Loading rhel8/default-icl
  Loading requirement: dot rhel8/slurm singularity/current rhel8/global
    cuda/11.4 vgl/2.5.1/64 intel-oneapi-compilers/2022.1.0/gcc/b6zld2mz
    intel-oneapi-mpi/2021.6.0/intel/guxuvcpm
Changed directory to /rds/user/mm2075/hpc-work/Pipelines/micapipe.

JobID: 25573523
======
Time: Sun 20 Aug 15:24:38 BST 2023
Running on master node: cpu-q-336
Current directory: /rds/user/mm2075/hpc-work/Pipelines/micapipe

Nodes allocated:
================
cpu-q-336

numtasks=1, numnodes=1, mpi_tasks_per_node=1 (OMP_NUM_THREADS=1)

Executing command:
==================
/home/mm2075/rds/hpc-work/Pipelines/micapipe/batch_run_micapipe_all.sh 35843 20230327 

Some packages in this Docker container are non-free
If you are considering commercial use of this container, please consult the relevant license:
https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Licence
INFO: /home/mm2075/matlab/startup.m does not exist ... creating


micapipe -bids /home/mm2075/rds/hpc-work/Pipelines/micapipe/test_dataset_BIDS -sub 35843 -out /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives -ses 20230327 -tmpDir /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327 -fs_licence /opt/freesurfer-7.3.2/license.txt -proc_func


-------------------------------------------------------------
	MICA pipeline - (Version v0.2.0 'Northern flicker') 
		Subject: 35843 Session: ses-20230327
-------------------------------------------------------------
		Freesurfer licence:	/opt/freesurfer-7.3.2/license.txt

[ INFO ]..... Inputs: 
		Topup Config     :	DEFAULT
		ICA fix training :	DEFAULT
		Main scan        :	DEFAULT
		Phase scan       :	DEFAULT
		Reverse Phase    :	DEFAULT
		Perform NSR      :	0
		Perform GSR      :	0
		No FIX           :	0
		Longitudinal ses :	FALSE
		Drop TR          :	FALSE
		Surface          :	fastsurfer

[ INFO ]..... No run number specified for func scan and did not find more than one run for main scan - all good! 

[ INFO ]..... Using default json scan: /home/mm2075/rds/hpc-work/Pipelines/micapipe/test_dataset_BIDS/sub-35843/ses-20230327/func/sub-35843_ses-20230327_task-rest_acq-AP_bold.json 

[ INFO ]..... No run number specified for phase reversals and did not find more than one phase reversal scan - all good! 

[ WARNING ]..... Subject 35843 doesn't have a Main Phase Scan (pe): TOPUP will run only if a rpe is provided 

[ WARNING ]..... Subject 35843 doesn't have Reverse Phase Scan (rpe): TOPUP will be skipped 

[ INFO ]..... Will use default config file for TOPUP: /opt/fsl-6.0.2/etc/flirtsch/b02b0_1.cnf 

[ INFO ]..... ICA-FIX pipeline will be run! 

[ INFO ]..... Will use default training file for ICA-FIX: /opt/micapipe/functions/MICAMTL_training_15HC_15PX.RData 

[ INFO ]..... Global, white matter and CSF signal regression will not be performed (default) 


-------------------------------------------------------------
	functional MRI processing
		micapipe v0.2.0 'Northern flicker', container_micapipe-v0.2.0 
-------------------------------------------------------------

