`mritotal` subcommands not found #3103

tsalo · 2023-10-06T12:57:03Z

What happened?

I am processing multi-echo data with a T1w, and the recon-all step failed because the following mritotal subcommands were missing: mincresample, mincblur, volume_cog, minctracc, check_scale, and autocrop.

What command did you use?

singularity run --home /cbica/home/salot \
    --cleanenv -B /cbica/home/salot/datasets/mobile-phenomics/dset:/data \
    /cbica/home/salot/datasets/mobile-phenomics/singularity/fmriprep-23_1_5dev.simg \
    /data \
    /data/derivatives/fmriprep \
    participant \
    --participant-label 01 \
    -w /cbica/home/salot/datasets/mobile-phenomics/work \
    --nprocs 1 \
    --omp-nthreads 1 \
    --output-spaces func T1w MNI152NLin6Asym \
    --me-t2s-fit-method curvefit \
    --output-layout bids \
    --me-output-echos \
    --project-goodvoxels \
    --cifti-output \
    --bids-filter-file /cbica/home/salot/datasets/mobile-phenomics/code/bids_filter.json \
    --fs-license-file /cbica/home/salot/datasets/mobile-phenomics/freesurfer_license.txt \
    --skip_bids_validation

What version of fMRIPrep are you running?

23.2.0.dev39+g36404281

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.

fs-check-version --s sub-01 --o /tmp/tmp.wtCyBh
	Thu Oct  5 11:59:44 EDT 2023

	setenv SUBJECTS_DIR /data/derivatives/fmriprep/sourcedata/freesurfer
	cd /cbica/home/salot/datasets/mobile-phenomics/work/fmriprep_23_2_wf/single_subject_01_wf/anat_preproc_wf/surface_recon_wf/autorecon1
	/opt/freesurfer/bin/fs-check-version --s sub-01 --o /tmp/tmp.wtCyBh
	-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 2119fmn035 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
	pid 146995
	Current FS Version freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275
	Subject does not have a bstampfile, copying /opt/freesurfer/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 /data/derivatives/fmriprep/sourcedata/freesurfer
	Actual FREESURFER_HOME /opt/freesurfer
	Linux 2119fmn035 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01

	 mri_convert /cbica/home/salot/datasets/mobile-phenomics/work/fmriprep_23_2_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-01_ses-1_T1w_noise_corrected.nii.gz /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/orig/001.mgz 

	mri_convert /cbica/home/salot/datasets/mobile-phenomics/work/fmriprep_23_2_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-01_ses-1_T1w_noise_corrected.nii.gz /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/orig/001.mgz 
	reading from /cbica/home/salot/datasets/mobile-phenomics/work/fmriprep_23_2_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/denoise/mapflow/_denoise0/sub-01_ses-1_T1w_noise_corrected.nii.gz...
	TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
	i_ras = (1, 0, 0)
	j_ras = (0, 1, 0)
	k_ras = (-0, -0, 1)
	writing to /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/orig/001.mgz...
	#--------------------------------------------
	#@# MotionCor Thu Oct  5 11:59:46 EDT 2023
	Found 1 runs
	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/orig/001.mgz
	Checking for (invalid) multi-frame inputs...
	Only one run found so motion
	correction will not be performed. I'll
	copy the run to rawavg and continue.

	 cp /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/orig/001.mgz /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/rawavg.mgz 


	 mri_info /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/rawavg.mgz 

	rawavg.mgz ========================================
	Volume information for /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/rawavg.mgz
	          type: MGH
	    dimensions: 176 x 256 x 256
	   voxel sizes: 1.000000, 0.976563, 0.976563
	          type: FLOAT (3)
	           fov: 250.000
	           dof: 1
	        xstart: -88.0, xend: 88.0
	        ystart: -125.0, yend: 125.0
	        zstart: -125.0, zend: 125.0
	            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
	       nframes: 1
	       PhEncDir: UNKNOWN
	       FieldStrength: 0.000000
	ras xform present
	    xform info: x_r =   1.0000, y_r =   0.0000, z_r =  -0.0000, c_r =     0.3428
	              : x_a =   0.0000, y_a =   1.0000, z_a =  -0.0000, c_a =    19.7935
	              : x_s =   0.0000, y_s =   0.0000, z_s =   1.0000, c_s =   -20.9975

