I am trying to use --fs-no-recall to skip any surface processing to save time, but I keep receiving this error:
Here is the command I am running:
singularity run jpetucci-fmriprep_icsaci-master-rec.simg my_dataset no-reconall-2/results participant --participant-label 01 --fs-no-reconall --fs-license-file license.txt -w no-reconall-2/reports
Thank you!
Hi @rosaleen,
Do you think you could post the entire log somewhere? Most of what you have there are warnings, unrelated to the inu_n4 node that it says failed.
Best,
Chris
Here’s the entirety of the crash log:
Node: fmriprep_wf.single_subject_01_wf.anat_preproc_wf.brain_extraction_wf.inu_n4
Working directory: /gpfs/group/xxl213/default/Rosaleen/no-reconall-2/reports/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/inu_n4
Node inputs:
args =
bias_image =
bspline_fitting_distance = 200.0
bspline_order =
convergence_threshold = 1e-07
copy_header = True
dimension = 3
environ = {‘NSLOTS’: ‘8’}
input_image = [’/gpfs/group/xxl213/default/Rosaleen/no-reconall-2/reports/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0/sub-01_T1w_ras_valid_maths.nii.gz’]
mask_image =
n_iterations = [50, 50, 50, 50]
num_threads = 8
output_image =
save_bias = False
shrink_factor = 4
weight_image =
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/plugins/multiproc.py”, line 69, in run_node
result[‘result’] = node.run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 472, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 1259, in _run_interface
self.config[‘execution’][‘stop_on_first_crash’])))
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 1181, in _collate_results
(self.name, ‘\n’.join(msg)))
Exception: Subnodes of node: inu_n4 failed:
Subnode 0 failed
Error: Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/utils.py”, line 99, in nodelist_runner
result = node.run(updatehash=updatehash)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 472, in run
result = self._run_interface(execute=True)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 563, in _run_interface
return self._run_command(execute)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 643, in _run_command
result = self._interface.run(cwd=outdir)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 375, in run
runtime = self._run_interface(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/ants/segmentation.py”, line 438, in _run_interface
runtime, correct_return_codes)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 758, in _run_interface
self.raise_exception(runtime)
File “/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 695, in raise_exception
).format(**runtime.dictcopy()))
RuntimeError: Command:
N4BiasFieldCorrection --bspline-fitting [ 200 ] -d 3 --input-image /gpfs/group/xxl213/default/Rosaleen/no-reconall-2/reports/fmriprep_wf/single_subject_01_wf/anat_preproc_wf/brain_extraction_wf/truncate_images/mapflow/_truncate_images0/sub-01_T1w_ras_valid_maths.nii.gz --convergence [ 50x50x50x50, 1e-07 ] --output sub-01_T1w_ras_valid_maths_corrected.nii.gz --shrink-factor 4
Standard output:
Standard error:
Killed
Return code: 137
This looks likely to be an out-of-memory error, and possibly the reason that disabling FreeSurfer’s recon-all triggers this is that it frees up a higher-memory process to run at the same time as inu_n4.
How much memory do you have available? If you add --mem-mb constraint, the scheduler should do a better job at avoiding running too-large processes at the same time.
That worked, thanks!
MANAGED BY INCF