[ INFO ]..... MICA pipe - Software versions 
		MRtrix3.....	3.0.1
		            	/opt/miniconda-22.11.1/envs/micapipe/bin/mrinfo
		FSL.........	6.0
		            	/opt/fsl-6.0.2
		ANFI........	 Jun  9 2023 (Version AFNI_23.1.08 'Publius Helvius Pertinax')
		            	/opt/afni-latest/3dresample
		ANTS........	 0.0.0.0
		            	/opt/ants-2.3.4/
		WorkBench...	1.3.2
		            	/usr/bin/wb_command
		FreeSurfer..	freesurfer-linux-ubuntu18_x86_64-7.3.2-20220804-6354275
		            	/opt/freesurfer-7.3.2
		fix.........	/opt/fix1.068/fix
		            	/opt/fix1.068
		python......	3.9.16
		            	/opt/miniconda-22.11.1/envs/micapipe/bin/python
		R...........	3.6.3
		            	/usr/bin/R
		conda.......	conda 22.11.1
		            	/opt/miniconda-22.11.1/condabin/conda

[ INFO ]..... Variables for functional processing 
		T1 nativepro       :	/home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/anat/sub-35843_ses-20230327_space-nativepro_T1w.nii.gz
		T1 surface      :	/home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/fastsurfer/sub-35843_ses-20230327/mri/orig.mgz
		mainScan         :	/home/mm2075/rds/hpc-work/Pipelines/micapipe/test_dataset_BIDS/sub-35843/ses-20230327/func/sub-35843_ses-20230327_task-rest_acq-AP_bold.nii.gz
		mainScan json    :	/home/mm2075/rds/hpc-work/Pipelines/micapipe/test_dataset_BIDS/sub-35843/ses-20230327/func/sub-35843_ses-20230327_task-rest_acq-AP_bold.json
		Main phase scan    :	file not found
		Main reverse phase :	file not found
		TOPUP config file  :	/opt/fsl-6.0.2/etc/flirtsch/b02b0_1.cnf
		ICA-FIX training   :	/opt/micapipe/functions/MICAMTL_training_15HC_15PX.RData
		Saving temporal dir:	FALSE
		Parallel processing      :	6 threads
		proc_fun outputs:	/home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold
		tagMRI:	se_task-rest_acq-AP_bold

mm2075 @ cpu-q-336 Sun Aug 20 15:24:45 BST 2023:
COMMAND -->   mkdir -p /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327  

[ INFO ]..... Processing mainScan scan 
		func file:	/home/mm2075/rds/hpc-work/Pipelines/micapipe/test_dataset_BIDS/sub-35843/ses-20230327/func/sub-35843_ses-20230327_task-rest_acq-AP_bold.nii.gz

mm2075 @ cpu-q-336 Sun Aug 20 15:24:45 BST 2023:
COMMAND -->   3dresample -orient LPI -prefix /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/mainScan_reo.nii.gz -inset /home/mm2075/rds/hpc-work/Pipelines/micapipe/test_dataset_BIDS/sub-35843/ses-20230327/func/sub-35843_ses-20230327_task-rest_acq-AP_bold.nii.gz  
*+ WARNING:   If you are performing spatial transformations on an oblique dset,
  such as /home/mm2075/rds/hpc-work/Pipelines/micapipe/test_dataset_BIDS/sub-35843/ses-20230327/func/sub-35843_ses-20230327_task-rest_acq-AP_bold.nii.gz,
  or viewing/combining it with volumes of differing obliquity,
  you should consider running: 
     3dWarp -deoblique 
  on this and  other oblique datasets in the same session.
 See 3dWarp -help for details.
++ Oblique dataset:/home/mm2075/rds/hpc-work/Pipelines/micapipe/test_dataset_BIDS/sub-35843/ses-20230327/func/sub-35843_ses-20230327_task-rest_acq-AP_bold.nii.gz is 8.380401 degrees from plumb.