	talairach xfm : 
	Orientation   : RAS
	Primary Slice Direction: axial

	voxel to ras transform:
	                1.0000   0.0000  -0.0000   -87.6572
	                0.0000   0.9766  -0.0000  -105.2066
	                0.0000   0.0000   0.9766  -145.9976
	                0.0000   0.0000   0.0000     1.0000

	voxel-to-ras determinant 0.953675

	ras to voxel transform:
	                1.0000   0.0000   0.0000    87.6572
	                0.0000   1.0240   0.0000   107.7315
	                0.0000   0.0000   1.0240   149.5014
	                0.0000   0.0000   0.0000     1.0000
	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01

	 mri_convert /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/rawavg.mgz /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/orig.mgz --conform 

	mri_convert /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/rawavg.mgz /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/orig.mgz --conform 
	reading from /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/rawavg.mgz...
	TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
	i_ras = (1, 0, 0)
	j_ras = (0, 1, 0)
	k_ras = (-0, -0, 1)
	changing data type from float to uchar (noscale = 0)...
	MRIchangeType: Building histogram -0.000953734 1414.2 1000, flo=0, fhi=0.999, dest_type=0
	Reslicing using trilinear interpolation 
	writing to /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/orig.mgz...

	 mri_add_xform_to_header -c /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/transforms/talairach.xfm /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/orig.mgz /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/orig.mgz 

	INFO: extension is mgz

	 mri_info /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/orig.mgz 

	orig.mgz ========================================
	Volume information for /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/orig.mgz
	          type: MGH
	    dimensions: 256 x 256 x 256
	   voxel sizes: 1.000000, 1.000000, 1.000000
	          type: UCHAR (0)
	           fov: 256.000
	           dof: 1
	        xstart: -128.0, xend: 128.0
	        ystart: -128.0, yend: 128.0
	        zstart: -128.0, zend: 128.0
	            TR: 0.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 degrees
	       nframes: 1
	       PhEncDir: UNKNOWN
	       FieldStrength: 0.000000
	ras xform present
	    xform info: x_r =  -1.0000, y_r =   0.0000, z_r =   0.0000, c_r =     0.3428
	              : x_a =   0.0000, y_a =   0.0000, z_a =   1.0000, c_a =    19.7935
	              : x_s =   0.0000, y_s =  -1.0000, z_s =   0.0000, c_s =   -20.9975

	talairach xfm : /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/transforms/talairach.xfm
	Orientation   : LIA
	Primary Slice Direction: coronal

	voxel to ras transform:
	               -1.0000   0.0000   0.0000   128.3428
	                0.0000   0.0000   1.0000  -108.2065
	                0.0000  -1.0000   0.0000   107.0025
	                0.0000   0.0000   0.0000     1.0000

	voxel-to-ras determinant -1

	ras to voxel transform:
	               -1.0000  -0.0000  -0.0000   128.3428
	               -0.0000  -0.0000  -1.0000   107.0025
	               -0.0000   1.0000  -0.0000   108.2065
	               -0.0000  -0.0000  -0.0000     1.0000
	#--------------------------------------------
	#@# Talairach Thu Oct  5 11:59:53 EDT 2023
	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri

