Hi,

I keep getting the same error every time I run fmriprep on subjects from the OASIS3 dataset. There are 5-7 T1 scans over 3-4 time points for most subjects, and the registration is failing every time with the return code -9. I can’t seem to find any indication of what that return code means, so I don’t know what to try to dix. Does anybody have an idea?

Thanks, Blaise

cat /n/scratch2/bdf1/OASIS/derivatives/fmriprep/sub-OAS30004/log/20190719-151129_2b54c614-de57-4bd6-9c95-9c721b09df7d/crash-20190719-153017-bdf1-t1_merge-59cde0ed-a554-4c50-8cc7-fd158f28f7ae.txt Node: fmriprep_wf.single_subject_OAS30004_wf.anat_preproc_wf.anat_template_wf.t1_merge Working directory: /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/t1_merge

Node inputs:

args = <undefined> auto_detect_sensitivity = True average_metric = <undefined> environ = {'SUBJECTS_DIR': '/home/bdf1/software/freesurfer/subjects', 'OMP_NUM_THREADS': '4'} fixed_timepoint = True in_files = ['/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz', '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30004_ses-d1101_run-02_T1w_corrected.nii.gz', '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30004_ses-d2229_run-01_T1w_corrected.nii.gz', '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30004_ses-d2229_run-02_T1w_corrected.nii.gz', '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30004_ses-d2232_run-01_T1w_ras_corrected.nii.gz', '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30004_ses-d2232_run-02_T1w_corrected.nii.gz', '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30004_ses-d3457_T1w_ras_corrected.nii.gz'] in_intensity_scales = <undefined> initial_timepoint = 1 initial_transforms = <undefined> intensity_scaling = True no_iteration = True num_threads = 7 out_file = sub-OAS30004_ses-d1101_run-01_T1w_template.nii.gz outlier_sensitivity = <undefined> scaled_intensity_outputs = <undefined> subjects_dir = /home/bdf1/software/freesurfer/subjects subsample_threshold = 200 transform_outputs = True

Traceback (most recent call last): File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py", line 69, in run_node result['result'] = node.run(updatehash=updatehash) File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 472, in run result = self._run_interface(execute=True) File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 563, in _run_interface return self._run_command(execute) File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_command result = self._interface.run(cwd=outdir) File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/interfaces/freesurfer/base.py", line 265, in run return super(FSCommandOpenMP, self).run(**inputs) File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/interfaces/freesurfer/base.py", line 144, in run return super(FSCommand, self).run(**inputs) File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 375, in run runtime = self._run_interface(runtime) File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 758, in _run_interface self.raise_exception(runtime) File "/home/bdf1/software/anaconda3/envs/fmriprep141sing/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 695, in raise_exception ).format(**runtime.dictcopy())) RuntimeError: Command: mri_robust_template --satit --fixtp --mov /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30004_ses-d1101_run-02_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30004_ses-d2229_run-01_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30004_ses-d2229_run-02_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30004_ses-d2232_run-01_T1w_ras_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30004_ses-d2232_run-02_T1w_corrected.nii.gz /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30004_ses-d3457_T1w_ras_corrected.nii.gz --inittp 1 --iscale --noit --template sub-OAS30004_ses-d1101_run-01_T1w_template.nii.gz --subsample 200 --lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp1.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp2.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp3.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp4.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp5.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp6.lta /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/t1_merge/tp7.lta Standard output: $Id: mri_robust_template.cpp,v 1.54 2016/05/05 21:17:08 mreuter Exp $

