Hi there,
While running smriprep, I got the following error:
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220406-12:26:27,663 nipype.workflow ERROR:
could not run node: smriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1w_conform
220406-12:26:27,663 nipype.workflow INFO:
crashfile: /out/smriprep/sub-01/log/20220406-122305_fd77ae4c-3a32-4794-ba5a-7359a4fac5cb/crash-20220406-122609-smriprep-_t1w_conform2-50d356c3-881f-4027-a619-5c4e94013b64.txt
220406-12:26:27,663 nipype.workflow ERROR:
could not run node: smriprep_wf.single_subject_01_wf.anat_preproc_wf.anat_template_wf.t1w_conform
220406-12:26:27,663 nipype.workflow INFO:
crashfile: /out/smriprep/sub-01/log/20220406-122305_fd77ae4c-3a32-4794-ba5a-7359a4fac5cb/crash-20220406-122611-smriprep-_t1w_conform4-b8371d26-6ff6-4360-b3dd-e27090747064.txt
220406-12:26:27,663 nipype.workflow INFO:
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RUNNING: docker run --rm -e DOCKER_VERSION_8395080871=20.10.7 -u 1000 -v /home/ec2-user/.licenses/freesurfer/license.txt:/opt/freesurfer/license.txt:ro -v /home/ec2-user/brain-mri-processing/data:/data:ro -v /home/ec2-user/output:/out nipreps/smriprep:0.8.3 /data /out participant --participant-label 01 --nthreads 4 --mem-gb 8 --resource-monitor --verbose
This is the content of the second crashfile that the error mentions:
Node: _t1w_conform4
Working directory: /tmp/work/smriprep_wf/single_subject_01_wf/anat_preproc_wf/anat_template_wf/t1w_conform/mapflow/_t1w_conform4
Node inputs:
in_file = /data/sub-01/ses-20130525/anat/sub-01_ses-20130525_run-5_T1w.nii.gz
target_shape = (256, 484, 484)
target_zooms = (1.0, 0.5289255976676941, 0.5289255976676941)
Traceback (most recent call last):
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
result = self._run_interface(execute=True)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
return self._run_command(execute)
File "/opt/conda/lib/python3.8/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
result = self._interface.run(cwd=outdir)
File "/opt/conda/lib/python3.8/site-packages/nipype/interfaces/base/core.py", line 428, in run
runtime = self._run_interface(runtime)
File "/opt/conda/lib/python3.8/site-packages/niworkflows/interfaces/images.py", line 561, in _run_interface
data = nli.resample_img(reoriented, target_affine, target_shape).dataobj
File "/opt/conda/lib/python3.8/site-packages/nilearn/image/resampling.py", line 503, in resample_img
raise BoundingBoxError("The field of view given "
nilearn.image.resampling.BoundingBoxError: The field of view given by the target affine does not contain any of the data
Could anyone help me on this, please?