	 mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 

	/usr/bin/bc
	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri
	/opt/freesurfer/bin/mri_nu_correct.mni
	--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
	nIters 1
	mri_nu_correct.mni 7.3.2
	Linux 2119fmn035 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
	Thu Oct  5 11:59:53 EDT 2023
	tmpdir is ./tmp.mri_nu_correct.mni.147338
	cd /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri
	AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.147338/nu0.mgz --dtype uchar
	AntsN4BiasFieldCorrectionFs done
	mri_convert ./tmp.mri_nu_correct.mni.147338/nu0.mgz orig_nu.mgz --like orig.mgz --conform
	mri_convert ./tmp.mri_nu_correct.mni.147338/nu0.mgz orig_nu.mgz --like orig.mgz --conform 
	reading from ./tmp.mri_nu_correct.mni.147338/nu0.mgz...
	TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
	i_ras = (-1, 0, 0)
	j_ras = (0, 0, -1)
	k_ras = (0, 1, 0)
	INFO: transform src into the like-volume: orig.mgz
	writing to orig_nu.mgz...
 
 
	Thu Oct  5 12:02:52 EDT 2023
	mri_nu_correct.mni done

	 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 

	talairach_avi log file is transforms/talairach_avi.log...
	mv -f /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt
	Started at Thu Oct 5 12:02:52 EDT 2023
	Ended   at Thu Oct  5 12:03:13 EDT 2023
	talairach_avi done

	 cp transforms/talairach.auto.xfm transforms/talairach.xfm 

	lta_convert --src orig.mgz --trg /opt/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox
	7.3.2

	--src: orig.mgz src image (geometry).
	--trg: /opt/freesurfer/average/mni305.cor.mgz trg image (geometry).
	--inmni: transforms/talairach.xfm input MNI/XFM transform.
	--outlta: transforms/talairach.xfm.lta output LTA.
	--s: fsaverage subject name
	--ltavox2vox: output LTA as VOX_TO_VOX transform.
	 LTA read, type : 1
	 1.66768  -0.46606   0.82159   44.75748;
	-97.32905   112.43233   88.45214   1715.59375;
	 34.04164  -20.57554  -35.31321  -2123.05322;
	 0.00000   0.00000   0.00000   1.00000;
	setting subject to fsaverage
	Writing  LTA to file transforms/talairach.xfm.lta...
	lta_convert successful.
	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/transforms /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri 
	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri 
	#--------------------------------------------
	#@# Talairach Failure Detection Thu Oct  5 12:03:15 EDT 2023
	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri

	 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

	ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)

	Manual Talairach alignment may be necessary, or
	include the -notal-check flag to skip this test,
	making sure the -notal-check flag follows -all
	or -autorecon1 in the command string.
	See:

	http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

	INFO: Retrying Talairach align using 3T-based atlas...

	#--------------------------------------------
	#@# Talairach Thu Oct  5 12:03:15 EDT 2023
	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri

	 mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 

	/usr/bin/bc
	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri
	/opt/freesurfer/bin/mri_nu_correct.mni
	--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
	nIters 1
	mri_nu_correct.mni 7.3.2
	Linux 2119fmn035 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
	Thu Oct  5 12:03:15 EDT 2023
	tmpdir is ./tmp.mri_nu_correct.mni.147997
	cd /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri
	AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.147997/nu0.mgz --dtype uchar
	AntsN4BiasFieldCorrectionFs done
	mri_convert ./tmp.mri_nu_correct.mni.147997/nu0.mgz orig_nu.mgz --like orig.mgz --conform
	mri_convert ./tmp.mri_nu_correct.mni.147997/nu0.mgz orig_nu.mgz --like orig.mgz --conform 
	reading from ./tmp.mri_nu_correct.mni.147997/nu0.mgz...
	TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
	i_ras = (-1, 0, 0)
	j_ras = (0, 0, -1)
	k_ras = (0, 1, 0)
	INFO: transform src into the like-volume: orig.mgz
	writing to orig_nu.mgz...
 
