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Error in cortribbon node with T2 in fmriprep 23.0.2 #3000

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liuzhenqi77 opened this issue Apr 28, 2023 · 2 comments
Closed

Error in cortribbon node with T2 in fmriprep 23.0.2 #3000

liuzhenqi77 opened this issue Apr 28, 2023 · 2 comments
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@liuzhenqi77
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What happened?

fmriprep 23.0.2 crashed at cortribbon node, the same data and parameters was tested fine in 22.1.1. On a different server and dataset (without T2), there was no error in fmriprep 23.0.2.

The crashed node was anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon when running the command recon-all -parallel -subjid sub-CC110033 -sd /out/sourcedata/freesurfer -T2pial -cortribbon.

I suspect that it might be related to the recently cortical ribbon and/or T2 changes.

nipreps/smriprep/pull/322
nipreps/smriprep/pull/319

What command did you use?

singularity exec \
    --cleanenv \
    -B <some-binds> \
    /path/to/singularity/fmriprep-22.1.1.sif \
        fmriprep /data /out participant \
            --participant-label $subject \
            -vvv \
            --output-spaces MNI152NLin2009cAsym:res-2 MNI152NLin6Asym:res-2 anat fsnative fsaverage fsaverage6 \
            --medial-surface-nan \
            --cifti-output 91k \
            --use-aroma \
            --fs-license-file /opt/freesurfer/license.txt \
            --output-layout bids \
            --work-dir /wd \
            --resource-monitor \
            --write-graph \
            --stop-on-first-crash \
            --notrack

What version of fMRIPrep are you running?

23.0.2

How are you running fMRIPrep?

Singularity

Is your data BIDS valid?

Yes

Are you reusing any previously computed results?

No

Please copy and paste any relevant log output.

230427-16:56:26,223 nipype.workflow DEBUG:
	 Allocating fmriprep_23_0_wf.single_subject_CC110037_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon ID=206 (0.20GB, 2 threads). Free: 226.02GB, 62 threads.
230427-16:56:26,224 nipype.workflow DEBUG:
	 [Node] Not cached "/wd/fmriprep_23_0_wf/single_subject_CC110037_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/cortribbon".
230427-16:56:26,224 nipype.workflow DEBUG:
	 Checking hash "fmriprep_23_0_wf.single_subject_CC110037_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon" locally: cached=False, updated=False.
230427-16:56:26,224 nipype.workflow DEBUG:
	 [MultiProc] Submitted task fmriprep_23_0_wf.single_subject_CC110037_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon (taskid=159).
230427-16:56:27,562 nipype.workflow INFO:
	 [Node] Setting-up "fmriprep_23_0_wf.single_subject_CC110037_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon" in "/wd/fmriprep_23_0_wf/single_subject_CC110037_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/cortribbon".
230427-16:56:27,644 nipype.workflow INFO:
	 [Node] Executing "cortribbon" <smriprep.interfaces.freesurfer.ReconAll>
230427-16:56:27,645 nipype.interface INFO:
	 resume recon-all : recon-all -parallel -subjid sub-CC110037 -sd /out/sourcedata/freesurfer -T2pial -cortribbon
230427-16:56:27,645 nipype.interface INFO:
	 resume recon-all : recon-all -parallel -subjid sub-CC110037 -sd /out/sourcedata/freesurfer -T2pial -cortribbon
230427-16:56:28,136 nipype.workflow DEBUG:
	 Progress: 499 jobs, 210/1/0 (done/running/ready), 1/288 (pending_tasks/waiting).
230427-16:56:28,136 nipype.workflow DEBUG:
	 Tasks currently running: 1. Pending: 1.
230427-16:56:28,137 nipype.workflow INFO:
	 [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 226.02/226.22, Free processors: 62/64.
                     Currently running:
                       * fmriprep_23_0_wf.single_subject_CC110037_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon
230427-16:59:48,425 nipype.workflow INFO:
	 [Node] Finished "cortribbon", elapsed time 200.780046s.
230427-16:59:48,432 nipype.workflow WARNING:
	 [Node] Error on "fmriprep_23_0_wf.single_subject_CC110037_wf.anat_preproc_wf.surface_recon_wf.autorecon_resume_wf.cortribbon" (/wd/fmriprep_23_0_wf/single_subject_CC110037_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/cortribbon)
230427-16:59:50,334 nipype.workflow DEBUG:
	 Clearing 206 from queue
230427-16:59:50,334 nipype.utils DEBUG:
	 Loading pkl: /wd/fmriprep_23_0_wf/single_subject_CC110037_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/cortribbon/result_cortribbon.pklz
230427-16:59:50,337 nipype.workflow DEBUG:
	 Resolving paths in outputs loaded from results file.
230427-16:59:50,340 nipype.workflow ERROR:
	 Node cortribbon failed to run on host nc10518.narval.calcul.quebec.
230427-16:59:50,342 nipype.workflow ERROR:
	 Saving crash info to /out/sub-CC110037/log/20230427-132229_38798902-e1f4-4309-b339-53d99aa97d9e/crash-20230427-165950-zqliu-cortribbon-5b5fece2-c3c1-4fcf-acb3-33ed7f6afe08.txt
Traceback (most recent call last):
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
    result["result"] = node.run(updatehash=updatehash)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/lib/python3.9/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
    raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node cortribbon.

Cmdline:
	recon-all -parallel -subjid sub-CC110037 -sd /out/sourcedata/freesurfer -T2pial -cortribbon
Stdout:
	fs-check-version --s sub-CC110037 --o /tmp/tmp.7xNH8O
	Thu Apr 27 16:56:28 UTC 2023

	setenv SUBJECTS_DIR /out/sourcedata/freesurfer
	cd /wd/fmriprep_23_0_wf/single_subject_CC110037_wf/anat_preproc_wf/surface_recon_wf/autorecon_resume_wf/cortribbon
	/opt/freesurfer/bin/fs-check-version --s sub-CC110037 --o /tmp/tmp.7xNH8O
	-rwxrwxr-x. 1 root root 18565 Aug  4  2022 /opt/freesurfer/bin/fs-check-version

	freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
	$Id$
	Linux nc10518.narval.calcul.quebec 4.18.0-425.19.2.el8_7.x86_64 #1 SMP Tue Apr 4 22:38:11 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
	pid 714686
	Current FS Version freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
	bstampfile exists /out/sourcedata/freesurfer/sub-CC110037/scripts/build-stamp.txt
	Subject FS Version: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
	No constraints on version because REQ=UnSet and FsVerFile=NotThere
	#@#% fs-check-version match = 1
	fs-check-version Done
	INFO: SUBJECTS_DIR is /out/sourcedata/freesurfer
	Actual FREESURFER_HOME /opt/freesurfer
	-rw-rw-r--. 1 zqliu zqliu 261478 Apr 27 16:35 /out/sourcedata/freesurfer/sub-CC110037/scripts/recon-all.log
	Linux nc10518.narval.calcul.quebec 4.18.0-425.19.2.el8_7.x86_64 #1 SMP Tue Apr 4 22:38:11 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
	/out/sourcedata/freesurfer/sub-CC110037/mri/transforms /out/sourcedata/freesurfer/sub-CC110037 
	/out/sourcedata/freesurfer/sub-CC110037 
	#--------------------------------------------
	#@# Refine Pial Surfs w/ T2/FLAIR Thu Apr 27 16:56:29 UTC 2023

	 bbregister --s sub-CC110037 --mov /out/sourcedata/freesurfer/sub-CC110037/mri/orig/T2raw.mgz --lta /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.auto.lta --init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 --no-coreg-ref-mask 

	tmp /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014
	Log file is /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.auto.log
	Thu Apr 27 16:56:30 UTC 2023

	setenv SUBJECTS_DIR /out/sourcedata/freesurfer
	cd /out/sourcedata/freesurfer/sub-CC110037/scripts
	/opt/freesurfer/bin/bbregister --s sub-CC110037 --mov /out/sourcedata/freesurfer/sub-CC110037/mri/orig/T2raw.mgz --lta /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.auto.lta --init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 --no-coreg-ref-mask

	bbregister 7.3.2
	Linux nc10518.narval.calcul.quebec 4.18.0-425.19.2.el8_7.x86_64 #1 SMP Tue Apr 4 22:38:11 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux
	FREESURFER_HOME /opt/freesurfer
	mri_convert /out/sourcedata/freesurfer/sub-CC110037/mri/orig/T2raw.mgz /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/template.nii
	mri_convert /out/sourcedata/freesurfer/sub-CC110037/mri/orig/T2raw.mgz /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/template.nii 
	reading from /out/sourcedata/freesurfer/sub-CC110037/mri/orig/T2raw.mgz...
	TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
	i_ras = (0.047074, -0.998891, 0)
	j_ras = (0.067921, 0.00320101, 0.997686)
	k_ras = (0.99658, 0.0469649, -0.0679967)
	writing to /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/template.nii...
	mri_coreg --s sub-CC110037 --mov /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/template.nii --regdat /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/reg.init.dat --reg /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask

	$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $
	cwd /out/sourcedata/freesurfer/sub-CC110037/scripts
	cmdline mri_coreg --s sub-CC110037 --mov /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/template.nii --regdat /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/reg.init.dat --reg /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask 
	sysname  Linux
	hostname nc10518.narval.calcul.quebec
	machine  x86_64
	user     zqliu
	dof    6
	nsep    1
	cras0    1
	ftol    0.000100
	linmintol    0.010000
	bf       1
	bflim    30.000000
	bfnsamp    30
	SmoothRef 0
	SatPct    99.990000
	MovOOB 0
	optschema 1
	Seed 53
	Reading in mov /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/template.nii
	INFO: This is an unsigined short.
	Reading in ref /out/sourcedata/freesurfer/sub-CC110037/mri/brainmask.mgz
	Setting cras translation parameters to align volume centers
	Creating random numbers for coordinate dithering
	Performing intensity dithering
	Performing intensity dithering on mov with computed dither
	Init matrix params -1.0087 -0.0245 -0.9649  0.0000  0.0000  0.0000  1.0000  1.0000  1.0000  0.0000  0.0000  0.0000 
	Initial parameters to be opt -1.0087 -0.0245 -0.9649  0.0000  0.0000  0.0000 
	Separation list (1):  4   min = 4
	DoSmoothing 1
	DoCoordDither 1
	DoIntensityDither 1
	nitersmax 4
	ftol 1.000e-04
	linmintol 1.000e-02
	SatPct 99.990000
	Hist FWHM 7.000000 7.000000
	nthreads 4
	movsat = 278.0000
	mov gstd 1.8914 1.8914 1.8914
	Smoothing mov
	refsat = 115.0000
	ref gstd 1.8914 1.8914 1.8914
	Smoothing ref
	COREGpreproc() done
	Testing if mov and target overlap
	Init cost   -1.0566453519
	nhits = 191039 out of 16777216, Percent Overlap:  72.9
	Initial  RefRAS-to-MovRAS
	 1.00000   0.00000   0.00000  -1.00871;
	 0.00000   1.00000   0.00000  -0.02452;
	 0.00000   0.00000   1.00000  -0.96486;
	 0.00000   0.00000   0.00000   1.00000;
	Initial  RefVox-to-MovVox
	-0.04707  -0.00000  -0.99889   260.86069;
	-0.06792  -0.99769   0.00320   262.95673;
	-0.99658   0.06800   0.04697   207.90633;
	 0.00000   0.00000   0.00000   1.00000;
	sep = 4 -----------------------------------
	COREGoptBruteForce() 30 1 30
	Turning on MovOOB for BruteForce Search
	#BF# sep= 4 iter=0 lim=30.0 delta=2.00   0.99129  -0.02452   1.03514   0.00000   0.00000   0.00000   -1.0494026
	Turning  MovOOB back off after brute force search


	---------------------------------
	Init Powel Params dof = 6: 0.991287 -0.024521 1.035141 0.000000 0.000000 0.000000 
	Starting OpenPowel2(), sep = 4
	InitialCost        -1.0575037003 
	#@#  4  188  0.99129 -0.02452 1.03514 0.00000 0.00000 0.00000   -1.0575037
	fs_powell::minimize
	  nparams 6
	  maxfev 4
	  ftol   0.000100
	  linmin_xtol_   0.010000
	  powell nthiter 0: fret = -1.057504
	#@#  4  191  -0.62675 -0.02452 1.03514 0.00000 0.00000 0.00000   -1.0575118
	#@#  4  192  0.17766 -0.02452 1.03514 0.00000 0.00000 0.00000   -1.0580053
	#@#  4  196  0.20217 -0.02452 1.03514 0.00000 0.00000 0.00000   -1.0580059
	#@#  4  198  0.19217 -0.02452 1.03514 0.00000 0.00000 0.00000   -1.0580060
	#@#  4  204  0.19217 0.35745 1.03514 0.00000 0.00000 0.00000   -1.0580188
	#@#  4  205  0.19217 0.19525 1.03514 0.00000 0.00000 0.00000   -1.0580359
	#@#  4  214  0.19217 0.20525 0.41711 0.00000 0.00000 0.00000   -1.0585365
	#@#  4  216  0.19217 0.20525 0.22728 0.00000 0.00000 0.00000   -1.0585685
	#@#  4  245  0.19217 0.20525 0.21728 0.00000 0.02921 0.01204   -1.0585690
	  powell nthiter 1: fret = -1.058569
	#@#  4  255  0.20217 0.20525 0.21728 0.00000 0.02921 0.01204   -1.0585692
	#@#  4  256  0.21217 0.20525 0.21728 0.00000 0.02921 0.01204   -1.0585700
	#@#  4  270  0.21217 0.18473 0.21728 0.00000 0.02921 0.01204   -1.0585701
	#@#  4  279  0.21217 0.17473 0.22786 0.00000 0.02921 0.01204   -1.0585703
	#@#  4  287  0.21217 0.17473 0.22786 -0.02507 0.02921 0.01204   -1.0585710
	Powell done niters total = 1
	OptTimeSec  4.2 sec
	OptTimeMin  0.07 min
	nEvals 309
	Final optimized parameters   0.21216717   0.17472816   0.22785757  -0.02507343   0.02920930   0.01203908 
	Final matrix parameters  0.2122  0.1747  0.2279 -0.0251  0.0292  0.0220  1.0000  1.0000  1.0000  0.0000  0.0000  0.0000 
	Final cost   -1.058570926802958
 

	---------------------------------
	Final  RefRAS-to-MovRAS
	 1.00000   0.00021   0.00051   0.21217;
	-0.00021   1.00000  -0.00044   0.17473;
	-0.00051   0.00044   1.00000   0.22786;
	 0.00000   0.00000   0.00000   1.00000;
	Final  RefVox-to-MovVox
	-0.04728  -0.00046  -0.99888   260.80142;
	-0.06741  -0.99772   0.00365   264.12225;
	-0.99660   0.06751   0.04714   209.09550;
	 0.00000   0.00000   0.00000   1.00000;
	Final matrix parameters  0.2122  0.1747  0.2279 -0.0251  0.0292  0.0120  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000 
	Final opt parameters  0.2122  0.1747  0.2279 -0.0251  0.0292  0.0120 
	nhits = 190988 out of 16777216, Percent Overlap:  72.9
	mri_coreg RunTimeSec 54.7 sec
	To check run:
	   tkregisterfv --mov /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/template.nii --targ /out/sourcedata/freesurfer/sub-CC110037/mri/brainmask.mgz --reg /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/mri_coreg.lta --s sub-CC110037 --surfs 

	mri_coreg done

	mri_segreg --mov /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/template.nii --init-reg /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/reg.init.dat --out-reg /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-abs 2 --gm-gt-wm 0.5
	7.3.2
	setenv SUBJECTS_DIR /out/sourcedata/freesurfer
	cd /out/sourcedata/freesurfer/sub-CC110037/scripts
	mri_segreg --mov /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/template.nii --init-reg /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/reg.init.dat --out-reg /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-abs 2 --gm-gt-wm 0.5 
	sysname  Linux
	hostname nc10518.narval.calcul.quebec
	machine  x86_64
	user     zqliu
	movvol /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/template.nii
	regfile /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/reg.init.dat
	subject sub-CC110037
	dof 6
	outregfile /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/bbr.pass1.dat
	UseMask 0
	UseLH 1
	UseRH 1
	nsubsamp 100
	PenaltySign  -1
	PenaltySlope 0.500000
	PenaltyCenter 0.000000
	surfname white
	GMProjAbs 2.000000
	WMProjAbs 2.000000
	lhcostfile (null)
	rhcostfile (null)
	interp  trilinear (1)
	frame  0
	TolPowell 0.000100
	nMaxItersPowell 36
	n1dmin  3
	Profile   0
	Gdiag_no  -1
	AddNoise  0 (0)
	SynthSeed 1683025149
	TransRandMax 0.000000
	RotRandMax 0.000000
	Translations 0.000000 0.000000 0.000000
	Rotations   0.000000 0.000000 0.000000
	Input reg
	-0.04728   0.99888  -0.00046   1.16679;
	 0.99660   0.04714  -0.06751   0.20580;
	-0.06741  -0.00365  -0.99772  -0.25299;
	 0.00000   0.00000   0.00000   1.00000;