--satit: Will estimate SAT iteratively! --fixtp: Will map everything to init TP! --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30004_ses-d1101_run-02_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30004_ses-d2229_run-01_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30004_ses-d2229_run-02_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30004_ses-d2232_run-01_T1w_ras_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30004_ses-d2232_run-02_T1w_corrected.nii.gz as movable/source volume. --mov: Using /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30004_ses-d3457_T1w_ras_corrected.nii.gz as movable/source volume. Total: 7 input volumes --inittp: Using TP 1 as target for initialization --iscale: Enableing intensity scaling! --noit: Will output only first template (no iterations)! --template: Using sub-OAS30004_ses-d1101_run-01_T1w_template.nii.gz as template output volume. --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms Setting iscale ... reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30004_ses-d1101_run-02_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30004_ses-d1101_run-02_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30004_ses-d2229_run-01_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30004_ses-d2229_run-01_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30004_ses-d2229_run-02_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30004_ses-d2229_run-02_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30004_ses-d2232_run-01_T1w_ras_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30004_ses-d2232_run-01_T1w_ras_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30004_ses-d2232_run-02_T1w_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30004_ses-d2232_run-02_T1w_corrected.nii.gz' to bspline ... MRItoBSpline degree 3 reading source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30004_ses-d3457_T1w_ras_corrected.nii.gz'... converting source '/n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30004_ses-d3457_T1w_ras_corrected.nii.gz' to bspline ... MRItoBSpline degree 3

MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) :

[init] ========================= TP 5 to TP 1 ============================== Register TP 5 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct4/sub-OAS30004_ses-d2232_run-01_T1w_ras_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz )

[init] ========================= TP 6 to TP 1 ============================== Register TP 6 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct5/sub-OAS30004_ses-d2232_run-02_T1w_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz )

[init] ========================= TP 3 to TP 1 ============================== Register TP 3 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct2/sub-OAS30004_ses-d2229_run-01_T1w_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz )

[init] ========================= TP 4 to TP 1 ============================== Register TP 4 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct3/sub-OAS30004_ses-d2229_run-02_T1w_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz )

[init] ========================= TP 7 to TP 1 ============================== Register TP 7 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct6/sub-OAS30004_ses-d3457_T1w_ras_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz )

[init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct1/sub-OAS30004_ses-d1101_run-02_T1w_corrected.nii.gz ) to TP 1 ( /n/scratch2/bdf1/OASIS/work/fmriprep_wf/single_subject_OAS30004_wf/anat_preproc_wf/anat_template_wf/n4_correct/mapflow/_n4_correct0/sub-OAS30004_ses-d1101_run-01_T1w_corrected.nii.gz )

-- Original : (0.999994, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (0.999996, 0.999996, 0.999996)mm and (176, 257, 257) voxels. -- Reslicing using cubic bspline -- Original : (1, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (1, 1, 1)mm and (177, 256, 256) voxels. -- Reslicing using cubic bspline -- Original : (0.999994, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (0.999996, 0.999996, 0.999996)mm and (176, 257, 257) voxels. -- Reslicing using cubic bspline -- Original : (1, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (1, 1, 1)mm and (177, 256, 256) voxels. -- Reslicing using cubic bspline -- Original : (0.999994, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (0.999996, 0.999996, 0.999996)mm and (176, 257, 257) voxels. -- Reslicing using cubic bspline -- Original : (0.999994, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (0.999996, 0.999996, 0.999996)mm and (176, 257, 257) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 MRItoBSpline degree 3 MRItoBSpline degree 3 MRItoBSpline degree 3 MRItoBSpline degree 3 MRItoBSpline degree 3 -- Original : (0.999996, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (1, 1, 1)mm and (177, 256, 256) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.999996, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (0.999996, 0.999996, 0.999996)mm and (176, 257, 257) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.999996, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (0.999996, 0.999996, 0.999996)mm and (176, 257, 257) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.999996, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (0.999996, 0.999996, 0.999996)mm and (176, 257, 257) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.999996, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (0.999996, 0.999996, 0.999996)mm and (176, 257, 257) voxels. -- Reslicing using cubic bspline -- Original : (0.999996, 1, 1)mm and (176, 256, 256) voxels. -- Resampled: (1, 1, 1)mm and (177, 256, 256) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 MRItoBSpline degree 3

- Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter:

- Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter:

- Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter:

- Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter:

- Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) - running loop to estimate saturation parameter:

- Max Resolution used: 2 -- gpS ( 44 , 64 , 64 ) -- gpT ( 44 , 64 , 64 ) Standard error:

Return code: -9

------------------------------------------------------- Blaise Frederick Associate Professor of Psychiatry/Biophysicist Harvard Medical School/McLean Hospital bbfrederick@mclean.harvard.edu http://www.nirs-fmri.net