 
	Thu Oct  5 12:06:18 EDT 2023
	mri_nu_correct.mni done

	 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm --atlas 3T18yoSchwartzReactN32_as_orig 

	talairach_avi log file is transforms/talairach_avi.log...
	mv -f /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4_vox2vox.txt /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/transforms/talsrcimg_to_3T18yoSchwartzReactN32_as_orig_t4_vox2vox.txt
	Started at Thu Oct 5 12:06:18 EDT 2023
	Ended   at Thu Oct  5 12:06:39 EDT 2023
	talairach_avi done

	 cp transforms/talairach.auto.xfm transforms/talairach.xfm 

	lta_convert --src orig.mgz --trg /opt/freesurfer/average/mni305.cor.mgz --inxfm transforms/talairach.xfm --outlta transforms/talairach.xfm.lta --subject fsaverage --ltavox2vox
	7.3.2

	--src: orig.mgz src image (geometry).
	--trg: /opt/freesurfer/average/mni305.cor.mgz trg image (geometry).
	--inmni: transforms/talairach.xfm input MNI/XFM transform.
	--outlta: transforms/talairach.xfm.lta output LTA.
	--s: fsaverage subject name
	--ltavox2vox: output LTA as VOX_TO_VOX transform.
	 LTA read, type : 1
	 0.08458   0.84734   7.62671   424.87531;
	 2.83673   1.75668  -15.85732  -1243.33643;
	 2.46005  -0.35815  -9.77660  -648.98743;
	 0.00000   0.00000   0.00000   1.00000;
	setting subject to fsaverage
	Writing  LTA to file transforms/talairach.xfm.lta...
	lta_convert successful.
	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri/transforms /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri 
	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri 
	#--------------------------------------------
	#@# Talairach Failure Detection Thu Oct  5 12:06:41 EDT 2023
	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri

	 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 

	ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)

	Manual Talairach alignment may be necessary, or
	include the -notal-check flag to skip this test,
	making sure the -notal-check flag follows -all
	or -autorecon1 in the command string.
	See:

	http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

	INFO: Trying MINC mritotal to perform Talairach align...

	#--------------------------------------------
	#@# Talairach Thu Oct  5 12:06:41 EDT 2023
	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri

	 mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50 

	/usr/bin/bc
	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri
	/opt/freesurfer/bin/mri_nu_correct.mni
	--no-rescale --i orig.mgz --o orig_nu.mgz --ants-n4 --n 1 --proto-iters 1000 --distance 50
	nIters 1
	mri_nu_correct.mni 7.3.2
	Linux 2119fmn035 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
	Thu Oct  5 12:06:41 EDT 2023
	tmpdir is ./tmp.mri_nu_correct.mni.149794
	cd /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri
	AntsN4BiasFieldCorrectionFs -i orig.mgz -o ./tmp.mri_nu_correct.mni.149794/nu0.mgz --dtype uchar
	AntsN4BiasFieldCorrectionFs done
	mri_convert ./tmp.mri_nu_correct.mni.149794/nu0.mgz orig_nu.mgz --like orig.mgz --conform
	mri_convert ./tmp.mri_nu_correct.mni.149794/nu0.mgz orig_nu.mgz --like orig.mgz --conform 
	reading from ./tmp.mri_nu_correct.mni.149794/nu0.mgz...
	TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
	i_ras = (-1, 0, 0)
	j_ras = (0, 0, -1)
	k_ras = (0, 1, 0)
	INFO: transform src into the like-volume: orig.mgz
	writing to orig_nu.mgz...
 
