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. 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
http://lists.humanconnectome.org/mailman/listinfo/hcp-users
