Dear dHCP Expertes,
I am using dHCP example codes (dhcp-dual-echo-time-fieldmap) from dhcp-neonatal-fmri-pipeline (Files · master · Sean Fitzgibbon / dhcp-neonatal-fmri-pipeline · GitLab). I am using dHCP data release 2. I get the following error in the command line from the “FIX” part of the analysis:
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 ‘[’/Users/parinazbabaeeghazvini/Documents/GitHub/fix/fix’, ‘-f’, ‘/Users/parinazbabaeeghazvini/Desktop/sourcedata/derivatives/dhcp-fmri-pipeline1/sub-CC00060XX03/ses-12501/denoise’]’ returned non-zero exit status 1.
And the “error log” returns the following error:
Error Time: 09/21/2022 12:01:14
Error using call_fsl (line 36)
FSL call (/bin/sh -c ‘. /usr/local/fsl/etc/fslconf/fsl.sh; cluster --in=/Users/parinazbabaeeghazvini/Desktop/sourcedata/derivatives/dhcp-fmri-pipeline1/sub-CC00060XX03/ses-12501/denoise/fix/dummyabs --thresh=2.500000 > /Users/parinazbabaeeghazvini/Desktop/sourcedata/derivatives/dhcp-fmri-pipeline1/sub-CC00060XX03/ses-12501/denoise/fix/dummy1’) failed, option – unrecognized
Usage: cluster graphfile
-C k - generate no more than k clusters (0)
0 : no limit
-c k - use clustering method k (0)
0 : use modularity
1 : use modularity quality
-o - output file (stdout)
-v - verbose mode
-? - print usage
Would you please help me to fix the error?
Thank you for your time and consideration,
Parinaz.