Hi everyone,
A little bit of context: I’m writing a workflow that takes the functional files processed through fmriprep and smooths them using SPM. I’m currently running Nipype on the Sherlock server using a singularity container that contains Nipype (version: 0.13.1) and Jupyter.
My pipeline (ostensibly) takes the functional files, unzips them, smooths them, and puts them in a new directory. Here’s what it looks like:
infosource = pe.Node(util.IdentityInterface(fields=['subject_id']), name = 'infosource')
infosource.iterables = ('subject_id', ['sub-04', 'sub-05'])
datasource = pe.Node(nio.DataGrabber(infields=['subject_id']), name = 'datasource')
datasource.inputs.base_directory = in_dir
datasource.inputs.template = '%s/func/*preproc.nii.gz'
datasource.inputs.sort_filelist = True
gunzip = pe.MapNode(interface = misc.Gunzip(),
iterfield=['in_file'],
name='gunzip')
smooth = pe.Node(interface= spm.Smooth(),
name = 'smooth')
datasink = pe.Node(interface=nio.DataSink(), name="datasink", iterfield = 'container')
datasink.inputs.base_directory = out_dir
smoothingWorkflow = pe.Workflow(name = 'smoothingWorkflow', base_dir=working_dir)
smoothingWorkflow.connect([
(infosource, datasource, [('subject_id', 'subject_id')]),
(infosource, datasink, [('subject_id', 'container')]),
(datasource, gunzip, [('outfiles', 'in_file')]),
(gunzip, smooth, [('out_file', 'in_files')]),
(smooth, datasink, [('smoothed_files', 'func')])
])
smoothingWorkflow.run()
However, I get the following error when I try to execute the smoothing node:
RuntimeError: Command:
/opt/spm12/run_spm12.sh /opt/mcr/v85/ script /scratch/users/nvelez/myProject/smoothing_wf/smoothingWorkflow/_subject_id_sub-04/smooth/pyscript_smooth.m
Standard output:
Standard error:
Failed to create a directory required to extract the CTF file.
Please make sure that you have appropriate permissions and re-run the
application.
Error initializing CTF Archive
Return code: 255
Interface MatlabCommand failed to run.
Interface Smooth failed to run.
Does anyone know what might be causing this error? I thought that I might be writing temporary files on a directory where I have no business writing, so I tried changing the working directory to a directory within $SCRATCH, but this didn’t seem to fix it.
Thanks in advance!