mm2075 @ cpu-q-336 Sun Aug 20 15:25:21 BST 2023:
COMMAND -->   fslreorient2std /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/mainScan_reo.nii.gz /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/mainScan_reo.nii.gz  

mm2075 @ cpu-q-336 Sun Aug 20 15:25:55 BST 2023:
COMMAND -->   fslmaths /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/mainScan_reo.nii.gz -Tmean /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/mainScan_reoMean.nii.gz  

mm2075 @ cpu-q-336 Sun Aug 20 15:26:05 BST 2023:
COMMAND -->   3dvolreg -Fourier -twopass -base /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/mainScan_reoMean.nii.gz -zpad 4 -prefix /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/mainScan_mc.nii.gz -1Dfile /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_mainScan.1D -1Dmatrix_save /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/mainScan_mat_mc.1D /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/mainScan_reo.nii.gz  
++ 3dvolreg: AFNI version=AFNI_23.1.08 (Jun  9 2023) [64-bit]
++ Authored by: RW Cox
++ Coarse del was 10, replaced with 6
++ Max displacement in automask = 0.88 (mm) at sub-brick 126
++ Max delta displ  in automask = 0.41 (mm) at sub-brick 379

mm2075 @ cpu-q-336 Sun Aug 20 15:38:40 BST 2023:
COMMAND -->   fslmaths /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/mainScan_mc.nii.gz -Tmean /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/mainScan_mcMean.nii.gz  

mm2075 @ cpu-q-336 Sun Aug 20 15:38:52 BST 2023:
COMMAND -->   fsl_motion_outliers -i /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/mainScan_reo.nii.gz -o /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_spikeRegressors_FD.1D -s /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_metric_FD.1D --fd  
terminate called after throwing an instance of 'NiftiIO::NiftiException'
  what():  Error: short write, output file will be truncated
Aborted

mm2075 @ cpu-q-336 Sun Aug 20 15:40:25 BST 2023:
COMMAND -->   mv /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_mainScan.1D /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se.1D  

[ WARNING ]..... No pe or rpe (AP, PA) acquisition were found, TOPUP will be skip!!!!!!! 

mm2075 @ cpu-q-336 Sun Aug 20 15:40:25 BST 2023:
COMMAND -->   mv -v /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/mainScan_mc.nii.gz /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se.nii.gz  
copied '/home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/mainScan_mc.nii.gz' -> '/home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se.nii.gz'
mv: setting attribute 'system.posix_acl_access' for 'system.posix_acl_access': Invalid argument
mv: preserving permissions for ‘/home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se.nii.gz’: Invalid argument
removed '/home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/mainScan_mc.nii.gz'

[ INFO ]..... !!!!!  goin str8 to ICA-FIX yo  !!!!! 

[ INFO ]..... Generating a func binary mask 

mm2075 @ cpu-q-336 Sun Aug 20 15:40:26 BST 2023:
COMMAND -->   fslmaths /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se.nii.gz -Tmean /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_mean.nii.gz  

mm2075 @ cpu-q-336 Sun Aug 20 15:40:37 BST 2023:
COMMAND -->   N4BiasFieldCorrection -d 3 -i /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_mean.nii.gz -r -o /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_mean.nii.gz  

mm2075 @ cpu-q-336 Sun Aug 20 15:40:39 BST 2023:
COMMAND -->   mri_synthstrip -i /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_mean.nii.gz -o /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_brain.nii.gz -m /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_brain_mask.nii.gz  
Configuring model on the CPU
Running SynthStrip model version 1
Input image read from: /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_mean.nii.gz
Masked image saved to: /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_brain.nii.gz
Binary brain mask saved to: /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_brain_mask.nii.gz
If you use SynthStrip in your analysis, please cite:
----------------------------------------------------
SynthStrip: Skull-Stripping for Any Brain Image.
A Hoopes, JS Mora, AV Dalca, B Fischl, M Hoffmann.
NeuroImage 206 (2022), 119474.