	Loading mov
	INFO: This is an unsigined short.
	ExcludeZeroVoxels 1
	Reading in targ vol /out/sourcedata/freesurfer/sub-CC110037/mri/orig.mgz
	Projecting LH Surfs
	Loading lh.white surf
	GM Proj: 0 0.500000 2.000000
	WM Proj: 0 0.500000 2.000000
	Projecting RH Surfs
	Loading rh.white surf
	Projecting RH Surfs
	Using lh.cortex.label
	Using rh.cortex.label
	Computing relative cost
	 0  -25.0 -25.0 -25.0   1.013100
	 1  -25.0 -25.0  25.0   1.009040
	 2  -25.0  25.0 -25.0   0.992883
	 3  -25.0  25.0  25.0   0.947395
	 4   25.0 -25.0 -25.0   1.019692
	 5   25.0 -25.0  25.0   1.020254
	 6   25.0  25.0 -25.0   1.027812
	 7   25.0  25.0  25.0   1.000285
	REL:  8  0.071670    8.030461  1.003808 rel = 0.0713985 
	Initial costs ----------------
	Number of surface hits 2628
	WM  Intensity    84.6720 +/-  15.4200
	Ctx Intensity   122.2086 +/-  20.8196
	Pct Contrast     35.9859 +/-  20.8561
	Cost   0.0717
	RelCost   0.0714

	------------------------------------
	Brute force preopt -4 4 4, n = 729
	     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      0.9749   0.9749  0.0
	     5  -4.0000  -4.0000  -4.0000  -4.0000   0.0000   4.0000      0.9681   0.9681  0.0
	     7  -4.0000  -4.0000  -4.0000  -4.0000   4.0000   0.0000      0.8823   0.8823  0.0
	    15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.8510   0.8510  0.0
	    39  -4.0000  -4.0000   0.0000   0.0000   0.0000  -4.0000      0.8052   0.8052  0.0
	    97  -4.0000   0.0000  -4.0000   0.0000   4.0000   0.0000      0.7540   0.7540  0.0
	   121  -4.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.7335   0.7335  0.0
	   282   0.0000  -4.0000   0.0000   0.0000   0.0000  -4.0000      0.6290   0.6290  0.0
	   340   0.0000   0.0000  -4.0000   0.0000   4.0000   0.0000      0.6081   0.6081  0.0
	   355   0.0000   0.0000   0.0000  -4.0000   0.0000   0.0000      0.5872   0.5872  0.0
	   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.0717   0.0717  0.0
	Brute Force --------------------------
	Min cost was 0.071670
	Number of iterations   729
	Search time 1.227875 sec
	Parameters at best (transmm, rotdeg)
	  0.000   0.000   0.000  0.000  0.000  0.000 
	--------------------------------------------

	Starting Powell Minimization
	Init Powel Params dof = 6
	0 0
	1 0
	2 0
	3 0
	4 0
	5 0
	fs_powell::minimize
	  nparams 6
	  maxfev 36
	  ftol   0.000100
	  linmin_xtol_   0.001000
	  powell nthiter 0: fret = 0.071670
	   7  0.084  0.000  0.000  0.000  0.000  0.000   0.0698822351
	   8  0.150  0.000  0.000  0.000  0.000  0.000   0.0694800648
	   9  0.147  0.000  0.000  0.000  0.000  0.000   0.0694456720
	  10  0.127  0.000  0.000  0.000  0.000  0.000   0.0693391843
	  12  0.126  0.000  0.000  0.000  0.000  0.000   0.0693387767
	  14  0.120  0.000  0.000  0.000  0.000  0.000   0.0693325732
	  16  0.121  0.000  0.000  0.000  0.000  0.000   0.0693322424
	  25  0.121 -0.068  0.000  0.000  0.000  0.000   0.0682256174
	  27  0.121 -0.069  0.000  0.000  0.000  0.000   0.0682255274
	  34  0.121 -0.069  0.382  0.000  0.000  0.000   0.0663790273
	  35  0.121 -0.069  0.220  0.000  0.000  0.000   0.0609174419
	  36  0.121 -0.069  0.205  0.000  0.000  0.000   0.0607095765
	  39  0.121 -0.069  0.198  0.000  0.000  0.000   0.0606969796
	  40  0.121 -0.069  0.199  0.000  0.000  0.000   0.0606964506
	  48  0.121 -0.069  0.199  0.028  0.000  0.000   0.0606555079
	  49  0.121 -0.069  0.199  0.026  0.000  0.000   0.0606451751
	  50  0.121 -0.069  0.199  0.017  0.000  0.000   0.0606301735
	  52  0.121 -0.069  0.199  0.018  0.000  0.000   0.0606287311
	  53  0.121 -0.069  0.199  0.021  0.000  0.000   0.0606281349
	  55  0.121 -0.069  0.199  0.020  0.000  0.000   0.0606281162
	  62  0.121 -0.069  0.199  0.020 -0.025  0.000   0.0603659364
	  63  0.121 -0.069  0.199  0.020 -0.089  0.000   0.0599880733
	  66  0.121 -0.069  0.199  0.020 -0.065  0.000   0.0598408969
	  67  0.121 -0.069  0.199  0.020 -0.067  0.000   0.0598160079
	  68  0.121 -0.069  0.199  0.020 -0.073  0.000   0.0597829451
	  79  0.121 -0.069  0.199  0.020 -0.073 -0.013   0.0596842943
	  80  0.121 -0.069  0.199  0.020 -0.073 -0.037   0.0596060215
	  82  0.121 -0.069  0.199  0.020 -0.073 -0.030   0.0595897830
	  92  0.134 -0.077  0.221  0.022 -0.081 -0.033   0.0595419083
	  93  0.132 -0.075  0.216  0.022 -0.079 -0.032   0.0595326126
	  95  0.131 -0.075  0.215  0.022 -0.079 -0.032   0.0595322454
	  96  0.131 -0.075  0.215  0.022 -0.079 -0.032   0.0595320185
	  97  0.131 -0.075  0.215  0.022 -0.079 -0.032   0.0595320123
	  powell nthiter 1: fret = 0.059532
	 107  0.138 -0.075  0.215  0.022 -0.079 -0.032   0.0595103710
	 109  0.137 -0.075  0.215  0.022 -0.079 -0.032   0.0595102446
	 120  0.137 -0.128  0.215  0.022 -0.079 -0.032   0.0594564756
	 121  0.137 -0.106  0.215  0.022 -0.079 -0.032   0.0592907954
	 123  0.137 -0.107  0.215  0.022 -0.079 -0.032   0.0592905543
	 133  0.137 -0.107  0.215  0.022 -0.079 -0.068   0.0592681264
	 134  0.137 -0.107  0.215  0.022 -0.079 -0.051   0.0592187757
	 135  0.137 -0.107  0.215  0.022 -0.079 -0.052   0.0592163481
	 136  0.137 -0.107  0.215  0.022 -0.079 -0.055   0.0592131636
	 150  0.137 -0.107  0.215  0.021 -0.079 -0.055   0.0592129150
	 161  0.137 -0.107  0.215  0.021 -0.080 -0.055   0.0592084874
	 162  0.137 -0.107  0.215  0.021 -0.082 -0.055   0.0592084468
	 173  0.139 -0.108  0.219  0.021 -0.083 -0.056   0.0592046933
	 176  0.139 -0.108  0.218  0.021 -0.083 -0.056   0.0592046575
	  powell nthiter 2: fret = 0.059205
	 188  0.149 -0.108  0.218  0.021 -0.083 -0.056   0.0591574285
	 201  0.149 -0.107  0.218  0.021 -0.083 -0.056   0.0591536206
	 202  0.149 -0.098  0.218  0.021 -0.083 -0.056   0.0591493617
	 204  0.149 -0.102  0.218  0.021 -0.083 -0.056   0.0591444832
	 216  0.149 -0.102  0.218  0.021 -0.083 -0.063   0.0591149111
	 218  0.149 -0.102  0.218  0.021 -0.083 -0.065   0.0591139543
	 228  0.149 -0.102  0.218  0.018 -0.083 -0.065   0.0591123151
	 241  0.149 -0.102  0.218  0.018 -0.080 -0.065   0.0591068343
	 242  0.149 -0.102  0.218  0.018 -0.081 -0.065   0.0591054765
	 254  0.148 -0.102  0.218  0.018 -0.080 -0.065   0.0591054095
	 257  0.158 -0.095  0.217  0.015 -0.078 -0.073   0.0589883209
	 262  0.164 -0.091  0.217  0.014 -0.077 -0.079   0.0589326361
	 264  0.165 -0.091  0.217  0.014 -0.076 -0.079   0.0589318060
	 266  0.164 -0.091  0.217  0.014 -0.076 -0.079   0.0589315902
	  powell nthiter 3: fret = 0.058932
	 278  0.173 -0.096  0.232  0.015 -0.082 -0.081   0.0589312798
	 279  0.169 -0.093  0.224  0.014 -0.079 -0.080   0.0589153509
	 280  0.169 -0.093  0.224  0.014 -0.079 -0.080   0.0589149974
	 282  0.168 -0.093  0.223  0.014 -0.079 -0.080   0.0589147173
	 295  0.168 -0.119  0.223  0.014 -0.079 -0.080   0.0588476551
	 296  0.168 -0.114  0.223  0.014 -0.079 -0.080   0.0588257718
	 297  0.168 -0.110  0.223  0.014 -0.079 -0.080   0.0588206947
	 298  0.168 -0.109  0.223  0.014 -0.079 -0.080   0.0588206443
	 309  0.168 -0.109  0.223  0.014 -0.079 -0.082   0.0588150787
	 312  0.168 -0.109  0.223  0.014 -0.079 -0.083   0.0588150515
	 322  0.168 -0.109  0.223  0.010 -0.079 -0.083   0.0588077291
	 323  0.168 -0.109  0.223  0.008 -0.079 -0.083   0.0588067490
	 335  0.168 -0.109  0.223  0.008 -0.084 -0.083   0.0588034196
	 336  0.168 -0.109  0.223  0.008 -0.082 -0.083   0.0587997059
	 343  0.172 -0.107  0.223  0.007 -0.081 -0.087   0.0587861448
	 344  0.172 -0.107  0.223  0.007 -0.081 -0.086   0.0587858239
	 345  0.171 -0.107  0.223  0.007 -0.081 -0.086   0.0587856272
	 349  0.171 -0.107  0.223  0.007 -0.081 -0.086   0.0587854140
	  powell nthiter 4: fret = 0.058785
	 362  0.170 -0.106  0.221  0.007 -0.080 -0.086   0.0587843836
	 363  0.170 -0.107  0.221  0.007 -0.080 -0.086   0.0587843019
	 364  0.170 -0.107  0.221  0.007 -0.080 -0.086   0.0587842612
	 377  0.170 -0.130  0.221  0.007 -0.080 -0.086   0.0587790593
	 379  0.170 -0.119  0.221  0.007 -0.080 -0.086   0.0587502829
	 380  0.170 -0.118  0.221  0.007 -0.080 -0.086   0.0587499583
	 391  0.170 -0.118  0.221  0.007 -0.080 -0.087   0.0587488656
	 402  0.170 -0.118  0.221  0.005 -0.080 -0.087   0.0587460095
	 403  0.170 -0.118  0.221  0.001 -0.080 -0.087   0.0587415941
	 417  0.170 -0.118  0.221  0.001 -0.081 -0.087   0.0587396131
	 420  0.180 -0.111  0.221 -0.002 -0.079 -0.096   0.0587288373
	 424  0.176 -0.114  0.221 -0.001 -0.080 -0.093   0.0587177564
	 436  0.182 -0.120  0.219 -0.008 -0.079 -0.099   0.0586177662
	 441  0.185 -0.125  0.218 -0.013 -0.078 -0.103   0.0585744461
	 442  0.187 -0.127  0.217 -0.016 -0.078 -0.105   0.0585688563
	 443  0.186 -0.127  0.218 -0.016 -0.078 -0.105   0.0585683873
	 444  0.186 -0.127  0.218 -0.016 -0.078 -0.105   0.0585682349
	 449  0.186 -0.126  0.218 -0.015 -0.078 -0.105   0.0585677620
	  powell nthiter 5: fret = 0.058568
	 460  0.186 -0.126  0.217 -0.016 -0.078 -0.104   0.0585665144
	 461  0.185 -0.126  0.215 -0.016 -0.077 -0.104   0.0585644981
	 464  0.184 -0.125  0.214 -0.016 -0.076 -0.104   0.0585641181
	 465  0.184 -0.125  0.214 -0.016 -0.077 -0.104   0.0585636856
	 472  0.178 -0.129  0.215 -0.014 -0.078 -0.099   0.0585304619
	 474  0.179 -0.129  0.215 -0.014 -0.078 -0.100   0.0585280458
	 475  0.180 -0.128  0.215 -0.015 -0.078 -0.100   0.0585280310
	 482  0.180 -0.128  0.215 -0.015 -0.078 -0.100   0.0585279732
	 495  0.180 -0.128  0.215 -0.015 -0.078 -0.092   0.0585245091
	 496  0.180 -0.128  0.215 -0.015 -0.078 -0.095   0.0585158324
	 508  0.180 -0.128  0.215 -0.012 -0.078 -0.095   0.0585133069
	 509  0.180 -0.128  0.215 -0.011 -0.078 -0.095   0.0585130633
	 520  0.180 -0.128  0.215 -0.011 -0.079 -0.095   0.0585086794
	 521  0.180 -0.128  0.215 -0.011 -0.080 -0.095   0.0585072335
	 524  0.185 -0.135  0.213 -0.019 -0.079 -0.102   0.0584547854
	 529  0.184 -0.134  0.213 -0.017 -0.079 -0.101   0.0584524012
	  powell nthiter 6: fret = 0.058452
	 558  0.183 -0.135  0.213 -0.017 -0.079 -0.100   0.0584515092
	 559  0.183 -0.134  0.213 -0.017 -0.079 -0.100   0.0584515066
	 564  0.183 -0.134  0.213 -0.017 -0.079 -0.100   0.0584514885
	 565  0.183 -0.134  0.213 -0.017 -0.079 -0.100   0.0584513133
	 576  0.183 -0.134  0.213 -0.017 -0.079 -0.099   0.0584505110
	 577  0.183 -0.134  0.213 -0.017 -0.079 -0.098   0.0584504971
	 587  0.183 -0.134  0.213 -0.004 -0.079 -0.098   0.0584460806
	 588  0.183 -0.134  0.213 -0.010 -0.079 -0.098   0.0584387940
	 589  0.183 -0.134  0.213 -0.011 -0.079 -0.098   0.0584386518
	 607  0.185 -0.137  0.212 -0.014 -0.079 -0.100   0.0584227609
	 608  0.186 -0.138  0.212 -0.014 -0.079 -0.101   0.0584225960
	 609  0.185 -0.137  0.212 -0.014 -0.079 -0.101   0.0584222117
	 612  0.185 -0.137  0.212 -0.014 -0.079 -0.101   0.0584220734
	 617  0.187 -0.141  0.211 -0.011 -0.078 -0.101   0.0584071358
	 622  0.188 -0.143  0.211 -0.009 -0.078 -0.101   0.0584040693
	  powell nthiter 7: fret = 0.058404
	 640  0.184 -0.141  0.204 -0.010 -0.076 -0.100   0.0583948945
	 641  0.185 -0.141  0.206 -0.009 -0.076 -0.100   0.0583930707
	 651  0.185 -0.141  0.206 -0.010 -0.076 -0.101   0.0583919683
	 652  0.186 -0.141  0.206 -0.010 -0.076 -0.101   0.0583913589
	 659  0.186 -0.141  0.206 -0.010 -0.076 -0.101   0.0583913306
	 672  0.186 -0.141  0.206 -0.010 -0.076 -0.104   0.0583826285
	 683  0.186 -0.141  0.206  0.001 -0.076 -0.104   0.0583623570
	 684  0.186 -0.141  0.206  0.000 -0.076 -0.104   0.0583617968
	 695  0.186 -0.141  0.206  0.000 -0.075 -0.104   0.0583588985
	 698  0.187 -0.144  0.205  0.004 -0.075 -0.105   0.0583565431
	 702  0.187 -0.143  0.205  0.002 -0.075 -0.105   0.0583559761
	 710  0.187 -0.143  0.205  0.002 -0.075 -0.105   0.0583556795
	  powell nthiter 8: fret = 0.058356
	 723  0.185 -0.142  0.203  0.002 -0.074 -0.104   0.0583531990
	 724  0.185 -0.142  0.203  0.002 -0.074 -0.104   0.0583527922
	 726  0.185 -0.142  0.202  0.002 -0.074 -0.104   0.0583527182
	 727  0.185 -0.142  0.202  0.002 -0.074 -0.104   0.0583526665
	 752  0.185 -0.142  0.202  0.002 -0.074 -0.105   0.0583484364
	 754  0.185 -0.142  0.202  0.002 -0.074 -0.107   0.0583433099
	 755  0.185 -0.142  0.202  0.002 -0.074 -0.108   0.0583431659
	 765  0.185 -0.142  0.202  0.004 -0.074 -0.108   0.0583414340
	 766  0.185 -0.142  0.202  0.005 -0.074 -0.108   0.0583413420
	 780  0.186 -0.145  0.201  0.008 -0.073 -0.109   0.0583320084
	 785  0.186 -0.146  0.201  0.009 -0.073 -0.109   0.0583318153
	 793  0.186 -0.146  0.201  0.009 -0.073 -0.109   0.0583317670
	 795  0.186 -0.149  0.197  0.015 -0.072 -0.113   0.0583247564
	 802  0.186 -0.148  0.197  0.014 -0.072 -0.112   0.0583241945
	  powell nthiter 9: fret = 0.058324
	 818  0.187 -0.149  0.199  0.014 -0.073 -0.112   0.0583212494
	 819  0.188 -0.149  0.200  0.014 -0.073 -0.112   0.0583210251
	 828  0.187 -0.150  0.200  0.015 -0.074 -0.111   0.0583177035
	 829  0.187 -0.150  0.200  0.015 -0.074 -0.111   0.0583174749
	 833  0.186 -0.150  0.200  0.015 -0.074 -0.111   0.0583174383
	 835  0.186 -0.150  0.200  0.015 -0.074 -0.111   0.0583172261
	 848  0.186 -0.150  0.200  0.015 -0.074 -0.114   0.0583036964
	 849  0.186 -0.150  0.200  0.015 -0.074 -0.118   0.0583029444
	 851  0.186 -0.150  0.200  0.015 -0.074 -0.117   0.0583018886
	 852  0.186 -0.150  0.200  0.015 -0.074 -0.116   0.0583018491
	 862  0.186 -0.150  0.200  0.013 -0.074 -0.116   0.0583015930
	 873  0.186 -0.150  0.200  0.013 -0.071 -0.116   0.0582986172
	 875  0.186 -0.150  0.200  0.013 -0.072 -0.116   0.0582975520
	 881  0.186 -0.151  0.199  0.016 -0.071 -0.117   0.0582946306
	  powell nthiter 10: fret = 0.058295
	 904  0.187 -0.152  0.200  0.016 -0.072 -0.117   0.0582942546
	 917  0.184 -0.154  0.200  0.017 -0.073 -0.115   0.0582816958
	 918  0.184 -0.154  0.200  0.017 -0.073 -0.115   0.0582816570
	 934  0.184 -0.154  0.200  0.017 -0.073 -0.116   0.0582786812
	 935  0.184 -0.154  0.200  0.017 -0.073 -0.118   0.0582781850
	 938  0.184 -0.154  0.200  0.017 -0.073 -0.117   0.0582776157
	 948  0.184 -0.154  0.200  0.014 -0.073 -0.117   0.0582761414
	 966  0.184 -0.155  0.199  0.017 -0.072 -0.119   0.0582751738
	 967  0.184 -0.155  0.199  0.016 -0.072 -0.119   0.0582751601
	 968  0.184 -0.155  0.199  0.017 -0.072 -0.119   0.0582751326
	 969  0.184 -0.155  0.199  0.017 -0.072 -0.119   0.0582748330
	 974  0.184 -0.155  0.199  0.017 -0.072 -0.119   0.0582747919
	 975  0.182 -0.158  0.199  0.017 -0.073 -0.120   0.0582645780
	 980  0.181 -0.160  0.199  0.018 -0.073 -0.121   0.0582626836
	 982  0.181 -0.160  0.199  0.018 -0.073 -0.121   0.0582625003
	  powell nthiter 11: fret = 0.058263
	1000  0.182 -0.161  0.201  0.018 -0.074 -0.122   0.0582617406
	1001  0.182 -0.161  0.201  0.018 -0.074 -0.122   0.0582616806
	1012  0.182 -0.161  0.201  0.018 -0.074 -0.121   0.0582616201
	1016  0.182 -0.161  0.201  0.018 -0.074 -0.121   0.0582615337
	1029  0.182 -0.161  0.201  0.018 -0.074 -0.120   0.0582601890
	1039  0.182 -0.161  0.201  0.012 -0.074 -0.120   0.0582600546
	1040  0.182 -0.161  0.201  0.015 -0.074 -0.120   0.0582582909
	1053  0.182 -0.161  0.201  0.015 -0.072 -0.120   0.0582529563
	1057  0.180 -0.164  0.201  0.015 -0.073 -0.122   0.0582514100
	1061  0.181 -0.163  0.201  0.015 -0.072 -0.121   0.0582506430
	1069  0.181 -0.163  0.201  0.015 -0.072 -0.121   0.0582506234
	  powell nthiter 12: fret = 0.058251
	1079  0.180 -0.162  0.200  0.015 -0.072 -0.121   0.0582506034
	1082  0.180 -0.162  0.200  0.015 -0.072 -0.121   0.0582504112
	1089  0.180 -0.163  0.198  0.017 -0.071 -0.122   0.0582501844
	1090  0.180 -0.163  0.199  0.016 -0.071 -0.122   0.0582500895
	1091  0.180 -0.163  0.199  0.016 -0.071 -0.122   0.0582495685
	1107  0.180 -0.163  0.199  0.016 -0.071 -0.118   0.0582484836
	1108  0.180 -0.163  0.199  0.016 -0.071 -0.120   0.0582465182
	1118  0.180 -0.163  0.199  0.011 -0.071 -0.120   0.0582456865
	1119  0.180 -0.163  0.199  0.013 -0.071 -0.120   0.0582450053
	1121  0.180 -0.163  0.199  0.015 -0.071 -0.120   0.0582449819
	1133  0.180 -0.163  0.199  0.015 -0.070 -0.120   0.0582435738
	1140  0.179 -0.164  0.199  0.015 -0.070 -0.120   0.0582431033
	1141  0.179 -0.164  0.199  0.015 -0.070 -0.120   0.0582429023
	1149  0.177 -0.165  0.196  0.014 -0.068 -0.119   0.0582405289
	1154  0.176 -0.166  0.195  0.014 -0.067 -0.118   0.0582397691
	1156  0.176 -0.166  0.194  0.014 -0.066 -0.118   0.0582395738
	1157  0.176 -0.166  0.194  0.014 -0.066 -0.118   0.0582394945
	1164  0.176 -0.166  0.194  0.014 -0.066 -0.118   0.0582394370
	  powell nthiter 13: fret = 0.058239
	1188  0.176 -0.167  0.193  0.017 -0.066 -0.119   0.0582392921
	1189  0.176 -0.167  0.193  0.016 -0.066 -0.119   0.0582387791
	1196  0.176 -0.167  0.193  0.016 -0.066 -0.119   0.0582387048
	1212  0.176 -0.167  0.193  0.016 -0.066 -0.119   0.0582386237
	1221  0.176 -0.167  0.193  0.010 -0.066 -0.119   0.0582357556
	1222  0.176 -0.167  0.193  0.012 -0.066 -0.119   0.0582353106
	1235  0.176 -0.167  0.193  0.012 -0.067 -0.119   0.0582338520
	1242  0.175 -0.167  0.192  0.011 -0.066 -0.118   0.0582333074
	  powell nthiter 14: fret = 0.058233
	1270  0.175 -0.168  0.191  0.014 -0.065 -0.120   0.0582326647
	1274  0.175 -0.168  0.191  0.014 -0.065 -0.120   0.0582324724
	1276  0.175 -0.168  0.191  0.014 -0.065 -0.120   0.0582324376
	1308  0.175 -0.168  0.191  0.010 -0.065 -0.120   0.0582313402
	1309  0.175 -0.168  0.191  0.011 -0.065 -0.120   0.0582312983
	1338  0.175 -0.168  0.191  0.011 -0.065 -0.120   0.0582311523
	Powell done niters = 14
	Computing relative cost
	 0  -25.0 -25.0 -25.0   1.003598
	 1  -25.0 -25.0  25.0   1.008154
	 2  -25.0  25.0 -25.0   0.988276
	 3  -25.0  25.0  25.0   0.959830
	 4   25.0 -25.0 -25.0   1.014564
	 5   25.0 -25.0  25.0   1.019405
	 6   25.0  25.0 -25.0   1.032183
	 7   25.0  25.0  25.0   1.003396
	REL:  8  0.058231    8.029406  1.003676 rel = 0.0580179 
	Number of iterations    14
	Min cost was 0.058231
	Number of FunctionCalls  1342
	TolPowell 0.000100
	nMaxItersPowell 36
	OptimizationTime 2.010238 sec
	Parameters at optimum (transmm)  0.17528 -0.16799  0.19085
	Parameters at optimum (rotdeg)  0.01144 -0.06544 -0.11973 
	Final costs ----------------
	Number of surface hits 2628
	WM  Intensity    84.4766 +/-  15.2521
	Ctx Intensity   121.9554 +/-  20.4306
	Pct Contrast     36.0308 +/-  20.6151
	Cost   0.0582
	RelCost   0.0714
	Reg at min cost was 
	-0.04512   0.99898   0.00054   1.34279;
	 0.99671   0.04506  -0.06731   0.03542;
	-0.06727  -0.00250  -0.99773  -0.06076;
	 0.00000   0.00000   0.00000   1.00000;

