I would use mode=1 Matt.
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: Saturday, April 6, 2019 at 2:46 PM To: Timothy Coalson <tsc...@mst.edu<mailto:tsc...@mst.edu>> Cc: HCP Users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: Re: [HCP-Users] MR ICA+FIX error 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<mailto: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<mailto: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 ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> 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. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