[ INFO ]..... High pass filter 

mm2075 @ cpu-q-336 Sun Aug 20 15:40:59 BST 2023:
COMMAND -->   3dTproject -input /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se.nii.gz -prefix /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_HP.nii.gz -passband 0.01 666  
++ 3dTproject: AFNI version=AFNI_23.1.08 (Jun  9 2023) [64-bit]
++ Authored by: Cox the Algebraic (Linear)
++ Setting up regressors
++ setting up stopband frequency mask
 + Block #0: 490 time points -- 7 stopband regressors
++ 1 Blocks * 3 polynomials -- 3 polort regressors
++ 490 retained time points MINUS 10 regressors ==> 480 D.O.F. left
++ no -mask option ==> processing all 495616 voxels in dataset
++ Compute pseudo-inverse of fixed orts
++ Loading dataset
++ Starting project-orization
++ Convert results to output dataset
++ Output dataset /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_HP.nii.gz
++ ===== clock time = 52s 785ms

mm2075 @ cpu-q-336 Sun Aug 20 15:41:52 BST 2023:
COMMAND -->   mkdir -p /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC  

[ INFO ]..... Running melodic 

mm2075 @ cpu-q-336 Sun Aug 20 15:41:52 BST 2023:
COMMAND -->   cp /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_HP.nii.gz /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC/filtered_func_data.nii.gz  

mm2075 @ cpu-q-336 Sun Aug 20 15:41:53 BST 2023:
COMMAND -->   melodic --in=/home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC/filtered_func_data.nii.gz --tr=0.735 --nobet --mask=/home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_brain_mask.nii.gz --bgthreshold=3 --mmthresh=0.5 --report --Oall --outdir=/home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC/filtered_func_data.ica --Omean=/home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC/mean_func.nii.gz  

[ INFO ]..... Creating a synthetic T1nativepro image for registration 

mm2075 @ cpu-q-336 Sun Aug 20 16:00:07 BST 2023:
COMMAND -->   flirt -applyisoxfm 2.3863637447357178,2.3863639831542969,2.4000000953674316 -in /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/anat/sub-35843_ses-20230327_space-nativepro_T1w_brain.nii.gz -ref /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/anat/sub-35843_ses-20230327_space-nativepro_T1w_brain.nii.gz -out /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/sub-35843_ses-20230327_space-nativepro_desc-T1wbold.nii.gz  

[ INFO ]..... Registering func MRI to nativepro 

mm2075 @ cpu-q-336 Sun Aug 20 16:00:11 BST 2023:
COMMAND -->   mri_synthseg --i /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/sub-35843_ses-20230327_space-nativepro_desc-T1wbold.nii.gz --o /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/T1bold_synthseg.nii.gz --robust --threads 6 --cpu  
Traceback (most recent call last):
  File "/opt/freesurfer-7.3.2/python/scripts/mri_synthseg", line 22, in <module>
    import tensorflow as tf
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/site-packages/tensorflow/__init__.py", line 41, in <module>
    from tensorflow.python.tools import module_util as _module_util
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/site-packages/tensorflow/python/__init__.py", line 106, in <module>
    from tensorflow.python.platform import test
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/site-packages/tensorflow/python/platform/test.py", line 24, in <module>
    from tensorflow.python.framework import test_util as _test_util
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/site-packages/tensorflow/python/framework/test_util.py", line 37, in <module>
    from absl.testing import parameterized
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/site-packages/absl/testing/parameterized.py", line 218, in <module>
    from absl.testing import absltest
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/site-packages/absl/testing/absltest.py", line 242, in <module>
    get_default_test_tmpdir(),
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/site-packages/absl/testing/absltest.py", line 180, in get_default_test_tmpdir
    tmpdir = os.path.join(tempfile.gettempdir(), 'absl_testing')
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/tempfile.py", line 286, in gettempdir
    tempdir = _get_default_tempdir()
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/tempfile.py", line 218, in _get_default_tempdir
    raise FileNotFoundError(_errno.ENOENT,
FileNotFoundError: [Errno 2] No usable temporary directory found in ['/tmp', '/var/tmp', '/usr/tmp', '/home/mica']