	Writing optimal reg to /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/bbr.pass1.dat, type = 14 
	Original Reg 
	-0.04728   0.99888  -0.00046   1.16679;
	 0.99660   0.04714  -0.06751   0.20580;
	-0.06741  -0.00365  -0.99772  -0.25299;
	 0.00000   0.00000   0.00000   1.00000;

	Original Reg - Optimal Reg
	-0.00216  -0.00010  -0.00100  -0.17599;
	-0.00011   0.00209  -0.00020   0.17038;
	-0.00014  -0.00115   0.00001  -0.19223;
	 0.00000   0.00000   0.00000   0.00000;

	Computing change in lh position
	LH rmsDiffMean 0.208812
	Computing change in rh position
	Surface-RMS-Diff-mm 0.251695 0.078387 0.426088
	mri_segreg done
	mri_segreg --mov /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/template.nii --init-reg /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/bbr.pass1.dat --out-reg /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/reg.curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5
	7.3.2
	setenv SUBJECTS_DIR /out/sourcedata/freesurfer
	cd /out/sourcedata/freesurfer/sub-CC110037/scripts
	mri_segreg --mov /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/template.nii --init-reg /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/bbr.pass1.dat --out-reg /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/reg.curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5 
	sysname  Linux
	hostname nc10518.narval.calcul.quebec
	machine  x86_64
	user     zqliu
	movvol /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/template.nii
	regfile /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/tmp.bbregister.715014/bbr.pass1.dat
	subject sub-CC110037
	dof 6
	outregfile /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.auto.dat
	UseMask 0
	UseLH 1
	UseRH 1
	nsubsamp 1
	PenaltySign  -1
	PenaltySlope 0.500000
	PenaltyCenter 0.000000
	surfname white
	GMProjAbs 2.000000
	WMProjAbs 1.000000
	lhcostfile (null)
	rhcostfile (null)
	interp  trilinear (1)
	frame  0
	TolPowell 0.000000
	nMaxItersPowell 36
	n1dmin  3
	Profile   0
	Gdiag_no  -1
	AddNoise  0 (0)
	SynthSeed 1682820521
	TransRandMax 0.000000
	RotRandMax 0.000000
	Translations 0.000000 0.000000 0.000000
	Rotations   0.000000 0.000000 0.000000
	Input reg
	-0.04512   0.99898   0.00054   1.34279;
	 0.99671   0.04506  -0.06731   0.03542;
	-0.06727  -0.00250  -0.99773  -0.06076;
	 0.00000   0.00000   0.00000   1.00000;

	Loading mov
	INFO: This is an unsigined short.
	ExcludeZeroVoxels 1
	Reading in targ vol /out/sourcedata/freesurfer/sub-CC110037/mri/orig.mgz
	Projecting LH Surfs
	Loading lh.white surf
	GM Proj: 0 0.500000 2.000000
	WM Proj: 0 0.500000 1.000000
	Projecting RH Surfs
	Loading rh.white surf
	Projecting RH Surfs
	Using lh.cortex.label
	Using rh.cortex.label
	Computing relative cost
	 0  -25.0 -25.0 -25.0   1.012625
	 1  -25.0 -25.0  25.0   1.022287
	 2  -25.0  25.0 -25.0   0.983847
	 3  -25.0  25.0  25.0   0.970758
	 4   25.0 -25.0 -25.0   1.023111
	 5   25.0 -25.0  25.0   1.007498
	 6   25.0  25.0 -25.0   0.996441
	 7   25.0  25.0  25.0   0.994886
	REL:  8  0.039803    8.011453  1.001432 rel = 0.0397461 
	Initial costs ----------------
	Number of surface hits 262238
	WM  Intensity    82.8130 +/-  12.7504
	Ctx Intensity   122.1445 +/-  20.2478
	Pct Contrast     37.8537 +/-  19.3342
	Cost   0.0398
	RelCost   0.0397

	------------------------------------
	Brute force preopt -0.1 0.1 0.1, n = 729
	     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.0450   0.0450  0.0
	     1  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.0000      0.0424   0.0424  0.0
	     4  -0.1000  -0.1000  -0.1000  -0.1000   0.0000   0.0000      0.0406   0.0406  0.0
	    15  -0.1000  -0.1000  -0.1000   0.0000   0.1000  -0.1000      0.0404   0.0404  0.0
	    32  -0.1000  -0.1000   0.0000  -0.1000   0.0000   0.1000      0.0401   0.0401  0.0
	    86  -0.1000   0.0000  -0.1000  -0.1000   0.0000   0.1000      0.0394   0.0394  0.0
	   113  -0.1000   0.0000   0.0000  -0.1000   0.0000   0.1000      0.0390   0.0390  0.0
	   250   0.0000  -0.1000  -0.1000  -0.1000   0.1000   0.0000      0.0380   0.0380  0.0
	   491   0.1000  -0.1000  -0.1000  -0.1000   0.0000   0.1000      0.0370   0.0370  0.0
	   494   0.1000  -0.1000  -0.1000  -0.1000   0.1000   0.1000      0.0364   0.0364  0.0
	   503   0.1000  -0.1000  -0.1000   0.0000   0.1000   0.1000      0.0364   0.0364  0.0
	Brute Force --------------------------
	Min cost was 0.036364
	Number of iterations   729
	Search time 1.212729 sec
	Parameters at best (transmm, rotdeg)
	  0.100  -0.100  -0.100  0.000  0.100  0.100 
	--------------------------------------------

