Dear Tim, I am getting the following error:
hcp_fix_multi_run - ABORTING: Unsupported MATLAB run mode value (FSL_FIX_MATLAB_MODE) in /usr/local/bin/gaurav_folder_new/HCP/Connectome_Project_3_22/Pipelines/ICAFIX/hcp_fix_multi_run/settings.sh: In settings.sh, I have set up the following: # Part III General settings # ========================= # This variable selects how we run the MATLAB portions of FIX. # It takes the values 0-2: # 0 - Try running the compiled version of the function # 1 - Use the MATLAB script version # 2 - Use Octave script version if [ -z "${FSL_FIX_MATLAB_MODE}" ]; then FSL_FIX_MATLAB_MODE=0 fi if [[ ${FSL_FIX_MATLAB_MODE} = 2 && -z ${FSL_FIX_OCTAVE} ]]; then echo "ERROR in $0: Can't find Octave command" exit 1 fi Not sure if this is needed but FSL_FIX_OCTAVE is disabled in my settings.sh since I tried to install octave via MacPorts and am getting the following errors: Error: Failed to build mpich-default: command execution failed Error: See /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_science_mpich/mpich-default/main.log for details. Error: Follow https://guide.macports.org/#project.tickets to report a bug. Error: Processing of port octave failed Thanks a lot, Leah. > On Apr 1, 2019, at 2:58 PM, Timothy Coalson <tsc...@mst.edu> wrote: > > I have pushed a change (it launched the matlab part without error, which is > where that path is used), try the latest master. > > Tim > > > On Mon, Apr 1, 2019 at 1:49 PM Marta Moreno <mmorenoort...@icloud.com > <mailto:mmorenoort...@icloud.com>> wrote: > Thanks for your response, Tim. > What should I do specifically to make it work. I am not sure I am following > the steps as written. > > Thanks again, > Leah. > > Sent from my iPhone > > On Apr 1, 2019, at 2:40 PM, Timothy Coalson <tsc...@mst.edu > <mailto:tsc...@mst.edu>> wrote: > >> Looks like mac's readlink is incapable of being easily useful for this - >> without -f, it doesn't even output anything if it isn't a symlink, while the >> point is to find the real location whether it is a symlink or not (because >> it needs other files from that directory). >> >> I guess I will make it test whether "$0" is a symlink first. >> >> Tim >> >> >> On Mon, Apr 1, 2019 at 9:31 AM Harms, Michael <mha...@wustl.edu >> <mailto:mha...@wustl.edu>> wrote: >> Tim will have to comment on the ‘readlink -f’ issue, since I think he >> introduced that particular syntax. >> >> >> >> Please keep posts cc’ed to the HCP-User list, so that we can archive the >> discussion, and other users can benefit from it. >> >> >> >> -- >> >> Michael Harms, Ph.D. >> >> ----------------------------------------------------------- >> >> Associate Professor of Psychiatry >> >> Washington University School of Medicine >> >> Department of Psychiatry, Box 8134 >> >> 660 South Euclid Ave. Tel: 314-747-6173 >> >> St. Louis, MO 63110 Email: mha...@wustl.edu >> <mailto:mha...@wustl.edu> >> >> >> From: Marta Moreno <mmorenoort...@icloud.com >> <mailto:mmorenoort...@icloud.com>> >> Date: Monday, April 1, 2019 at 9:21 AM >> To: "Harms, Michael" <mha...@wustl.edu <mailto:mha...@wustl.edu>> >> Subject: Re: [HCP-Users] ICA+FIX error >> >> >> >> Thanks for your response, Michael. The issue with single ICA+ FIX is solved >> after running fMRISurface again. >> >> >> >> The problem is now with MR ICA+FIX. I am copying the error below for your >> convenience. Matt said is probably related to the fact that I am using a MAC. >> >> >> >> bash-3.2$ hcp_fix_multi_run >> RS_fMRI_1/RS_fMRI_1.nii.gz@RS_fMRI_2/RS_fMRI_2.nii.gz RS_fMRI_MR 2000 TRUE >> >> Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - HCPPIPEDIR: >> /usr/local/bin/HCP/Pipelines >> >> Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - CARET7DIR: >> /Applications/workbench/bin_macosx64/ >> >> Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - FSLDIR: /usr/local/fsl >> >> Sat Mar 30 16:45:07 EDT 2019 - hcp_fix_multi_run - FSL_FIXDIR: >> /usr/local/bin/HCP/Pipelines/ICAFIX/hcp_fix_multi_run >> >> readlink: illegal option -- f >> >> usage: readlink [-n] [file …] >> >> >> >> Thanks!, >> >> Leah. >> >> >> On Apr 1, 2019, at 9:29 AM, Harms, Michael <mha...@wustl.edu >> <mailto:mha...@wustl.edu>> wrote: >> >> >> >> Check RS_fMRI_2_hp2000.ica/.fix.log for clues. Also, what’s in the stderr >> output from the run? >> >> >> >> >> >> -- >> >> Michael Harms, Ph.D. >> >> ----------------------------------------------------------- >> >> Associate Professor of Psychiatry >> >> Washington University School of Medicine >> >> Department of Psychiatry, Box 8134 >> >> 660 South Euclid Ave. Tel: 314-747-6173 >> >> St. Louis, MO 63110 Email: mha...@wustl.edu >> <mailto:mha...@wustl.edu> >> >> >> From: <hcp-users-boun...@humanconnectome.org >> <mailto:hcp-users-boun...@humanconnectome.org>> on behalf of Marta Moreno >> <mmorenoort...@icloud.com <mailto:mmorenoort...@icloud.com>> >> Date: Sunday, March 31, 2019 at 6:44 PM >> To: HCP Users <hcp-users@humanconnectome.org >> <mailto:hcp-users@humanconnectome.org>> >> Subject: [HCP-Users] ICA+FIX error >> >> >> >> Dear Experts, >> >> >> >> I am running hip_fix and getting the following error with just one of my >> subjects, please see below. It seams the script stoped at the end, in >> section "Rename some files (relative to the default names coded in >> fix_3_clean)”, first line: "$FSLDIR/bin/immv >> ${fmrihp}.ica/filtered_func_data_clean ${fmrihp}_clean”, which could not >> find a supported file with prefix ".ica/filtered_func_data_clean” >> >> >> >> (…) >> >> Sun Mar 31 19:18:12 EDT 2019 - hcp_fix - Done running FIX >> >> Sun Mar 31 19:18:13 EDT 2019 - hcp_fix - ABORTING: Something went wrong; >> RS_fMRI_2_hp2000.ica/Atlas_clean.dtseries.nii wasn't created >> >> >> >> How can I solve this problem? >> >> >> >> Thanks, >> >> >> >> Leah. >> >> >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org <mailto:HCP-Users@humanconnectome.org> >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> <http://lists.humanconnectome.org/mailman/listinfo/hcp-users> >> >> >> The materials in this message are private and may contain Protected >> Healthcare Information or other information of a sensitive nature. 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