mm2075 @ cpu-q-336 Sun Aug 20 16:00:23 BST 2023:
COMMAND -->   fslmaths /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/T1bold_synthseg.nii.gz -uthr 42 -thr 42 -bin -mul -39 -add /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/T1bold_synthseg.nii.gz /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/T1bold_synthsegGM.nii.gz  
Image Exception : #63 :: No image files match: /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/T1bold_synthseg
terminate called after throwing an instance of 'std::runtime_error'
  what():  No image files match: /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/T1bold_synthseg
/opt/micapipe/functions/utilities.sh: line 1084:   717 Aborted                 $l_command

mm2075 @ cpu-q-336 Sun Aug 20 16:00:23 BST 2023:
COMMAND -->   mri_synthseg --i /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_brain.nii.gz --o /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/func_brain_synthseg.nii.gz --robust --threads 6 --cpu  
Traceback (most recent call last):
  File "/opt/freesurfer-7.3.2/python/scripts/mri_synthseg", line 22, in <module>
    import tensorflow as tf
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/site-packages/tensorflow/__init__.py", line 41, in <module>
    from tensorflow.python.tools import module_util as _module_util
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/site-packages/tensorflow/python/__init__.py", line 106, in <module>
    from tensorflow.python.platform import test
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/site-packages/tensorflow/python/platform/test.py", line 24, in <module>
    from tensorflow.python.framework import test_util as _test_util
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/site-packages/tensorflow/python/framework/test_util.py", line 37, in <module>
    from absl.testing import parameterized
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/site-packages/absl/testing/parameterized.py", line 218, in <module>
    from absl.testing import absltest
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/site-packages/absl/testing/absltest.py", line 242, in <module>
    get_default_test_tmpdir(),
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/site-packages/absl/testing/absltest.py", line 180, in get_default_test_tmpdir
    tmpdir = os.path.join(tempfile.gettempdir(), 'absl_testing')
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/tempfile.py", line 286, in gettempdir
    tempdir = _get_default_tempdir()
  File "/opt/freesurfer-7.3.2/python/lib/python3.8/tempfile.py", line 218, in _get_default_tempdir
    raise FileNotFoundError(_errno.ENOENT,
FileNotFoundError: [Errno 2] No usable temporary directory found in ['/tmp', '/var/tmp', '/usr/tmp', '/home/mica']

mm2075 @ cpu-q-336 Sun Aug 20 16:00:28 BST 2023:
COMMAND -->   fslmaths /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/func_brain_synthseg.nii.gz -uthr 42 -thr 42 -bin -mul -39 -add /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/func_brain_synthseg.nii.gz /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/func_brain_synthsegGM.nii.gz  
Image Exception : #63 :: No image files match: /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/func_brain_synthseg
terminate called after throwing an instance of 'std::runtime_error'
  what():  No image files match: /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/func_brain_synthseg
/opt/micapipe/functions/utilities.sh: line 1084:   736 Aborted                 $l_command

mm2075 @ cpu-q-336 Sun Aug 20 16:00:28 BST 2023:
COMMAND -->   antsRegistrationSyN.sh -d 3 -f /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/T1bold_synthsegGM.nii.gz -m /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/func_brain_synthsegGM.nii.gz -o /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-se_task-rest_acq-AP_bold_to-nativepro_mode-image_desc-affine_ -t a -n 6 -p d  
Fixed image '/home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/T1bold_synthsegGM.nii.gz' does not exist.  See usage: '/opt/ants-2.3.4/antsRegistrationSyN.sh -h 1'

