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