	Starting Powell Minimization
	Init Powel Params dof = 6
	0 0.1
	1 -0.1
	2 -0.1
	3 0
	4 0.1
	5 0.1
	fs_powell::minimize
	  nparams 6
	  maxfev 36
	  ftol   0.000000
	  linmin_xtol_   0.001000
	  powell nthiter 0: fret = 0.040477
	   7 -0.120 -0.100 -0.100  0.000  0.100  0.100   0.0397947828
	  11 -0.178 -0.100 -0.100  0.000  0.100  0.100   0.0397344806
	  14 -0.172 -0.100 -0.100  0.000  0.100  0.100   0.0397268170
	  16 -0.171 -0.100 -0.100  0.000  0.100  0.100   0.0397267824
	  24 -0.171 -0.034 -0.100  0.000  0.100  0.100   0.0396396228
	  28 -0.171 -0.021 -0.100  0.000  0.100  0.100   0.0396308670
	  29 -0.171 -0.020 -0.100  0.000  0.100  0.100   0.0396307868
	  37 -0.171 -0.020  0.065  0.000  0.100  0.100   0.0391046498
	  38 -0.171 -0.020  0.048  0.000  0.100  0.100   0.0390964408
	  39 -0.171 -0.020  0.047  0.000  0.100  0.100   0.0390953210
	  41 -0.171 -0.020  0.026  0.000  0.100  0.100   0.0390903991
	  42 -0.171 -0.020  0.032  0.000  0.100  0.100   0.0390854726
	  52 -0.171 -0.020  0.032  0.073  0.100  0.100   0.0389841747
	  53 -0.171 -0.020  0.032  0.082  0.100  0.100   0.0389816303
	  57 -0.171 -0.020  0.032  0.081  0.100  0.100   0.0389815515
	  65 -0.171 -0.020  0.032  0.081  0.152  0.100   0.0389725008
	  66 -0.171 -0.020  0.032  0.081  0.129  0.100   0.0389340128
	  67 -0.171 -0.020  0.032  0.081  0.128  0.100   0.0389318265
	  68 -0.171 -0.020  0.032  0.081  0.117  0.100   0.0389266236
	  69 -0.171 -0.020  0.032  0.081  0.120  0.100   0.0389249582
	  80 -0.171 -0.020  0.032  0.081  0.120  0.078   0.0388956153
	  81 -0.171 -0.020  0.032  0.081  0.120  0.073   0.0388949735
	  82 -0.171 -0.020  0.032  0.081  0.120  0.074   0.0388947956
	  powell nthiter 1: fret = 0.038895
	  91 -0.083 -0.020  0.032  0.081  0.120  0.074   0.0388848047
	  92 -0.123 -0.020  0.032  0.081  0.120  0.074   0.0388732783
	  94 -0.141 -0.020  0.032  0.081  0.120  0.074   0.0388415986
	  96 -0.145 -0.020  0.032  0.081  0.120  0.074   0.0388403055
	  97 -0.146 -0.020  0.032  0.081  0.120  0.074   0.0388402068
	  98 -0.147 -0.020  0.032  0.081  0.120  0.074   0.0388402036
	 108 -0.147 -0.027  0.032  0.081  0.120  0.074   0.0388379067
	 109 -0.147 -0.028  0.032  0.081  0.120  0.074   0.0388377585
	 111 -0.147 -0.029  0.032  0.081  0.120  0.074   0.0388377472
	 120 -0.147 -0.029  0.041  0.081  0.120  0.074   0.0388373786
	 122 -0.147 -0.029  0.037  0.081  0.120  0.074   0.0388357355
	 133 -0.147 -0.029  0.037  0.094  0.120  0.074   0.0388320178
	 134 -0.147 -0.029  0.037  0.091  0.120  0.074   0.0388316597
	 136 -0.147 -0.029  0.037  0.090  0.120  0.074   0.0388316360
	 147 -0.147 -0.029  0.037  0.090  0.116  0.074   0.0388289531
	 159 -0.147 -0.029  0.037  0.090  0.116  0.072   0.0388282090
	  powell nthiter 2: fret = 0.038828
	 172 -0.145 -0.029  0.037  0.090  0.116  0.072   0.0388280594
	 181 -0.145 -0.024  0.037  0.090  0.116  0.072   0.0388274635
	 192 -0.145 -0.024  0.045  0.090  0.116  0.072   0.0388256383
	 194 -0.145 -0.024  0.043  0.090  0.116  0.072   0.0388251231
	 195 -0.145 -0.024  0.042  0.090  0.116  0.072   0.0388250749
	 205 -0.145 -0.024  0.042  0.096  0.116  0.072   0.0388232561
	 216 -0.145 -0.024  0.042  0.096  0.111  0.072   0.0388211542
	 227 -0.145 -0.024  0.042  0.096  0.111  0.073   0.0388208992
	 228 -0.145 -0.024  0.042  0.096  0.111  0.074   0.0388206858
	 232 -0.144 -0.020  0.047  0.103  0.107  0.076   0.0388146697
	 237 -0.143 -0.017  0.050  0.107  0.105  0.077   0.0388129020
	 241 -0.142 -0.017  0.050  0.107  0.104  0.077   0.0388128562
	  powell nthiter 3: fret = 0.038813
	 256 -0.143 -0.017  0.050  0.107  0.104  0.077   0.0388126536
	 266 -0.143 -0.013  0.050  0.107  0.104  0.077   0.0388119136
	 267 -0.143 -0.014  0.050  0.107  0.104  0.077   0.0388118673
	 278 -0.143 -0.014  0.050  0.107  0.104  0.079   0.0388117176
	 280 -0.143 -0.014  0.050  0.107  0.104  0.078   0.0388116066
	 289 -0.143 -0.014  0.050  0.099  0.104  0.078   0.0388087098
	 290 -0.143 -0.014  0.050  0.100  0.104  0.078   0.0388086811
	 300 -0.143 -0.014  0.050  0.100  0.109  0.078   0.0388086362
	 301 -0.143 -0.014  0.050  0.100  0.107  0.078   0.0388081079
	 304 -0.142 -0.009  0.055  0.106  0.102  0.080   0.0388066738
	 308 -0.142 -0.011  0.053  0.104  0.104  0.079   0.0388064250
	 309 -0.142 -0.011  0.053  0.104  0.104  0.079   0.0388064140
	 311 -0.142 -0.010  0.054  0.105  0.103  0.080   0.0388064116
	 320 -0.142 -0.010  0.054  0.105  0.103  0.080   0.0388064073
	  powell nthiter 4: fret = 0.038806
	 344 -0.142 -0.012  0.054  0.105  0.103  0.080   0.0388061248
	 366 -0.142 -0.012  0.054  0.100  0.103  0.080   0.0388051176
	 367 -0.142 -0.012  0.054  0.101  0.103  0.080   0.0388050227
	 378 -0.142 -0.012  0.054  0.101  0.105  0.080   0.0388047207
	 385 -0.141 -0.010  0.056  0.103  0.103  0.081   0.0388044596
	 387 -0.141 -0.011  0.056  0.103  0.103  0.080   0.0388044014
	 388 -0.141 -0.011  0.056  0.103  0.103  0.080   0.0388044011
	 389 -0.141 -0.011  0.056  0.103  0.103  0.080   0.0388043781
	 394 -0.141 -0.011  0.057  0.100  0.103  0.081   0.0388033911
	 397 -0.140 -0.012  0.060  0.096  0.103  0.082   0.0388030241
	 398 -0.140 -0.012  0.059  0.097  0.103  0.082   0.0388029615
	 401 -0.140 -0.012  0.059  0.098  0.103  0.082   0.0388029579
	 402 -0.140 -0.012  0.059  0.098  0.103  0.082   0.0388029575
	 403 -0.140 -0.012  0.059  0.098  0.103  0.082   0.0388029392
	  powell nthiter 5: fret = 0.038803
	 418 -0.138 -0.012  0.059  0.098  0.103  0.082   0.0388028900
	 420 -0.139 -0.012  0.059  0.098  0.103  0.082   0.0388028065
	 429 -0.139 -0.014  0.059  0.098  0.103  0.082   0.0388023782
	 448 -0.139 -0.013  0.060  0.099  0.103  0.082   0.0388023444
	 450 -0.139 -0.013  0.060  0.099  0.102  0.082   0.0388023234
	 464 -0.138 -0.013  0.062  0.097  0.102  0.083   0.0388021686
	 469 -0.138 -0.013  0.062  0.097  0.102  0.083   0.0388021481
	 470 -0.138 -0.013  0.062  0.097  0.102  0.083   0.0388021297
	 472 -0.138 -0.013  0.062  0.097  0.102  0.083   0.0388021263
	  powell nthiter 6: fret = 0.038802
	 490 -0.137 -0.013  0.062  0.097  0.102  0.083   0.0388020272
	 500 -0.137 -0.014  0.062  0.097  0.102  0.083   0.0388020057
	 510 -0.137 -0.014  0.062  0.097  0.102  0.084   0.0388019028
	 518 -0.137 -0.015  0.061  0.097  0.103  0.084   0.0388018498
	 520 -0.137 -0.014  0.061  0.097  0.102  0.084   0.0388018381
	 522 -0.137 -0.015  0.061  0.097  0.103  0.084   0.0388018338
	 543 -0.137 -0.015  0.062  0.096  0.103  0.084   0.0388018140
	 545 -0.137 -0.015  0.062  0.096  0.103  0.084   0.0388018013
	 546 -0.137 -0.015  0.062  0.096  0.103  0.084   0.0388017961
	 547 -0.137 -0.015  0.062  0.096  0.103  0.084   0.0388017649
	 550 -0.137 -0.015  0.062  0.096  0.103  0.084   0.0388017628
	 551 -0.137 -0.015  0.062  0.096  0.103  0.084   0.0388017593
	  powell nthiter 7: fret = 0.038802
	 624 -0.137 -0.015  0.062  0.096  0.103  0.084   0.0388017479
	  powell nthiter 8: fret = 0.038802
	Powell done niters = 8
	Computing relative cost
	 0  -25.0 -25.0 -25.0   1.011939
	 1  -25.0 -25.0  25.0   1.024021
	 2  -25.0  25.0 -25.0   0.982391
	 3  -25.0  25.0  25.0   0.970970
	 4   25.0 -25.0 -25.0   1.024425
	 5   25.0 -25.0  25.0   1.009692
	 6   25.0  25.0 -25.0   0.996309
	 7   25.0  25.0  25.0   0.990707
	REL:  8  0.038802    8.010454  1.001307 rel = 0.0387511 
	Number of iterations     8
	Min cost was 0.038802
	Number of FunctionCalls   702
	TolPowell 0.000000
	nMaxItersPowell 36
	OptimizationTime 29.447240 sec
	Parameters at optimum (transmm) -0.13688 -0.01464  0.06165
	Parameters at optimum (rotdeg)  0.09611  0.10254  0.08397 
	Final costs ----------------
	Number of surface hits 262238
	WM  Intensity    82.3481 +/-  12.5156
	Ctx Intensity   122.2796 +/-  20.0877
	Pct Contrast     38.4705 +/-  19.5464
	Cost   0.0388
	RelCost   0.0397
	Reg at min cost was 
	-0.04670   0.99891  -0.00115   1.20574;
	 0.99676   0.04653  -0.06564   0.02284;
	-0.06551  -0.00421  -0.99784  -0.00146;
	 0.00000   0.00000   0.00000   1.00000;

	Writing optimal reg to /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.auto.dat, type = 14 
	Original Reg 
	-0.04512   0.99898   0.00054   1.34279;
	 0.99671   0.04506  -0.06731   0.03542;
	-0.06727  -0.00250  -0.99773  -0.06076;
	 0.00000   0.00000   0.00000   1.00000;

	Original Reg - Optimal Reg
	 0.00158   0.00007   0.00169   0.13705;
	-0.00004  -0.00147  -0.00167   0.01257;
	-0.00175   0.00171   0.00011  -0.05931;
	 0.00000   0.00000   0.00000   0.00000;

	Computing change in lh position
	LH rmsDiffMean 0.170961
	Computing change in rh position
	Surface-RMS-Diff-mm 0.213590 0.080124 0.374245
	mri_segreg done
	MinCost: 0.038802 82.348139 122.279605 38.470469 
	tkregister2_cmdl --mov /out/sourcedata/freesurfer/sub-CC110037/mri/orig/T2raw.mgz --reg /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.auto.dat --noedit --ltaout /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.auto.lta
	INFO: no target volume specified, assuming FreeSurfer orig volume.
	target  volume orig
	movable volume /out/sourcedata/freesurfer/sub-CC110037/mri/orig/T2raw.mgz
	reg file       /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.auto.dat
	LoadVol        0
	ZeroCRAS       0
	7.3.2
	Diagnostic Level -1
	---- Input registration matrix --------
	-0.04670   0.99891  -0.00115   1.20574;
	 0.99676   0.04653  -0.06564   0.02284;
	-0.06551  -0.00421  -0.99784  -0.00146;
	 0.00000   0.00000   0.00000   1.00000;
	float2int = 0
	---------------------------------------
	INFO: loading target /out/sourcedata/freesurfer/sub-CC110037/mri/orig.mgz
	Ttarg: --------------------
	-1.00000   0.00000   0.00000   128.00000;
	 0.00000   0.00000   1.00000  -128.00000;
	 0.00000  -1.00000   0.00000   128.00000;
	 0.00000   0.00000   0.00000   1.00000;
	INFO: loading movable /out/sourcedata/freesurfer/sub-CC110037/mri/orig/T2raw.mgz
	Tmov: --------------------
	-1.00000   0.00000   0.00000   127.99995;
	 0.00000   0.00000   1.00000  -96.00000;
	 0.00000  -1.00000   0.00000   128.00006;
	 0.00000   0.00000   0.00000   1.00000;
	mkheaderreg = 0, float2int = 0
	---- Input registration matrix --------
	-0.04670   0.99891  -0.00115   1.20574;
	 0.99676   0.04653  -0.06564   0.02284;
	-0.06551  -0.00421  -0.99784  -0.00146;
	 0.00000   0.00000   0.00000   1.00000;
	Determinant 1
	subject = sub-CC110037
	RegMat ---------------------------
	-0.04670   0.99891  -0.00115   1.20574;
	 0.99676   0.04653  -0.06564   0.02284;
	-0.06551  -0.00421  -0.99784  -0.00146;
	 0.00000   0.00000   0.00000   1.00000;
	Cleaning up
 