mm2075 @ cpu-q-336 Sun Aug 20 16:00:28 BST 2023:
COMMAND -->   antsApplyTransforms -d 3 -i /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/T1bold_synthsegGM.nii.gz -r /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/func_brain_synthsegGM.nii.gz -t [/home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-se_task-rest_acq-AP_bold_to-nativepro_mode-image_desc-affine_0GenericAffine.mat,1] -o /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/T1bold_in_func.nii.gz -v -u int  
Using double precision for computations.
Input scalar image: /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/T1bold_synthsegGM.nii.gz
 file /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/T1bold_synthsegGM.nii.gz does not exist . 
Reference image: /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/func_brain_synthsegGM.nii.gz
 file /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/func_brain_synthsegGM.nii.gz does not exist . 
=============================================================================
The composite transform comprises the following transforms (in order): 
  1. inverse of /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-se_task-rest_acq-AP_bold_to-nativepro_mode-image_desc-affine_0GenericAffine.mat (type = AffineTransform)
=============================================================================
Default pixel value: 0
/opt/micapipe/functions/utilities.sh: line 1084:   744 Segmentation fault      $l_command

mm2075 @ cpu-q-336 Sun Aug 20 16:00:29 BST 2023:
COMMAND -->   antsRegistrationSyN.sh -d 3 -m /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/T1bold_in_func.nii.gz -f /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/func_brain_synthsegGM.nii.gz -o /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-nativepro_func_to-se_task-rest_acq-AP_bold_mode-image_desc-SyN_ -t s -n 6 -p d  
Fixed image '/home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/func_brain_synthsegGM.nii.gz' does not exist.  See usage: '/opt/ants-2.3.4/antsRegistrationSyN.sh -h 1'

mm2075 @ cpu-q-336 Sun Aug 20 16:00:29 BST 2023:
COMMAND -->   rm -rf /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/*Warped.nii.gz  

mm2075 @ cpu-q-336 Sun Aug 20 16:00:29 BST 2023:
COMMAND -->   antsApplyTransforms -d 3 -i /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_brain.nii.gz -r /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/sub-35843_ses-20230327_space-nativepro_desc-T1wbold.nii.gz -t /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-se_task-rest_acq-AP_bold_to-nativepro_mode-image_desc-affine_0GenericAffine.mat -t [/home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-nativepro_func_to-se_task-rest_acq-AP_bold_mode-image_desc-SyN_0GenericAffine.mat,1] -t /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-nativepro_func_to-se_task-rest_acq-AP_bold_mode-image_desc-SyN_1InverseWarp.nii.gz -o /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/anat/sub-35843_ses-20230327_space-nativepro_desc-se_task-rest_acq-AP_bold_mean.nii.gz -v -u int  
Using double precision for computations.
Input scalar image: /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_brain.nii.gz
Reference image: /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/sub-35843_ses-20230327_space-nativepro_desc-T1wbold.nii.gz
=============================================================================
The composite transform comprises the following transforms (in order): 
  1. /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-nativepro_func_to-se_task-rest_acq-AP_bold_mode-image_desc-SyN_1InverseWarp.nii.gz (type = DisplacementFieldTransform)
  2. inverse of /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-nativepro_func_to-se_task-rest_acq-AP_bold_mode-image_desc-SyN_0GenericAffine.mat (type = AffineTransform)
  3. /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-se_task-rest_acq-AP_bold_to-nativepro_mode-image_desc-affine_0GenericAffine.mat (type = AffineTransform)
=============================================================================
Default pixel value: 0
Interpolation type: LinearInterpolateImageFunction
Output warped image: /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/anat/sub-35843_ses-20230327_space-nativepro_desc-se_task-rest_acq-AP_bold_mean.nii.gz

