Thanks for your response, problem solved! Leah.
> On Apr 6, 2019, at 4:18 PM, Harms, Michael <mha...@wustl.edu> wrote: > > > This indicates that you aren’t using the version of hcp_fix_multi_run from > the v4.0.0 pipelines, which supports the use of all 3 matlab modes. > > -- > 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> on behalf of "Glasser, Matthew" > <glass...@wustl.edu> > Date: Saturday, April 6, 2019 at 2:57 PM > To: Marta Moreno <mmorenoort...@icloud.com>, NEUROSCIENCE tim <tsc...@mst.edu> > Cc: HCP Users <hcp-users@humanconnectome.org> > Subject: Re: [HCP-Users] MR ICA+FIX error > > 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 > <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_runRS_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 >>>>>> <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. >>>>> >>>>> >>>>> >>>>> 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 <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. 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 <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. 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