	Started at Thu Apr 27 16:56:30 UTC 2023 
	Ended   at Thu Apr 27 16:58:05 UTC 2023
	BBR-Run-Time-Sec 95
 
	bbregister Done
	To check results, run:
	tkregisterfv --mov /out/sourcedata/freesurfer/sub-CC110037/mri/orig/T2raw.mgz --reg /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.auto.lta --surfs  --sd /out/sourcedata/freesurfer
 

	 cp /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.auto.lta /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.lta 

	mri_convert -odt float -at /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.lta -rl /out/sourcedata/freesurfer/sub-CC110037/mri/orig.mgz /out/sourcedata/freesurfer/sub-CC110037/mri/orig/T2raw.mgz /out/sourcedata/freesurfer/sub-CC110037/mri/T2.prenorm.mgz 
	reading from /out/sourcedata/freesurfer/sub-CC110037/mri/orig/T2raw.mgz...
	TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
	i_ras = (0.047074, -0.998891, 0)
	j_ras = (0.067921, 0.00320101, 0.997686)
	k_ras = (0.99658, 0.0469649, -0.0679967)
	INFO: Reading transformation from file /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.lta...
	Reading transform with LTAreadEx()
	reading template info from volume /out/sourcedata/freesurfer/sub-CC110037/mri/orig.mgz...
	INFO: Applying transformation from file /out/sourcedata/freesurfer/sub-CC110037/mri/transforms/T2raw.lta...
	---------------------------------
	INFO: Transform Matrix (linear_ras_to_ras)
	 1.00000   0.00037  -0.00241  -0.04407;
	-0.00037   1.00000   0.00104  -0.19614;
	 0.00241  -0.00104   1.00000   0.01878;
	 0.00000   0.00000   0.00000   1.00000;
	---------------------------------
	Applying LTAtransformInterp (resample_type 1)
	changing data type from ushrt to float (noscale = 0)...
	MRIchangeType: Building histogram 0 332 1000, flo=0, fhi=0.999, dest_type=3
	writing to /out/sourcedata/freesurfer/sub-CC110037/mri/T2.prenorm.mgz...

	 mri_normalize -seed 1234 -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /out/sourcedata/freesurfer/sub-CC110037/mri/aseg.presurf.mgz -surface /out/sourcedata/freesurfer/sub-CC110037/surf/lh.white identity.nofile -surface /out/sourcedata/freesurfer/sub-CC110037/surf/rh.white identity.nofile /out/sourcedata/freesurfer/sub-CC110037/mri/T2.prenorm.mgz /out/sourcedata/freesurfer/sub-CC110037/mri/T2.norm.mgz 

	setting seed for random number genererator to 1234
	using Gaussian smoothing of bias field, sigma=0.500
	disabling nonmaximum suppression
	retaining  points that are at least 1.000mm from the boundary
	using segmentation for initial intensity normalization
	reading mri_src from /out/sourcedata/freesurfer/sub-CC110037/mri/T2.prenorm.mgz...
	Copying mri_dst from mri_src
	computing distance transform
	computing distance transform
	min_dist = 1
	Erasing Border planes 4
	Removing non-wm voxels
	48103 non wm control points removed
	Building bias image
	building Voronoi diagram...
	performing soap bubble smoothing, sigma = 0...
	smoothing bias field with sigma=0.500
	MRIapplyBiasCorrectionSameGeometry()
	NaN found at voxel (0, 0, 0, 0)
	error: Numerical argument out of domain
	error: WARNING: 16777216 NaNs found in volume /out/sourcedata/freesurfer/sub-CC110037/mri/T2.prenorm.mgz...

Additional information / screenshots

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@effigies
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Please reopen if this is still an issue in 23.1.x.

@effigies effigies closed this as not planned Won't fix, can't repro, duplicate, stale Aug 24, 2023
@FeHoff
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FeHoff commented Apr 15, 2024

We face the same problem in 23.2.1

	 [Node] Setting-up "fmriprep_23_2_wf.sub_CC122172_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.cortribbon" in "/var/lib/condor/execute/dir_3377921/ds/fmriprep_23_2_wf/sub_CC122172_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/cortribbon".
240412-19:19:22,414 nipype.workflow INFO:
	 [Node] Executing "cortribbon" <smriprep.interfaces.freesurfer.ReconAll>
240412-19:19:22,415 nipype.interface INFO:
	 resume recon-all : recon-all -parallel -subjid sub-CC122172 -sd /var/lib/condor/execute/dir_3377921/ds/freesurfer -T2pial -cortribbon
240412-19:19:22,415 nipype.interface INFO:
	 resume recon-all : recon-all -parallel -subjid sub-CC122172 -sd /var/lib/condor/execute/dir_3377921/ds/freesurfer -T2pial -cortribbon
240412-19:19:24,296 nipype.workflow INFO:
	 [MultiProc] Running 1 tasks, and 0 jobs ready. Free memory (GB): 1803.33/1803.53, Free processors: 0/2.
                     Currently running:
                       * fmriprep_23_2_wf.sub_CC122172_wf.anat_fit_wf.surface_recon_wf.autorecon_resume_wf.cortribbon
240412-19:23:00,485 nipype.workflow INFO:
	 [Node] Finished "cortribbon", elapsed time 218.07039s.
	 [Node] Error on "fmriprep_23_2_wf.sub_CC520197_wf.bold_task_movie_echo_1_wf.ds_report_t2star_hist" (/var/lib/condor/execute/dir_3221981/ds/fmriprep_23_2_wf/sub_CC520197_wf/bold_task_movie_echo_1_wf/ds_report_t2star_hist)
240411-06:53:38,763 nipype.workflow ERROR:
	 Node ds_report_t2star_hist failed to run on host cpu44.
240411-06:53:38,763 nipype.workflow ERROR:
	 Saving crash info to /var/lib/condor/execute/dir_3221981/ds/fmriprep/sub-CC520197/log/20240411-011301_32922eee-1096-48d0-81a9-d9f25d706913/crash-20240411-065338-fhoffstaedter-ds_report_t2star_hist-ce98fff5-fbb8-49e6-940c-a88b7d778a56.txt
Traceback (most recent call last):
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 344, in _send_procs_to_workers
    self.procs[jobid].run(updatehash=updatehash)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
    result = self._run_interface(execute=True)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
    return self._run_command(execute)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 722, in _run_command
    result = self._interface.run(cwd=outdir, ignore_exception=True)
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 388, in run
    self._check_mandatory_inputs()
  File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 275, in _check_mandatory_inputs
    raise ValueError(msg)
ValueError: DerivativesDataSink requires a value for input 'source_file'. For a list of required inputs, see DerivativesDataSink.help()


	fs-check-version --s sub-CC122172 --o /tmp/tmp.k0VL0z
	Fri Apr 12 19:19:22 CEST 2024

	setenv SUBJECTS_DIR /var/lib/condor/execute/dir_3377921/ds/freesurfer
	cd /var/lib/condor/execute/dir_3377921/ds/fmriprep_23_2_wf/sub_CC122172_wf/anat_fit_wf/surface_recon_wf/autorecon_resume_wf/cortribbon
	/opt/freesurfer/bin/fs-check-version --s sub-CC122172 --o /tmp/tmp.k0VL0z
	-rwxrwxr-x 1 root root 18565 Aug  4  2022 /opt/freesurfer/bin/fs-check-version

	freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
	$Id$
	Linux cpu44 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 x86_64 x86_64 GNU/Linux
	pid 2670809
	Current FS Version freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
	bstampfile exists /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/scripts/build-stamp.txt
	Subject FS Version: freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
	No constraints on version because REQ=UnSet and FsVerFile=NotThere
	#@#% fs-check-version match = 1
	fs-check-version Done
	INFO: SUBJECTS_DIR is /var/lib/condor/execute/dir_3377921/ds/freesurfer
	Actual FREESURFER_HOME /opt/freesurfer
	-rw-rw-r-- 1 fhoffstaedter BnB 251176 Apr 12 18:07 /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/scripts/recon-all.log
	Linux cpu44 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 x86_64 x86_64 GNU/Linux
	/var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172 
	/var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172 
	#--------------------------------------------
	#@# Refine Pial Surfs w/ T2/FLAIR Fri Apr 12 19:19:23 CEST 2024

	 bbregister --s sub-CC122172 --mov /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/orig/T2raw.mgz --lta /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.auto.lta --init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 --no-coreg-ref-mask 

	tmp /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012
	Log file is /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.auto.log
	Fri Apr 12 19:19:23 CEST 2024

	setenv SUBJECTS_DIR /var/lib/condor/execute/dir_3377921/ds/freesurfer
	cd /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/scripts
	/opt/freesurfer/bin/bbregister --s sub-CC122172 --mov /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/orig/T2raw.mgz --lta /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.auto.lta --init-coreg --T2 --gm-proj-abs 2 --wm-proj-abs 1 --no-coreg-ref-mask

	bbregister 7.3.2
	Linux cpu44 6.1.0-18-amd64 #1 SMP PREEMPT_DYNAMIC Debian 6.1.76-1 (2024-02-01) x86_64 x86_64 x86_64 GNU/Linux
	FREESURFER_HOME /opt/freesurfer
	mri_convert /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/orig/T2raw.mgz /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/template.nii
	mri_convert /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/orig/T2raw.mgz /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/template.nii 
	reading from /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/orig/T2raw.mgz...
	TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
	i_ras = (-0.003515, -0.999994, 0)
	j_ras = (0.013944, -4.8995e-05, 0.999903)
	k_ras = (0.999897, -0.00351501, -0.013944)
	writing to /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/template.nii...
	mri_coreg --s sub-CC122172 --mov /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/template.nii --regdat /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/reg.init.dat --reg /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask

	$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $
	cwd /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/scripts
	cmdline mri_coreg --s sub-CC122172 --mov /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/template.nii --regdat /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/reg.init.dat --reg /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/mri_coreg.lta --nthreads 4 --dof 6 --sep 4 --ftol .0001 --linmintol .01 --no-ref-mask 
	sysname  Linux
	hostname cpu44
	machine  x86_64
	user     fhoffstaedter
	dof    6
	nsep    1
	cras0    1
	ftol    0.000100
	linmintol    0.010000
	bf       1
	bflim    30.000000
	bfnsamp    30
	SmoothRef 0
	SatPct    99.990000
	MovOOB 0
	optschema 1
	Seed 53
	Reading in mov /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/template.nii
	INFO: This is an unsigined short.
	Reading in ref /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/brainmask.mgz
	Setting cras translation parameters to align volume centers
	Creating random numbers for coordinate dithering
	Performing intensity dithering
	Performing intensity dithering on mov with computed dither
	Init matrix params -1.0087  0.0018 -0.9930  0.0000  0.0000  0.0000  1.0000  1.0000  1.0000  0.0000  0.0000  0.0000 
	Initial parameters to be opt -1.0087  0.0018 -0.9930  0.0000  0.0000  0.0000 
	Separation list (1):  4   min = 4
	DoSmoothing 1
	DoCoordDither 1
	DoIntensityDither 1
	nitersmax 4
	ftol 1.000e-04
	linmintol 1.000e-02
	SatPct 99.990000
	Hist FWHM 7.000000 7.000000
	nthreads 4
	movsat = 360.0000
	mov gstd 1.8914 1.8914 1.8914
	Smoothing mov
	refsat = 115.0000
	ref gstd 1.8914 1.8914 1.8914
	Smoothing ref
	COREGpreproc() done
	Testing if mov and target overlap
	Init cost   -1.0561328336
	nhits = 194203 out of 16777216, Percent Overlap:  74.1
	Initial  RefRAS-to-MovRAS
	 1.00000   0.00000   0.00000  -1.00865;
	 0.00000   1.00000   0.00000   0.00177;
	 0.00000   0.00000   1.00000  -0.99300;
	 0.00000   0.00000   0.00000   1.00000;
	Initial  RefVox-to-MovVox
	 0.00352  -0.00000  -0.99999   254.55096;
	-0.01394  -0.99990  -0.00005   256.77167;
	-0.99990   0.01394  -0.00351   221.65706;
	 0.00000   0.00000   0.00000   1.00000;
	sep = 4 -----------------------------------
	COREGoptBruteForce() 30 1 30
	Turning on MovOOB for BruteForce Search
	#BF# sep= 4 iter=0 lim=30.0 delta=2.00   0.99135   0.00177   1.00700   0.00000   0.00000   0.00000   -1.0502478
	Turning  MovOOB back off after brute force search


	---------------------------------
	Init Powel Params dof = 6: 0.991348 0.001770 1.007004 0.000000 0.000000 0.000000 
	Starting OpenPowel2(), sep = 4
	InitialCost        -1.0576514006 
	#@#  4  188  0.99135 0.00177 1.00700 0.00000 0.00000 0.00000   -1.0576514
	fs_powell::minimize
	  nparams 6
	  maxfev 4
	  ftol   0.000100
	  linmin_xtol_   0.010000
	  powell nthiter 0: fret = -1.057651
	#@#  4  191  -0.62669 0.00177 1.00700 0.00000 0.00000 0.00000   -1.0577430
	#@#  4  192  0.12862 0.00177 1.00700 0.00000 0.00000 0.00000   -1.0581867
	#@#  4  196  0.16637 0.00177 1.00700 0.00000 0.00000 0.00000   -1.0581877
	#@#  4  197  0.15637 0.00177 1.00700 0.00000 0.00000 0.00000   -1.0581883
	#@#  4  200  0.15637 1.00177 1.00700 0.00000 0.00000 0.00000   -1.0582325
	#@#  4  204  0.15637 0.61980 1.00700 0.00000 0.00000 0.00000   -1.0583571
	#@#  4  205  0.15637 0.43540 1.00700 0.00000 0.00000 0.00000   -1.0583624
	#@#  4  206  0.15637 0.50055 1.00700 0.00000 0.00000 0.00000   -1.0583652
	#@#  4  213  0.15637 0.50055 0.38897 0.00000 0.00000 0.00000   -1.0583684
	#@#  4  215  0.15637 0.50055 0.69352 0.00000 0.00000 0.00000   -1.0584245
	#@#  4  217  0.15637 0.50055 0.71352 0.00000 0.00000 0.00000   -1.0584248
	#@#  4  227  0.15637 0.50055 0.71352 -0.19709 0.00000 0.00000   -1.0584344
	#@#  4  228  0.15637 0.50055 0.71352 -0.17808 0.00000 0.00000   -1.0584353
	#@#  4  229  0.15637 0.50055 0.71352 -0.14226 0.00000 0.00000   -1.0584372
	#@#  4  240  0.15637 0.50055 0.71352 -0.12151 -0.15578 0.00000   -1.0584469
	#@#  4  250  0.15637 0.50055 0.71352 -0.12151 -0.15578 -0.13359   -1.0584480
	  powell nthiter 1: fret = -1.058448
	#@#  4  266  0.13492 0.50055 0.71352 -0.12151 -0.15578 -0.14390   -1.0584482
	#@#  4  273  0.13492 0.47371 0.71352 -0.12151 -0.15578 -0.14390   -1.0584486
	#@#  4  281  0.13492 0.48371 0.67360 -0.12151 -0.15578 -0.14390   -1.0584490
	#@#  4  282  0.13492 0.48371 0.68381 -0.12151 -0.15578 -0.14390   -1.0584494
	#@#  4  290  0.13492 0.48371 0.68381 -0.24746 -0.15578 -0.14390   -1.0584496
	#@#  4  291  0.13492 0.48371 0.68381 -0.18836 -0.15578 -0.14390   -1.0584508
	#@#  4  302  0.13492 0.48371 0.68381 -0.18836 -0.13147 -0.14390   -1.0584512
	Powell done niters total = 1
	OptTimeSec 14.1 sec
	OptTimeMin  0.23 min
	nEvals 315
	Final optimized parameters   0.13492247   0.48370636   0.68381065  -0.18835609  -0.13146910  -0.14390282 
	Final matrix parameters  0.1349  0.4837  0.6838 -0.1884 -0.1315 -0.1539  1.0000  1.0000  1.0000  0.0000  0.0000  0.0000 
	Final cost   -1.058451164101897
 