 
	Thu Oct  5 12:09:40 EDT 2023
	mri_nu_correct.mni done

	 talairach --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 

	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri
	/opt/freesurfer/bin/talairach
	--i orig_nu.mgz --xfm transforms/talairach.auto.xfm
	talairach 7.3.2
	Linux 2119fmn035 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
	Thu Oct  5 12:09:40 EDT 2023
	tmpdir is transforms/tmp.talairach.150141
	/data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/mri
	mri_convert orig_nu.mgz transforms/tmp.talairach.150141/src.mnc
	mri_convert orig_nu.mgz transforms/tmp.talairach.150141/src.mnc 
	reading from orig_nu.mgz...
	TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
	i_ras = (-1, 0, 0)
	j_ras = (0, 0, -1)
	k_ras = (0, 1, 0)
	writing to transforms/tmp.talairach.150141/src.mnc...
	--------------------------------------------
	mritotal -verbose -debug -clobber -modeldir /opt/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.150141/src.mnc transforms/talairach.auto.xfm
	mritotal: couldn't find program "mincresample"
	mritotal: couldn't find program "mincblur"
	mritotal: couldn't find program "volume_cog"
	mritotal: couldn't find program "minctracc"
	mritotal: couldn't find program "check_scale"
	mritotal: couldn't find program "autocrop"
	ERROR: mritotal failed, see transforms/talairach.log
	Linux 2119fmn035 3.10.0-1160.el7.x86_64 #1 SMP Mon Oct 19 16:18:59 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux

	recon-all -s sub-01 exited with ERRORS at Thu Oct  5 12:09:44 EDT 2023

	For more details, see the log file /data/derivatives/fmriprep/sourcedata/freesurfer/sub-01/scripts/recon-all.log
	To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

Additional information / screenshots

No response

The text was updated successfully, but these errors were encountered:

effigies · 2023-10-06T13:02:37Z

Do you have a subject that reliably hits this? If so, would you mind removing these from the exclude file, rebuilding the Docker image, and verifying that it runs all the way through without needing us to de-exclude even more files?

tsalo · 2023-10-08T15:32:05Z

It turns out the failure was happening on an image I improperly defaced, so now I'm not sure if this issue is valid. On the one hand, at least for some bad T1ws, recon-all will try to call these mritotal subcommands, but, at least in my case, recon-all should fail, even if the subcommands were available.

effigies · 2023-10-08T22:56:34Z

Yeah, I think we should put these back in.

When FreeSurfer has trouble with an image, it can reach for some more obscure tools. Closes nipreps#3103

When FreeSurfer has trouble with an image, it can reach for some more obscure tools. Closes #3103

tsalo added the bug label Oct 6, 2023

tsalo mentioned this issue Oct 6, 2023

mritotal: Command not found. #3088

Closed

effigies added this to the 23.2.0 milestone Nov 21, 2023

effigies added a commit to effigies/fmriprep that referenced this issue Nov 21, 2023

DOCKER: Restore mritotal subcommands

7458817

When FreeSurfer has trouble with an image, it can reach for some more obscure tools. Closes nipreps#3103

effigies mentioned this issue Nov 21, 2023

DOCKER: Restore mritotal subcommands #3149

Merged

effigies closed this as completed in #3149 Nov 21, 2023

effigies added a commit that referenced this issue Nov 21, 2023

DOCKER: Restore mritotal subcommands (#3149)

d9e92a9

When FreeSurfer has trouble with an image, it can reach for some more obscure tools. Closes #3103

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`mritotal` subcommands not found #3103

`mritotal` subcommands not found #3103

tsalo commented Oct 6, 2023 •

edited

effigies commented Oct 6, 2023

tsalo commented Oct 8, 2023

effigies commented Oct 8, 2023

mritotal subcommands not found #3103

mritotal subcommands not found #3103

Comments

tsalo commented Oct 6, 2023 • edited

What happened?

What command did you use?

What version of fMRIPrep are you running?

How are you running fMRIPrep?

Is your data BIDS valid?

Are you reusing any previously computed results?

Please copy and paste any relevant log output.

Additional information / screenshots

effigies commented Oct 6, 2023

tsalo commented Oct 8, 2023

effigies commented Oct 8, 2023

`mritotal` subcommands not found #3103

`mritotal` subcommands not found #3103

tsalo commented Oct 6, 2023 •

edited