mm2075 @ cpu-q-336 Sun Aug 20 16:00:30 BST 2023:
COMMAND -->   antsApplyTransforms -d 3 -i /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/anat/sub-35843_ses-20230327_space-nativepro_T1w_brain.nii.gz -r /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_brain.nii.gz -t /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-nativepro_func_to-se_task-rest_acq-AP_bold_mode-image_desc-SyN_1Warp.nii.gz -t /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-nativepro_func_to-se_task-rest_acq-AP_bold_mode-image_desc-SyN_0GenericAffine.mat -t [/home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-se_task-rest_acq-AP_bold_to-nativepro_mode-image_desc-affine_0GenericAffine.mat,1] -o /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-T1w.nii.gz -v -u int  
Using double precision for computations.
Input scalar image: /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/anat/sub-35843_ses-20230327_space-nativepro_T1w_brain.nii.gz
Reference image: /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_brain.nii.gz
=============================================================================
The composite transform comprises the following transforms (in order): 
  1. inverse of /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-se_task-rest_acq-AP_bold_to-nativepro_mode-image_desc-affine_0GenericAffine.mat (type = AffineTransform)
  2. /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-nativepro_func_to-se_task-rest_acq-AP_bold_mode-image_desc-SyN_0GenericAffine.mat (type = AffineTransform)
  3. /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-nativepro_func_to-se_task-rest_acq-AP_bold_mode-image_desc-SyN_1Warp.nii.gz (type = DisplacementFieldTransform)
=============================================================================
Default pixel value: 0
Interpolation type: LinearInterpolateImageFunction
Output warped image: /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-T1w.nii.gz

mm2075 @ cpu-q-336 Sun Aug 20 16:00:32 BST 2023:
COMMAND -->   cp /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-T1w.nii.gz /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC/filtered_func_data.ica/T1w2fmri_brain.nii.gz  

[ INFO ]..... Creating transformations file: func space <<>> T1nativepro 

[ INFO ]..... Getting ICA-FIX requirements 

mm2075 @ cpu-q-336 Sun Aug 20 16:00:32 BST 2023:
COMMAND -->   mkdir -p /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC/reg /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC/mc  

mm2075 @ cpu-q-336 Sun Aug 20 16:00:32 BST 2023:
COMMAND -->   cp /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se.1D /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC/mc/prefiltered_func_data_mcf.par  

mm2075 @ cpu-q-336 Sun Aug 20 16:00:32 BST 2023:
COMMAND -->   cp /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_brain_mask.nii.gz /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC/mask.nii.gz  

mm2075 @ cpu-q-336 Sun Aug 20 16:00:32 BST 2023:
COMMAND -->   cp /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC/filtered_func_data.ica/mean.nii.gz /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC/mean_func.nii.gz  

mm2075 @ cpu-q-336 Sun Aug 20 16:00:32 BST 2023:
COMMAND -->   fslroi /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC/filtered_func_data.nii.gz /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC/reg/example_func.nii.gz 245 1  

mm2075 @ cpu-q-336 Sun Aug 20 16:00:40 BST 2023:
COMMAND -->   cp /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/anat/sub-35843_ses-20230327_space-nativepro_T1w_brain.nii.gz /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC/reg/highres.nii.gz  

mm2075 @ cpu-q-336 Sun Aug 20 16:00:40 BST 2023:
COMMAND -->   antsApplyTransforms -v 1 -o Linear[/home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/highres2example_func.mat,0] -t /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-nativepro_func_to-se_task-rest_acq-AP_bold_mode-image_desc-SyN_0GenericAffine.mat -t [/home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-se_task-rest_acq-AP_bold_to-nativepro_mode-image_desc-affine_0GenericAffine.mat,1]  
Using double precision for computations.
=============================================================================
The composite transform comprises the following transforms (in order): 
  1. inverse of /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-se_task-rest_acq-AP_bold_to-nativepro_mode-image_desc-affine_0GenericAffine.mat (type = AffineTransform)
  2. /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/xfm/sub-35843_ses-20230327_from-nativepro_func_to-se_task-rest_acq-AP_bold_mode-image_desc-SyN_0GenericAffine.mat (type = AffineTransform)
=============================================================================
Default pixel value: 0

mm2075 @ cpu-q-336 Sun Aug 20 16:00:40 BST 2023:
COMMAND -->   ConvertTransformFile 3 /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/highres2example_func.mat /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/highres2example_func.txt  

mm2075 @ cpu-q-336 Sun Aug 20 16:00:40 BST 2023:
COMMAND -->   lta_convert --initk /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/highres2example_func.txt --outfsl /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/itk2fsl_highres2example_func.mat --src /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/anat/sub-35843_ses-20230327_space-nativepro_T1w.nii.gz --trg /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_brain.nii.gz  
7.3.2