	---------------------------------
	Final  RefRAS-to-MovRAS
	 0.99999  -0.00251  -0.00229   0.13492;
	 0.00250   0.99999  -0.00329   0.48371;
	 0.00230   0.00328   0.99999   0.68381;
	 0.00000   0.00000   0.00000   1.00000;
	Final  RefVox-to-MovVox
	 0.00602  -0.00330  -0.99998   254.10783;
	-0.01625  -0.99986   0.00320   258.47726;
	-0.99985   0.01623  -0.00607   222.73515;
	 0.00000   0.00000   0.00000   1.00000;
	Final matrix parameters  0.1349  0.4837  0.6838 -0.1884 -0.1315 -0.1439  0.0000  0.0000  0.0000  0.0000  0.0000  0.0000 
	Final opt parameters  0.1349  0.4837  0.6838 -0.1884 -0.1315 -0.1439 
	nhits = 192985 out of 16777216, Percent Overlap:  73.6
	mri_coreg RunTimeSec 71.1 sec
	To check run:
	   tkregisterfv --mov /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/template.nii --targ /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/brainmask.mgz --reg /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/mri_coreg.lta --s sub-CC122172 --surfs 

	mri_coreg done

	mri_segreg --mov /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/template.nii --init-reg /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/reg.init.dat --out-reg /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-abs 2 --gm-gt-wm 0.5
	7.3.2
	setenv SUBJECTS_DIR /var/lib/condor/execute/dir_3377921/ds/freesurfer
	cd /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/scripts
	mri_segreg --mov /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/template.nii --init-reg /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/reg.init.dat --out-reg /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/bbr.pass1.dat --subsamp-brute 100 --subsamp 100 --tol 1e-4 --tol1d 1e-3 --brute -4 4 4 --surf white --gm-proj-abs 2 --gm-gt-wm 0.5 
	sysname  Linux
	hostname cpu44
	machine  x86_64
	user     fhoffstaedter
	movvol /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/template.nii
	regfile /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/reg.init.dat
	subject sub-CC122172
	dof 6
	outregfile /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/bbr.pass1.dat
	UseMask 0
	UseLH 1
	UseRH 1
	nsubsamp 100
	PenaltySign  -1
	PenaltySlope 0.500000
	PenaltyCenter 0.000000
	surfname white
	GMProjAbs 2.000000
	WMProjAbs 2.000000
	lhcostfile (null)
	rhcostfile (null)
	interp  trilinear (1)
	frame  0
	TolPowell 0.000100
	nMaxItersPowell 36
	n1dmin  3
	Profile   0
	Gdiag_no  -1
	AddNoise  0 (0)
	SynthSeed 1713413618
	TransRandMax 0.000000
	RotRandMax 0.000000
	Translations 0.000000 0.000000 0.000000
	Rotations   0.000000 0.000000 0.000000
	Input reg
	 0.00602   0.99998  -0.00330   1.54045;
	 0.99985  -0.00607  -0.01623   0.05424;
	-0.01625  -0.00320  -0.99986  -0.82460;
	 0.00000   0.00000   0.00000   1.00000;

	Loading mov
	INFO: This is an unsigined short.
	ExcludeZeroVoxels 1
	Reading in targ vol /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/orig.mgz
	Projecting LH Surfs
	Loading lh.white surf
	GM Proj: 0 0.500000 2.000000
	WM Proj: 0 0.500000 2.000000
	Projecting RH Surfs
	Loading rh.white surf
	Projecting RH Surfs
	Using lh.cortex.label
	Using rh.cortex.label
	Computing relative cost
	 0  -25.0 -25.0 -25.0   1.042037
	 1  -25.0 -25.0  25.0   0.993437
	 2  -25.0  25.0 -25.0   1.027815
	 3  -25.0  25.0  25.0   1.016161
	 4   25.0 -25.0 -25.0   1.014790
	 5   25.0 -25.0  25.0   0.981310
	 6   25.0  25.0 -25.0   1.003595
	 7   25.0  25.0  25.0   0.987409
	REL:  8  0.142995    8.066554  1.008319 rel = 0.141815 
	Initial costs ----------------
	Number of surface hits 2780
	WM  Intensity   107.9987 +/-  21.5304
	Ctx Intensity   153.7275 +/-  35.0954
	Pct Contrast     33.6018 +/-  24.9724
	Cost   0.1430
	RelCost   0.1418

	------------------------------------
	Brute force preopt -4 4 4, n = 729
	     0  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000      1.0029   1.0029  0.0
	     1  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   0.0000      0.9928   0.9928  0.0
	     2  -4.0000  -4.0000  -4.0000  -4.0000  -4.0000   4.0000      0.9687   0.9687  0.0
	    15  -4.0000  -4.0000  -4.0000   0.0000   4.0000  -4.0000      0.9592   0.9592  0.0
	    21  -4.0000  -4.0000  -4.0000   4.0000   0.0000  -4.0000      0.9292   0.9292  0.0
	    24  -4.0000  -4.0000  -4.0000   4.0000   4.0000  -4.0000      0.9225   0.9225  0.0
	    38  -4.0000  -4.0000   0.0000   0.0000  -4.0000   4.0000      0.8969   0.8969  0.0
	    39  -4.0000  -4.0000   0.0000   0.0000   0.0000  -4.0000      0.8269   0.8269  0.0
	    46  -4.0000  -4.0000   0.0000   4.0000  -4.0000   0.0000      0.8262   0.8262  0.0
	    48  -4.0000  -4.0000   0.0000   4.0000   0.0000  -4.0000      0.8246   0.8246  0.0
	    63  -4.0000  -4.0000   4.0000   0.0000  -4.0000  -4.0000      0.8000   0.8000  0.0
	   118  -4.0000   0.0000   0.0000   0.0000  -4.0000   0.0000      0.6988   0.6988  0.0
	   340   0.0000   0.0000  -4.0000   0.0000   4.0000   0.0000      0.6567   0.6567  0.0
	   355   0.0000   0.0000   0.0000  -4.0000   0.0000   0.0000      0.6269   0.6269  0.0
	   364   0.0000   0.0000   0.0000   0.0000   0.0000   0.0000      0.1430   0.1430  0.0
	Brute Force --------------------------
	Min cost was 0.142995
	Number of iterations   729
	Search time 0.718500 sec
	Parameters at best (transmm, rotdeg)
	  0.000   0.000   0.000  0.000  0.000  0.000 
	--------------------------------------------

	Starting Powell Minimization
	Init Powel Params dof = 6
	0 0
	1 0
	2 0
	3 0
	4 0
	5 0
	fs_powell::minimize
	  nparams 6
	  maxfev 36
	  ftol   0.000100
	  linmin_xtol_   0.001000
	  powell nthiter 0: fret = 0.142995
	   5 -0.618  0.000  0.000  0.000  0.000  0.000   0.1351795434
	   7 -0.380  0.000  0.000  0.000  0.000  0.000   0.1311628239
	  10 -0.329  0.000  0.000  0.000  0.000  0.000   0.1310331078
	  11 -0.351  0.000  0.000  0.000  0.000  0.000   0.1310202069
	  13 -0.362  0.000  0.000  0.000  0.000  0.000   0.1308771749
	  29 -0.362 -0.002  0.000  0.000  0.000  0.000   0.1308732946
	  33 -0.362 -0.002  1.000  0.000  0.000  0.000   0.0874278314
	  38 -0.362 -0.002  0.997  0.000  0.000  0.000   0.0873912375
	  41 -0.362 -0.002  0.987  0.000  0.000  0.000   0.0873453610
	  42 -0.362 -0.002  0.989  0.000  0.000  0.000   0.0873438710
	  49 -0.362 -0.002  0.989  0.382  0.000  0.000   0.0851048136
	  50 -0.362 -0.002  0.989  0.286  0.000  0.000   0.0833645093
	  51 -0.362 -0.002  0.989  0.226  0.000  0.000   0.0825540297
	  54 -0.362 -0.002  0.989  0.229  0.000  0.000   0.0825526085
	  63 -0.362 -0.002  0.989  0.229 -0.289  0.000   0.0788663803
	  64 -0.362 -0.002  0.989  0.229 -0.279  0.000   0.0785339621
	  65 -0.362 -0.002  0.989  0.229 -0.182  0.000   0.0777585253
	  67 -0.362 -0.002  0.989  0.229 -0.215  0.000   0.0772434962
	  69 -0.362 -0.002  0.989  0.229 -0.212  0.000   0.0772400782
	  73 -0.362 -0.002  0.989  0.229 -0.211  0.000   0.0772392286
	  86 -0.362 -0.002  0.989  0.229 -0.211  0.008   0.0772244160
	  87 -0.362 -0.002  0.989  0.229 -0.211  0.006   0.0772210861
	  90 -0.362 -0.002  0.989  0.229 -0.211  0.005   0.0772206415
	  powell nthiter 1: fret = 0.077221
	 100 -0.311 -0.002  0.989  0.229 -0.211  0.005   0.0759061911
	 101 -0.325 -0.002  0.989  0.229 -0.211  0.005   0.0757118718
	 114 -0.325 -0.022  0.989  0.229 -0.211  0.005   0.0756604899
	 116 -0.325 -0.016  0.989  0.229 -0.211  0.005   0.0756397784
	 117 -0.325 -0.015  0.989  0.229 -0.211  0.005   0.0756391003
	 128 -0.325 -0.015  0.985  0.229 -0.211  0.005   0.0756314795
	 139 -0.325 -0.015  0.985  0.235 -0.211  0.005   0.0756198380
	 150 -0.325 -0.015  0.985  0.235 -0.188  0.005   0.0755701511
	 151 -0.325 -0.015  0.985  0.235 -0.193  0.005   0.0754910629
	 152 -0.325 -0.015  0.985  0.235 -0.199  0.005   0.0754589925
	 165 -0.325 -0.015  0.985  0.235 -0.199  0.006   0.0754536213
	 166 -0.325 -0.015  0.985  0.235 -0.199  0.009   0.0754465353
	 176 -0.311 -0.020  0.983  0.238 -0.194  0.010   0.0754395051
	 177 -0.318 -0.017  0.984  0.237 -0.196  0.010   0.0754096656
	 178 -0.318 -0.017  0.984  0.237 -0.196  0.010   0.0754095609
	 179 -0.317 -0.018  0.984  0.237 -0.196  0.010   0.0754091064
	 181 -0.317 -0.018  0.984  0.237 -0.196  0.010   0.0754090344
	 185 -0.317 -0.018  0.984  0.237 -0.196  0.010   0.0754089049
	  powell nthiter 2: fret = 0.075409
	 198 -0.317 -0.018  0.984  0.237 -0.196  0.011   0.0754085829
	 213 -0.317 -0.019  0.984  0.237 -0.196  0.011   0.0754077420
	 223 -0.317 -0.019  0.982  0.237 -0.196  0.011   0.0754027482
	 236 -0.317 -0.019  0.982  0.235 -0.196  0.011   0.0754014357
	 249 -0.317 -0.019  0.982  0.235 -0.191  0.011   0.0753761923
	 250 -0.317 -0.019  0.982  0.235 -0.190  0.011   0.0753760678
	 261 -0.317 -0.019  0.982  0.235 -0.190  0.011   0.0753760632
	 263 -0.317 -0.019  0.982  0.235 -0.190  0.011   0.0753759261
	  powell nthiter 3: fret = 0.075376
	 289 -0.317 -0.037  0.982  0.235 -0.190  0.011   0.0753422989
	 291 -0.317 -0.038  0.982  0.235 -0.190  0.011   0.0753420991
	 304 -0.317 -0.038  0.980  0.235 -0.190  0.011   0.0753413768
	 313 -0.317 -0.038  0.980  0.234 -0.190  0.011   0.0753410599
	 314 -0.317 -0.038  0.980  0.232 -0.190  0.011   0.0753409550
	 316 -0.317 -0.038  0.980  0.231 -0.190  0.011   0.0753406331
	 319 -0.317 -0.038  0.980  0.230 -0.190  0.011   0.0753402513
	 328 -0.317 -0.038  0.980  0.230 -0.179  0.011   0.0753225691
	 329 -0.317 -0.038  0.980  0.230 -0.180  0.011   0.0753129558
	 330 -0.317 -0.038  0.980  0.230 -0.184  0.011   0.0752937241
	 340 -0.315 -0.039  0.980  0.230 -0.183  0.011   0.0752841816
	 342 -0.314 -0.039  0.980  0.230 -0.183  0.011   0.0752840057
	 344 -0.314 -0.039  0.980  0.230 -0.183  0.011   0.0752837530
	 348 -0.311 -0.059  0.978  0.226 -0.176  0.011   0.0752076303
	 355 -0.311 -0.059  0.978  0.226 -0.176  0.011   0.0752075411
	 356 -0.311 -0.059  0.978  0.226 -0.176  0.011   0.0752072273
	 362 -0.311 -0.059  0.978  0.226 -0.176  0.011   0.0752071171
	  powell nthiter 4: fret = 0.075207
	 375 -0.311 -0.059  0.978  0.226 -0.176  0.013   0.0752055492
	 386 -0.311 -0.058  0.978  0.226 -0.176  0.013   0.0752054779
	 399 -0.311 -0.058  0.971  0.226 -0.176  0.013   0.0751891985
	 400 -0.311 -0.058  0.973  0.226 -0.176  0.013   0.0751857783
	 411 -0.311 -0.058  0.973  0.221 -0.176  0.013   0.0751835216
	 412 -0.311 -0.058  0.973  0.223 -0.176  0.013   0.0751831184
	 413 -0.311 -0.058  0.973  0.224 -0.176  0.013   0.0751827938
	 421 -0.317 -0.056  0.974  0.223 -0.178  0.012   0.0751681248
	 422 -0.315 -0.056  0.974  0.223 -0.177  0.012   0.0751656490
	 423 -0.315 -0.056  0.974  0.223 -0.177  0.012   0.0751655282
	 435 -0.314 -0.064  0.973  0.221 -0.174  0.012   0.0751626664
	 436 -0.314 -0.061  0.973  0.222 -0.175  0.012   0.0751607885
	 437 -0.314 -0.061  0.973  0.222 -0.175  0.012   0.0751607361
	 440 -0.314 -0.061  0.973  0.222 -0.176  0.012   0.0751607346
	 442 -0.314 -0.061  0.973  0.222 -0.176  0.012   0.0751607255
	 443 -0.314 -0.061  0.973  0.222 -0.176  0.012   0.0751607078
	  powell nthiter 5: fret = 0.075161
	 457 -0.314 -0.061  0.973  0.222 -0.176  0.013   0.0751601659
	 469 -0.314 -0.057  0.973  0.222 -0.176  0.013   0.0751559187
	 484 -0.314 -0.057  0.971  0.222 -0.176  0.013   0.0751554244
	 486 -0.314 -0.057  0.972  0.222 -0.176  0.013   0.0751543777
	 495 -0.314 -0.057  0.972  0.215 -0.176  0.013   0.0751466455
	 497 -0.314 -0.057  0.972  0.213 -0.176  0.013   0.0751461187
	 506 -0.318 -0.055  0.973  0.212 -0.177  0.013   0.0751424814
	 507 -0.317 -0.056  0.972  0.213 -0.176  0.013   0.0751403931
	 517 -0.315 -0.064  0.972  0.211 -0.174  0.013   0.0751294185
	 519 -0.316 -0.062  0.972  0.211 -0.174  0.013   0.0751288268
	 527 -0.316 -0.062  0.972  0.211 -0.174  0.013   0.0751287886
	 528 -0.317 -0.063  0.970  0.201 -0.173  0.014   0.0751214209
	  powell nthiter 6: fret = 0.075129
	 563 -0.316 -0.061  0.966  0.211 -0.174  0.015   0.0751149643
	 564 -0.316 -0.061  0.968  0.211 -0.174  0.015   0.0751090363
	 573 -0.316 -0.061  0.968  0.202 -0.174  0.015   0.0751002198
	 575 -0.316 -0.061  0.968  0.205 -0.174  0.015   0.0750989635
	 576 -0.316 -0.061  0.968  0.204 -0.174  0.015   0.0750988406
	 584 -0.319 -0.060  0.968  0.203 -0.175  0.015   0.0750960465
	 585 -0.317 -0.060  0.968  0.203 -0.175  0.015   0.0750943618
	 588 -0.317 -0.060  0.968  0.203 -0.175  0.015   0.0750942689
	 600 -0.317 -0.061  0.968  0.203 -0.175  0.015   0.0750941772
	 605 -0.317 -0.061  0.968  0.203 -0.175  0.015   0.0750939379
	  powell nthiter 7: fret = 0.075094
	 629 -0.317 -0.059  0.968  0.203 -0.175  0.015   0.0750934870
	 643 -0.317 -0.059  0.966  0.203 -0.175  0.015   0.0750888699
	 655 -0.317 -0.059  0.966  0.201 -0.175  0.015   0.0750877378
	 676 -0.317 -0.060  0.965  0.201 -0.174  0.015   0.0750877243
	 677 -0.317 -0.060  0.966  0.201 -0.174  0.015   0.0750874750
	 679 -0.317 -0.060  0.966  0.201 -0.174  0.015   0.0750872587
	Powell done niters = 7
	Computing relative cost
	 0  -25.0 -25.0 -25.0   1.029650
	 1  -25.0 -25.0  25.0   0.988140
	 2  -25.0  25.0 -25.0   0.997678
	 3  -25.0  25.0  25.0   1.011442
	 4   25.0 -25.0 -25.0   1.005741
	 5   25.0 -25.0  25.0   0.998003
	 6   25.0  25.0 -25.0   0.986425
	 7   25.0  25.0  25.0   0.988588
	REL:  8  0.075087    8.005666  1.000708 rel = 0.0750341 
	Number of iterations     7
	Min cost was 0.075087
	Number of FunctionCalls   684
	TolPowell 0.000100
	nMaxItersPowell 36
	OptimizationTime 0.638214 sec
	Parameters at optimum (transmm) -0.31708 -0.06005  0.96552
	Parameters at optimum (rotdeg)  0.20105 -0.17433  0.01478 
	Final costs ----------------
	Number of surface hits 2780
	WM  Intensity   106.0819 +/-  19.1014
	Ctx Intensity   154.7749 +/-  32.7686
	Pct Contrast     36.0763 +/-  22.9644
	Cost   0.0751
	RelCost   0.1418
	Reg at min cost was 
	 0.00580   0.99998  -0.00025   1.22585;
	 0.99990  -0.00580  -0.01272  -0.00252;
	-0.01272  -0.00018  -0.99992   0.14581;
	 0.00000   0.00000   0.00000   1.00000;

