Hi Everyone,
I am trying to preprocess my single-band fMRI data using dhcp-dual-echo-time-fieldmap from this page (dhcp/examples/dhcp-dual-echo-time-fieldmap.py · master · Sean Fitzgibbon / dhcp-neonatal-fmri-pipeline · GitLab) because we only have DTI fieldmaps. The pipeline can not perform motion correction (mcdc). Here is the error message that I get:
[2022-09-15 22:17:13,568 - dhcp.func.mcdc.mcdc ] INFO : start
[2022-09-15 22:17:13,569 - dhcp.func.mcdc.mcdc ] INFO : BEGIN: motion correction and susceptibility distortion correction
[2022-09-15 22:17:13,570 - dhcp.util.util.timed ] INFO : BEGIN eddy_mcdc
[2022-09-15 22:17:13,572 - root.eddy_mcdc ] INFO : start
[2022-09-15 22:17:13,574 - root.eddy_mcdc ] INFO : Performing slice-to-volume (S2V) motion correction
[2022-09-15 22:17:13,574 - root.eddy_mcdc ] INFO : NO distortion correction
[2022-09-15 22:17:13,579 - dhcp.util.shellops.run ] INFO : /usr/local/fsl/bin/eddy --imain=/Users/parinazbabaeeghazvini/Desktop/sourcedata1/derivatives/dhcp-fmri-pipeline1/sub-NYS220/ses-001/import/func.nii.gz --mask=/Users/parinazbabaeeghazvini/Desktop/sourcedata1/derivatives/dhcp-fmri-pipeline1/sub-NYS220/ses-001/import/func_brainmask.nii.gz --index=/Users/parinazbabaeeghazvini/Desktop/sourcedata1/derivatives/dhcp-fmri-pipeline1/sub-NYS220/ses-001/mcdc/index.txt --bvals=/Users/parinazbabaeeghazvini/Desktop/sourcedata1/derivatives/dhcp-fmri-pipeline1/sub-NYS220/ses-001/mcdc/bvals --bvecs=/Users/parinazbabaeeghazvini/Desktop/sourcedata1/derivatives/dhcp-fmri-pipeline1/sub-NYS220/ses-001/mcdc/bvecs --acqp=/Users/parinazbabaeeghazvini/Desktop/sourcedata1/derivatives/dhcp-fmri-pipeline1/sub-NYS220/ses-001/mcdc/eddy.acqp --out=/Users/parinazbabaeeghazvini/Desktop/sourcedata1/derivatives/dhcp-fmri-pipeline1/sub-NYS220/ses-001/mcdc/func_mcdc --very_verbose --data_is_shelled --niter=10 --fwhm=10,10,5,5,0,0,0,0,0,0 --s2v_fwhm=0 --s2v_niter=10 --s2v_interp=trilinear --mporder=4 --nvoxhp=1000 --slspec=/Users/parinazbabaeeghazvini/.pyenv/versions/3.9.10/lib/python3.9/site-packages/dhcp_neonatal_fmri_pipeline-1.2.0-py3.9.egg/dhcp/resources/default_func.slorder --b0_only --field_mat=/usr/local/fsl/etc/flirtsch/ident.mat --dont_mask_output --s2v_lambda=1
Traceback (most recent call last):
File “/Users/parinazbabaeeghazvini/Desktop/dhcp_codes/dhcp-no-fieldmap.py”, line 169, in
mcdc.mcdc(
File “/Users/parinazbabaeeghazvini/.pyenv/versions/3.9.10/lib/python3.9/site-packages/dhcp_neonatal_fmri_pipeline-1.2.0-py3.9.egg/dhcp/func/mcdc.py”, line 195, in mcdc
eddy_mcdc(
File “/Users/parinazbabaeeghazvini/.pyenv/versions/3.9.10/lib/python3.9/site-packages/dhcp_neonatal_fmri_pipeline-1.2.0-py3.9.egg/dhcp/util/util.py”, line 51, in timed
result = f(*args, **kw)
File “/Users/parinazbabaeeghazvini/.pyenv/versions/3.9.10/lib/python3.9/site-packages/dhcp_neonatal_fmri_pipeline-1.2.0-py3.9.egg/dhcp/func/mcdc.py”, line 446, in eddy_mcdc
fsl.eddy(
File “/Users/parinazbabaeeghazvini/.pyenv/versions/3.9.10/lib/python3.9/site-packages/dhcp_neonatal_fmri_pipeline-1.2.0-py3.9.egg/dhcp/util/fslpy.py”, line 167, in eddy
shops.run(cmd)
File “/Users/parinazbabaeeghazvini/.pyenv/versions/3.9.10/lib/python3.9/site-packages/dhcp_neonatal_fmri_pipeline-1.2.0-py3.9.egg/dhcp/util/shellops.py”, line 41, in run
jobout = check_output(cmd)
File “/Users/parinazbabaeeghazvini/.pyenv/versions/3.9.10/lib/python3.9/subprocess.py”, line 424, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File “/Users/parinazbabaeeghazvini/.pyenv/versions/3.9.10/lib/python3.9/subprocess.py”, line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command ‘[’/usr/local/fsl/bin/eddy’, ‘–imain=/Users/parinazbabaeeghazvini/Desktop/sourcedata1/derivatives/dhcp-fmri-pipeline1/sub-NYS220/ses-001/import/func.nii.gz’, ‘–mask=/Users/parinazbabaeeghazvini/Desktop/sourcedata1/derivatives/dhcp-fmri-pipeline1/sub-NYS220/ses-001/import/func_brainmask.nii.gz’, ‘–index=/Users/parinazbabaeeghazvini/Desktop/sourcedata1/derivatives/dhcp-fmri-pipeline1/sub-NYS220/ses-001/mcdc/index.txt’, ‘–bvals=/Users/parinazbabaeeghazvini/Desktop/sourcedata1/derivatives/dhcp-fmri-pipeline1/sub-NYS220/ses-001/mcdc/bvals’, ‘–bvecs=/Users/parinazbabaeeghazvini/Desktop/sourcedata1/derivatives/dhcp-fmri-pipeline1/sub-NYS220/ses-001/mcdc/bvecs’, ‘–acqp=/Users/parinazbabaeeghazvini/Desktop/sourcedata1/derivatives/dhcp-fmri-pipeline1/sub-NYS220/ses-001/mcdc/eddy.acqp’, ‘–out=/Users/parinazbabaeeghazvini/Desktop/sourcedata1/derivatives/dhcp-fmri-pipeline1/sub-NYS220/ses-001/mcdc/func_mcdc’, ‘–very_verbose’, ‘–data_is_shelled’, ‘–niter=10’, ‘–fwhm=10,10,5,5,0,0,0,0,0,0’, ‘–s2v_fwhm=0’, ‘–s2v_niter=10’, ‘–s2v_interp=trilinear’, ‘–mporder=4’, ‘–nvoxhp=1000’, ‘–slspec=/Users/parinazbabaeeghazvini/.pyenv/versions/3.9.10/lib/python3.9/site-packages/dhcp_neonatal_fmri_pipeline-1.2.0-py3.9.egg/dhcp/resources/default_func.slorder’, ‘–b0_only’, ‘–field_mat=/usr/local/fsl/etc/flirtsch/ident.mat’, ‘–dont_mask_output’, ‘–s2v_lambda=1’]’ returned non-zero exit status 1.
Any help or suggestion is highly appreciated,
Parinaz.