--initk: /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/highres2example_func.txt input ITK txt transform.
--outfsl: /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/itk2fsl_highres2example_func.mat output FSL matrix.
--src: /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/anat/sub-35843_ses-20230327_space-nativepro_T1w.nii.gz src image (geometry).
--trg: /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_brain.nii.gz trg image (geometry).
INFO: using NIfTI-1 qform 
Transform: AffineTransform_double_3_3
 LTA read, type : 1
 0.97055   0.00100   0.00050   3.27221;
-0.00677   0.98680   0.05663   25.70387;
 0.00059  -0.08458   0.98000  -21.66463;
 0.00000   0.00000   0.00000   1.00000;
FSLOUTPUTTYPE NIFTI_GZ 
tkreg2FSL: mov det = 1, ref det = 13.6674
INFO: FSL2FreeSurfer: Mov volume is NIFTI with positive det,
      applying LR flip to registration matrix.
INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det,
      applying LR flip to registration matrix.
lta_convert successful.

mm2075 @ cpu-q-336 Sun Aug 20 16:00:41 BST 2023:
COMMAND -->   flirt -in /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/anat/sub-35843_ses-20230327_space-nativepro_T1w.nii.gz -out /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/T1w2fmri_brain_ants2fsl.nii.gz -ref /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-se_brain.nii.gz -applyxfm -init /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/itk2fsl_highres2example_func.mat  

mm2075 @ cpu-q-336 Sun Aug 20 16:00:43 BST 2023:
COMMAND -->   flirt -in /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/T1w2fmri_brain_ants2fsl.nii.gz -ref /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/func/desc-se_task-rest_acq-AP_bold/volumetric/sub-35843_ses-20230327_space-func_desc-T1w.nii.gz -omat /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ants2fsl_fixed.omat -cost mutualinfo -searchcost mutualinfo -dof 6  

mm2075 @ cpu-q-336 Sun Aug 20 16:00:59 BST 2023:
COMMAND -->   convert_xfm -concat /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ants2fsl_fixed.omat -omat /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC/reg/highres2example_func.mat /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/itk2fsl_highres2example_func.mat  

[ INFO ]..... Running ICA-FIX 

mm2075 @ cpu-q-336 Sun Aug 20 16:00:59 BST 2023:
COMMAND -->   fix /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC /opt/micapipe/functions/MICAMTL_training_15HC_15PX.RData 20 -m -h 100  
FIX Feature extraction for Melodic output directory: /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC
 create edge masks
 run FAST
 registration of standard space masks
 extract features
FIX Classifying components in Melodic directory: /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC using training file: /opt/micapipe/functions/MICAMTL_training_15HC_15PX.RData and threshold 20
FIX features not already generated, so creating them now.
FIX Feature extraction for Melodic output directory: /home/mm2075/rds/rds-cam-clin-qmin-nCu8GHKxWRw/data/micapipe/work_dir/sub-35843_ses-20230327/28606_micapipe_proc-func_sub-35843_ses-20230327/ICA_MELODIC
 create edge masks
 run FAST
 registration of standard space masks
 extract features
No valid labelling file specified

-------------------------------------------------------------

[ ERROR ]..... FIX failed, but MELODIC ran log file:
	 /home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/logs/proc_func_20-08-2023-3510.txt
/home/mm2075/rds/hpc-work/Pipelines/micapipe/derivatives/micapipe_v0.2.0/sub-35843/ses-20230327/logs/proc_func_20-08-2023-6440.txt

-------------------------------------------------------------



-------------------------------------------------------------
	GLOBAL micapipe running time with container_micapipe-v0.2.0 processing: 45.200 minutes 
-------------------------------------------------------------