	Writing optimal reg to /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/bbr.pass1.dat, type = 14 
	Original Reg 
	 0.00602   0.99998  -0.00330   1.54045;
	 0.99985  -0.00607  -0.01623   0.05424;
	-0.01625  -0.00320  -0.99986  -0.82460;
	 0.00000   0.00000   0.00000   1.00000;

	Original Reg - Optimal Reg
	 0.00022  -0.00001  -0.00305   0.31460;
	-0.00005  -0.00027  -0.00351   0.05676;
	-0.00353  -0.00302   0.00006  -0.97041;
	 0.00000   0.00000   0.00000   0.00000;

	Computing change in lh position
	LH rmsDiffMean 0.828673
	Computing change in rh position
	Surface-RMS-Diff-mm 0.913788 0.150637 1.270514
	mri_segreg done
	mri_segreg --mov /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/template.nii --init-reg /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/bbr.pass1.dat --out-reg /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/reg.curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5
	7.3.2
	setenv SUBJECTS_DIR /var/lib/condor/execute/dir_3377921/ds/freesurfer
	cd /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/scripts
	mri_segreg --mov /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/template.nii --init-reg /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/bbr.pass1.dat --out-reg /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.auto.dat --interp trilinear --wm-proj-abs 1 --tol 1e-8 --tol1d 1e-3 --c0 0 --mincost /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.auto.dat.mincost --dof 6 --nmax 36 --param /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.auto.dat.param --surf white --brute -0.1 0.1 0.1 --cur-reg /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/reg.curopt.dat --gm-proj-abs 2 --nsub 1 --gm-gt-wm 0.5 
	sysname  Linux
	hostname cpu44
	machine  x86_64
	user     fhoffstaedter
	movvol /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/template.nii
	regfile /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/tmp.bbregister.2671012/bbr.pass1.dat
	subject sub-CC122172
	dof 6
	outregfile /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.auto.dat
	UseMask 0
	UseLH 1
	UseRH 1
	nsubsamp 1
	PenaltySign  -1
	PenaltySlope 0.500000
	PenaltyCenter 0.000000
	surfname white
	GMProjAbs 2.000000
	WMProjAbs 1.000000
	lhcostfile (null)
	rhcostfile (null)
	interp  trilinear (1)
	frame  0
	TolPowell 0.000000
	nMaxItersPowell 36
	n1dmin  3
	Profile   0
	Gdiag_no  -1
	AddNoise  0 (0)
	SynthSeed 1713275222
	TransRandMax 0.000000
	RotRandMax 0.000000
	Translations 0.000000 0.000000 0.000000
	Rotations   0.000000 0.000000 0.000000
	Input reg
	 0.00580   0.99998  -0.00025   1.22585;
	 0.99990  -0.00580  -0.01272  -0.00252;
	-0.01272  -0.00018  -0.99992   0.14581;
	 0.00000   0.00000   0.00000   1.00000;

	Loading mov
	INFO: This is an unsigined short.
	ExcludeZeroVoxels 1
	Reading in targ vol /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/orig.mgz
	Projecting LH Surfs
	Loading lh.white surf
	GM Proj: 0 0.500000 2.000000
	WM Proj: 0 0.500000 1.000000
	Projecting RH Surfs
	Loading rh.white surf
	Projecting RH Surfs
	Using lh.cortex.label
	Using rh.cortex.label
	Computing relative cost
	 0  -25.0 -25.0 -25.0   1.027788
	 1  -25.0 -25.0  25.0   1.008880
	 2  -25.0  25.0 -25.0   1.007594
	 3  -25.0  25.0  25.0   0.996603
	 4   25.0 -25.0 -25.0   1.022383
	 5   25.0 -25.0  25.0   1.014322
	 6   25.0  25.0 -25.0   1.001144
	 7   25.0  25.0  25.0   1.000064
	REL:  8  0.061648    8.078778  1.009847 rel = 0.0610465 
	Initial costs ----------------
	Number of surface hits 277683
	WM  Intensity   104.2881 +/-  16.3912
	Ctx Intensity   153.9160 +/-  32.8478
	Pct Contrast     36.9405 +/-  22.4279
	Cost   0.0616
	RelCost   0.0610

	------------------------------------
	Brute force preopt -0.1 0.1 0.1, n = 729
	     0  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000      0.0576   0.0576  0.0
	     1  -0.1000  -0.1000  -0.1000  -0.1000  -0.1000   0.0000      0.0560   0.0560  0.0
	    10  -0.1000  -0.1000  -0.1000   0.0000  -0.1000   0.0000      0.0553   0.0553  0.0
	    19  -0.1000  -0.1000  -0.1000   0.1000  -0.1000   0.0000      0.0549   0.0549  0.0
	    20  -0.1000  -0.1000  -0.1000   0.1000  -0.1000   0.1000      0.0545   0.0545  0.0
	    36  -0.1000  -0.1000   0.0000   0.0000  -0.1000  -0.1000      0.0537   0.0537  0.0
	    45  -0.1000  -0.1000   0.0000   0.1000  -0.1000  -0.1000      0.0534   0.0534  0.0
	    46  -0.1000  -0.1000   0.0000   0.1000  -0.1000   0.0000      0.0530   0.0530  0.0
	   118  -0.1000   0.0000   0.0000   0.0000  -0.1000   0.0000      0.0529   0.0529  0.0
	   262   0.0000  -0.1000  -0.1000   0.1000  -0.1000   0.0000      0.0523   0.0523  0.0
	   288   0.0000  -0.1000   0.0000   0.1000  -0.1000  -0.1000      0.0520   0.0520  0.0
	Brute Force --------------------------
	Min cost was 0.052021
	Number of iterations   729
	Search time 0.616073 sec
	Parameters at best (transmm, rotdeg)
	  0.000  -0.100   0.000  0.100 -0.100 -0.100 
	--------------------------------------------

	Starting Powell Minimization
	Init Powel Params dof = 6
	0 0
	1 -0.1
	2 0
	3 0.1
	4 -0.1
	5 -0.1
	fs_powell::minimize
	  nparams 6
	  maxfev 36
	  ftol   0.000000
	  linmin_xtol_   0.001000
	  powell nthiter 0: fret = 0.062141
	   7  0.015 -0.100  0.000  0.100 -0.100 -0.100   0.0621370416
	  12  0.023 -0.100  0.000  0.100 -0.100 -0.100   0.0621340892
	  13  0.029 -0.100  0.000  0.100 -0.100 -0.100   0.0621340122
	  14  0.026 -0.100  0.000  0.100 -0.100 -0.100   0.0621338337
	  15  0.025 -0.100  0.000  0.100 -0.100 -0.100   0.0621338116
	  24  0.025 -0.093  0.000  0.100 -0.100 -0.100   0.0621320259
	  25  0.025 -0.092  0.000  0.100 -0.100 -0.100   0.0621319179
	  26  0.025 -0.090  0.000  0.100 -0.100 -0.100   0.0621318508
	  29  0.025 -0.091  0.000  0.100 -0.100 -0.100   0.0621318032
	  36  0.025 -0.091  0.117  0.100 -0.100 -0.100   0.0617944038
	  37  0.025 -0.091  0.101  0.100 -0.100 -0.100   0.0617711809
	  38  0.025 -0.091  0.092  0.100 -0.100 -0.100   0.0617663698
	  39  0.025 -0.091  0.089  0.100 -0.100 -0.100   0.0617657293
	  40  0.025 -0.091  0.086  0.100 -0.100 -0.100   0.0617652736
	  42  0.025 -0.091  0.083  0.100 -0.100 -0.100   0.0617651612
	  43  0.025 -0.091  0.082  0.100 -0.100 -0.100   0.0617651390
	  45  0.025 -0.091  0.081  0.100 -0.100 -0.100   0.0617651225
	  53  0.025 -0.091  0.081  0.105 -0.100 -0.100   0.0617602698
	  54  0.025 -0.091  0.081  0.131 -0.100 -0.100   0.0617492416
	  56  0.025 -0.091  0.081  0.129 -0.100 -0.100   0.0617476060
	  57  0.025 -0.091  0.081  0.122 -0.100 -0.100   0.0617469268
	  59  0.025 -0.091  0.081  0.125 -0.100 -0.100   0.0617465009
	  70  0.025 -0.091  0.081  0.125 -0.104 -0.100   0.0617449132
	  79  0.025 -0.091  0.081  0.125 -0.104  0.059   0.0612870084
	  83  0.025 -0.091  0.081  0.125 -0.104  0.062   0.0612863574
	  powell nthiter 1: fret = 0.061286
	  96  0.009 -0.091  0.081  0.125 -0.104  0.062   0.0612705980
	  97  0.010 -0.091  0.081  0.125 -0.104  0.062   0.0612698679
	  98  0.013 -0.091  0.081  0.125 -0.104  0.062   0.0612693839
	 108  0.013  0.013  0.081  0.125 -0.104  0.062   0.0612485688
	 109  0.013 -0.034  0.081  0.125 -0.104  0.062   0.0612454141
	 111  0.013 -0.056  0.081  0.125 -0.104  0.062   0.0612448345
	 113  0.013 -0.051  0.081  0.125 -0.104  0.062   0.0612448313
	 116  0.013 -0.050  0.081  0.125 -0.104  0.062   0.0612447084
	 117  0.013 -0.048  0.081  0.125 -0.104  0.062   0.0612445789
	 126  0.013 -0.048  0.119  0.125 -0.104  0.062   0.0611741474
	 128  0.013 -0.048  0.117  0.125 -0.104  0.062   0.0611740877
	 136  0.013 -0.048  0.117  0.060 -0.104  0.062   0.0611018481
	 137  0.013 -0.048  0.117  0.050 -0.104  0.062   0.0610929155
	 140  0.013 -0.048  0.117 -0.007 -0.104  0.062   0.0610512318
	 142  0.013 -0.048  0.117  0.015 -0.104  0.062   0.0610468756
	 143  0.013 -0.048  0.117  0.008 -0.104  0.062   0.0610420465
	 144  0.013 -0.048  0.117  0.006 -0.104  0.062   0.0610414102
	 146  0.013 -0.048  0.117  0.005 -0.104  0.062   0.0610413014
	 155  0.013 -0.048  0.117  0.005 -0.102  0.062   0.0610404631
	 156  0.013 -0.048  0.117  0.005 -0.101  0.062   0.0610403368
	 165  0.013 -0.048  0.117  0.005 -0.101  0.071   0.0610347225
	 167  0.013 -0.048  0.117  0.005 -0.101  0.070   0.0610347037
	  powell nthiter 2: fret = 0.061035
	 180  0.017 -0.048  0.117  0.005 -0.101  0.070   0.0610331525
	 181  0.018 -0.048  0.117  0.005 -0.101  0.070   0.0610329501
	 182  0.019 -0.048  0.117  0.005 -0.101  0.070   0.0610329019
	 190  0.019  0.014  0.117  0.005 -0.101  0.070   0.0610106306
	 191  0.019 -0.010  0.117  0.005 -0.101  0.070   0.0609983026
	 193  0.019 -0.024  0.117  0.005 -0.101  0.070   0.0609976772
	 194  0.019 -0.018  0.117  0.005 -0.101  0.070   0.0609967388
	 204  0.019 -0.018  0.129  0.005 -0.101  0.070   0.0609931998
	 205  0.019 -0.018  0.126  0.005 -0.101  0.070   0.0609926470
	 206  0.019 -0.018  0.127  0.005 -0.101  0.070   0.0609926132
	 216  0.019 -0.018  0.127 -0.012 -0.101  0.070   0.0609716711
	 218  0.019 -0.018  0.127 -0.016 -0.101  0.070   0.0609699584
	 221  0.019 -0.018  0.127 -0.017 -0.101  0.070   0.0609699236
	 229  0.019 -0.018  0.127 -0.017 -0.104  0.070   0.0609670989
	 231  0.019 -0.018  0.127 -0.017 -0.106  0.070   0.0609668845
	 240  0.019 -0.018  0.127 -0.017 -0.106  0.071   0.0609666739
	 241  0.019 -0.018  0.127 -0.017 -0.106  0.073   0.0609666725
	 244  0.019 -0.018  0.127 -0.017 -0.106  0.072   0.0609665020
	 245  0.026  0.011  0.137 -0.039 -0.110  0.075   0.0609599315
	 251  0.023 -0.000  0.133 -0.031 -0.108  0.074   0.0609505266
	 253  0.023 -0.002  0.132 -0.030 -0.108  0.074   0.0609497628
	 254  0.023 -0.003  0.132 -0.029 -0.108  0.074   0.0609495870
	 256  0.023 -0.003  0.132 -0.029 -0.108  0.074   0.0609495765
	  powell nthiter 3: fret = 0.060950
	 267 -0.047 -0.003  0.132 -0.029 -0.108  0.074   0.0609166482
	 273 -0.040 -0.003  0.132 -0.029 -0.108  0.074   0.0609112261
	 287 -0.040 -0.003  0.132 -0.029 -0.108  0.079   0.0609080459
	 301 -0.040 -0.003  0.133 -0.029 -0.108  0.079   0.0609077087
	 302 -0.040 -0.003  0.136 -0.029 -0.108  0.079   0.0609072403
	 304 -0.040 -0.003  0.135 -0.029 -0.108  0.079   0.0609072005
	 314 -0.040 -0.003  0.135 -0.037 -0.108  0.079   0.0609018779
	 316 -0.040 -0.003  0.135 -0.043 -0.108  0.079   0.0608999478
	 317 -0.040 -0.003  0.135 -0.044 -0.108  0.079   0.0608997953
	 327 -0.040 -0.003  0.135 -0.044 -0.107  0.079   0.0608994938
	 328 -0.040 -0.003  0.135 -0.044 -0.104  0.079   0.0608991843
	 330 -0.040 -0.003  0.135 -0.044 -0.105  0.079   0.0608991797
	 336 -0.037  0.008  0.139 -0.052 -0.107  0.080   0.0608815404
	 338 -0.037  0.010  0.140 -0.054 -0.107  0.080   0.0608810266
	 340 -0.037  0.010  0.140 -0.054 -0.107  0.080   0.0608809854
	 342 -0.037  0.010  0.139 -0.053 -0.107  0.080   0.0608809665
	 344 -0.037  0.010  0.139 -0.053 -0.107  0.080   0.0608809527
	  powell nthiter 4: fret = 0.060881
	 357 -0.039  0.010  0.139 -0.053 -0.107  0.080   0.0608801013
	 371 -0.039  0.010  0.139 -0.053 -0.107  0.081   0.0608797295
	 379 -0.039  0.010  0.128 -0.053 -0.107  0.081   0.0608698297
	 392 -0.039  0.010  0.128 -0.055 -0.107  0.081   0.0608694731
	 393 -0.039  0.010  0.128 -0.058 -0.107  0.081   0.0608690243
	 404 -0.039  0.010  0.128 -0.058 -0.103  0.081   0.0608661329
	 406 -0.039  0.010  0.128 -0.058 -0.102  0.081   0.0608659989
	 414 -0.039  0.011  0.128 -0.058 -0.102  0.082   0.0608655657
	 415 -0.039  0.012  0.129 -0.059 -0.102  0.082   0.0608654084
	 420 -0.039  0.012  0.129 -0.059 -0.102  0.082   0.0608653901
	 421 -0.040  0.014  0.118 -0.065 -0.097  0.083   0.0608619807
	 428 -0.040  0.014  0.118 -0.065 -0.097  0.083   0.0608619331
	 435 -0.040  0.014  0.118 -0.065 -0.097  0.083   0.0608619309
	  powell nthiter 5: fret = 0.060862
	 447 -0.039  0.014  0.118 -0.065 -0.097  0.083   0.0608614230
	 459 -0.039  0.014  0.118 -0.065 -0.097  0.086   0.0608603778
	 470 -0.039  0.013  0.118 -0.064 -0.097  0.086   0.0608603758
	 474 -0.039  0.013  0.118 -0.064 -0.097  0.086   0.0608603757
	 475 -0.039  0.013  0.118 -0.065 -0.097  0.086   0.0608603714
	 476 -0.039  0.013  0.118 -0.065 -0.097  0.086   0.0608603565
	 488 -0.039  0.013  0.118 -0.059 -0.097  0.086   0.0608593058
	 489 -0.039  0.013  0.118 -0.060 -0.097  0.086   0.0608592158
	 506 -0.040  0.014  0.116 -0.061 -0.096  0.086   0.0608588897
	 510 -0.040  0.014  0.116 -0.061 -0.096  0.086   0.0608588772
	  powell nthiter 6: fret = 0.060859
	 526 -0.038  0.014  0.116 -0.061 -0.096  0.086   0.0608587937
	 528 -0.037  0.014  0.116 -0.061 -0.096  0.086   0.0608587645
	 548 -0.037  0.014  0.116 -0.061 -0.096  0.086   0.0608587212
	 562 -0.037  0.014  0.116 -0.060 -0.096  0.086   0.0608587025
	 579 -0.037  0.014  0.116 -0.060 -0.096  0.086   0.0608586963
	 585 -0.037  0.014  0.116 -0.060 -0.096  0.086   0.0608586740
	  powell nthiter 7: fret = 0.060859
	 618 -0.037  0.014  0.116 -0.060 -0.096  0.086   0.0608586482
	 619 -0.037  0.015  0.116 -0.060 -0.096  0.086   0.0608586259
	 622 -0.037  0.015  0.116 -0.060 -0.096  0.086   0.0608586152
	 654 -0.037  0.015  0.116 -0.060 -0.096  0.086   0.0608586103
	 655 -0.037  0.015  0.116 -0.060 -0.096  0.086   0.0608586049
	  powell nthiter 8: fret = 0.060859
	 683 -0.037  0.015  0.116 -0.060 -0.096  0.087   0.0608585842
	 692 -0.037  0.015  0.116 -0.061 -0.096  0.087   0.0608585734
	 708 -0.037  0.015  0.116 -0.060 -0.096  0.087   0.0608585709
	 729 -0.037  0.015  0.116 -0.060 -0.096  0.087   0.0608585469
	 733 -0.037  0.015  0.116 -0.060 -0.096  0.087   0.0608585318
	  powell nthiter 9: fret = 0.060859
	 746 -0.040  0.015  0.116 -0.060 -0.096  0.087   0.0608584109
	 758 -0.040  0.015  0.116 -0.060 -0.096  0.090   0.0608575530
	 759 -0.040  0.015  0.116 -0.060 -0.096  0.089   0.0608575083
	 767 -0.040  0.018  0.117 -0.062 -0.096  0.089   0.0608571188
	 768 -0.040  0.017  0.117 -0.061 -0.096  0.089   0.0608570387
	 769 -0.040  0.017  0.117 -0.061 -0.096  0.089   0.0608570303
	 770 -0.040  0.017  0.117 -0.061 -0.096  0.089   0.0608570146
	 783 -0.040  0.017  0.117 -0.060 -0.096  0.089   0.0608570012
	 804 -0.040  0.017  0.116 -0.061 -0.096  0.089   0.0608569822
	 807 -0.040  0.017  0.116 -0.061 -0.096  0.089   0.0608569686
	 808 -0.040  0.017  0.116 -0.061 -0.096  0.089   0.0608569506
	 810 -0.040  0.017  0.116 -0.061 -0.096  0.089   0.0608569358
	 813 -0.043  0.019  0.116 -0.061 -0.096  0.092   0.0608545176
	 816 -0.047  0.022  0.116 -0.063 -0.096  0.096   0.0608517375
	 819 -0.050  0.024  0.116 -0.063 -0.096  0.098   0.0608509895
	 825 -0.050  0.024  0.116 -0.063 -0.096  0.098   0.0608509721
	 827 -0.050  0.024  0.116 -0.063 -0.096  0.098   0.0608509668
	 830 -0.050  0.024  0.116 -0.063 -0.096  0.098   0.0608509599
	 832 -0.050  0.024  0.116 -0.063 -0.096  0.098   0.0608509588
	  powell nthiter 10: fret = 0.060851
	 844 -0.048  0.024  0.116 -0.063 -0.096  0.098   0.0608501202
	 845 -0.047  0.024  0.116 -0.063 -0.096  0.098   0.0608500990
	 853 -0.047  0.024  0.116 -0.063 -0.096  0.098   0.0608499753
	 868 -0.046  0.025  0.117 -0.064 -0.096  0.098   0.0608495238
	 869 -0.046  0.026  0.117 -0.065 -0.096  0.098   0.0608494362
	 871 -0.046  0.026  0.117 -0.065 -0.096  0.098   0.0608494266
	 874 -0.046  0.026  0.117 -0.065 -0.096  0.098   0.0608494223
	 875 -0.046  0.026  0.117 -0.065 -0.096  0.098   0.0608494218
	 901 -0.049  0.028  0.117 -0.065 -0.096  0.101   0.0608487700
	  powell nthiter 11: fret = 0.060849
	 924 -0.048  0.028  0.117 -0.065 -0.096  0.101   0.0608487310
	 978 -0.048  0.028  0.117 -0.065 -0.097  0.101   0.0608485652
	 979 -0.048  0.028  0.117 -0.065 -0.098  0.101   0.0608485092
	 986 -0.049  0.029  0.117 -0.066 -0.098  0.102   0.0608483058
	 990 -0.049  0.029  0.117 -0.066 -0.098  0.102   0.0608482923
	 991 -0.049  0.029  0.117 -0.066 -0.098  0.102   0.0608482844
	 996 -0.049  0.029  0.117 -0.066 -0.098  0.102   0.0608482671
	  powell nthiter 12: fret = 0.060848
	1011 -0.050  0.029  0.117 -0.066 -0.098  0.102   0.0608480650
	1020 -0.050  0.029  0.117 -0.066 -0.098  0.102   0.0608480550
	1023 -0.050  0.029  0.117 -0.066 -0.098  0.102   0.0608480513
	1034 -0.050  0.030  0.117 -0.066 -0.098  0.102   0.0608480480
	1035 -0.050  0.029  0.117 -0.066 -0.098  0.102   0.0608480160
	1049 -0.050  0.029  0.117 -0.067 -0.098  0.102   0.0608479902
	1060 -0.050  0.029  0.117 -0.067 -0.099  0.102   0.0608478376
	1069 -0.050  0.029  0.117 -0.067 -0.099  0.102   0.0608478240
	1073 -0.050  0.029  0.117 -0.067 -0.099  0.102   0.0608478070
	1074 -0.051  0.030  0.118 -0.069 -0.100  0.102   0.0608477841
	  powell nthiter 13: fret = 0.060848
	1093 -0.050  0.030  0.117 -0.068 -0.099  0.102   0.0608477335
	1111 -0.050  0.030  0.117 -0.068 -0.099  0.102   0.0608477257
	  powell nthiter 14: fret = 0.060848
	Powell done niters = 14
	Computing relative cost
	 0  -25.0 -25.0 -25.0   1.027602
	 1  -25.0 -25.0  25.0   1.009385
	 2  -25.0  25.0 -25.0   1.007963
	 3  -25.0  25.0  25.0   0.996369
	 4   25.0 -25.0 -25.0   1.022250
	 5   25.0 -25.0  25.0   1.014382
	 6   25.0  25.0 -25.0   0.999880
	 7   25.0  25.0  25.0   1.001296
	REL:  8  0.060848    8.079127  1.009891 rel = 0.0602518 
	Number of iterations    14
	Min cost was 0.060848
	Number of FunctionCalls  1245
	TolPowell 0.000000
	nMaxItersPowell 36
	OptimizationTime 44.203924 sec
	Parameters at optimum (transmm) -0.05009  0.02957  0.11659
	Parameters at optimum (rotdeg) -0.06789 -0.09893  0.10222 
	Final costs ----------------
	Number of surface hits 277683
	WM  Intensity   104.0960 +/-  16.3321
	Ctx Intensity   153.8628 +/-  32.8083
	Pct Contrast     37.0830 +/-  22.5036
	Cost   0.0608
	RelCost   0.0610
	Reg at min cost was 
	 0.00404   0.99999   0.00150   1.17551;
	 0.99990  -0.00402  -0.01390   0.02941;
	-0.01389   0.00156  -0.99990   0.26452;
	 0.00000   0.00000   0.00000   1.00000;

	Writing optimal reg to /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.auto.dat, type = 14 
	Original Reg 
	 0.00580   0.99998  -0.00025   1.22585;
	 0.99990  -0.00580  -0.01272  -0.00252;
	-0.01272  -0.00018  -0.99992   0.14581;
	 0.00000   0.00000   0.00000   1.00000;

	Original Reg - Optimal Reg
	 0.00176  -0.00001  -0.00175   0.05034;
	 0.00001  -0.00178   0.00118  -0.03193;
	 0.00117  -0.00173  -0.00002  -0.11871;
	 0.00000   0.00000   0.00000   0.00000;

	Computing change in lh position
	LH rmsDiffMean 0.149675
	Computing change in rh position
	Surface-RMS-Diff-mm 0.145750 0.038514 0.268669
	mri_segreg done
	MinCost: 0.060848 104.095971 153.862790 37.083016 
	tkregister2_cmdl --mov /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/orig/T2raw.mgz --reg /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.auto.dat --noedit --ltaout /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.auto.lta
	INFO: no target volume specified, assuming FreeSurfer orig volume.
	target  volume orig
	movable volume /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/orig/T2raw.mgz
	reg file       /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.auto.dat
	LoadVol        0
	ZeroCRAS       0
	7.3.2
	Diagnostic Level -1
	---- Input registration matrix --------
	 0.00404   0.99999   0.00150   1.17551;
	 0.99990  -0.00402  -0.01390   0.02941;
	-0.01389   0.00156  -0.99990   0.26452;
	 0.00000   0.00000   0.00000   1.00000;
	float2int = 0
	---------------------------------------
	INFO: loading target /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/orig.mgz
	Ttarg: --------------------
	-1.00000   0.00000   0.00000   128.00000;
	 0.00000   0.00000   1.00000  -128.00000;
	 0.00000  -1.00000   0.00000   128.00000;
	 0.00000   0.00000   0.00000   1.00000;
	INFO: loading movable /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/orig/T2raw.mgz
	Tmov: --------------------
	-1.00000   0.00000   0.00000   128.00003;
	 0.00000   0.00000   1.00000  -96.00000;
	 0.00000  -1.00000   0.00000   128.00003;
	 0.00000   0.00000   0.00000   1.00000;
	mkheaderreg = 0, float2int = 0
	---- Input registration matrix --------
	 0.00404   0.99999   0.00150   1.17551;
	 0.99990  -0.00402  -0.01390   0.02941;
	-0.01389   0.00156  -0.99990   0.26452;
	 0.00000   0.00000   0.00000   1.00000;
	Determinant 1
	subject = sub-CC122172
	RegMat ---------------------------
	 0.00404   0.99999   0.00150   1.17551;
	 0.99990  -0.00402  -0.01390   0.02941;
	-0.01389   0.00156  -0.99990   0.26452;
	 0.00000   0.00000   0.00000   1.00000;
	Cleaning up
 
	Started at Fri Apr 12 19:19:23 CEST 2024 
	Ended   at Fri Apr 12 19:21:30 CEST 2024
	BBR-Run-Time-Sec 127
 
	bbregister Done
	To check results, run:
	tkregisterfv --mov /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/orig/T2raw.mgz --reg /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.auto.lta --surfs  --sd /var/lib/condor/execute/dir_3377921/ds/freesurfer
 

	 cp /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.auto.lta /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.lta 

	mri_convert -odt float -at /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.lta -rl /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/orig.mgz /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/orig/T2raw.mgz /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/T2.prenorm.mgz 
	reading from /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/orig/T2raw.mgz...
	TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
	i_ras = (-0.003515, -0.999994, 0)
	j_ras = (0.013944, -4.8995e-05, 0.999903)
	k_ras = (0.999897, -0.00351501, -0.013944)
	INFO: Reading transformation from file /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.lta...
	Reading transform with LTAreadEx()
	reading template info from volume /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/orig.mgz...
	INFO: Applying transformation from file /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/transforms/T2raw.lta...
	---------------------------------
	INFO: Transform Matrix (linear_ras_to_ras)
	 1.00000   0.00052  -0.00005  -0.04892;
	-0.00052   1.00000  -0.00150  -0.19873;
	 0.00005   0.00150   1.00000   0.20250;
	 0.00000   0.00000   0.00000   1.00000;
	---------------------------------
	Applying LTAtransformInterp (resample_type 1)
	changing data type from ushrt to float (noscale = 0)...
	MRIchangeType: Building histogram 0 407 1000, flo=0, fhi=0.999, dest_type=3
	writing to /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/T2.prenorm.mgz...

	 mri_normalize -seed 1234 -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/aseg.presurf.mgz -surface /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/surf/lh.white identity.nofile -surface /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/surf/rh.white identity.nofile /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/T2.prenorm.mgz /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/T2.norm.mgz 

	setting seed for random number genererator to 1234
	using Gaussian smoothing of bias field, sigma=0.500
	disabling nonmaximum suppression
	retaining  points that are at least 1.000mm from the boundary
	using segmentation for initial intensity normalization
	reading mri_src from /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/T2.prenorm.mgz...
	Copying mri_dst from mri_src
	computing distance transform
	computing distance transform
	min_dist = 1
	Erasing Border planes 4
	Removing non-wm voxels
	55817 non wm control points removed
	Building bias image
	building Voronoi diagram...
	performing soap bubble smoothing, sigma = 0...
	smoothing bias field with sigma=0.500
	MRIapplyBiasCorrectionSameGeometry()
	NaN found at voxel (128, 0, 0, 0)
	error: Numerical argument out of domain
	error: WARNING: 16777216 NaNs found in volume /var/lib/condor/execute/dir_3377921/ds/freesurfer/sub-CC122172/mri/T2.prenorm.mgz...

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@effigies @liuzhenqi77 @FeHoff