Re: [HCP-Users] Volumetric subcortical group-averaged data: what is the exact MNI template you used?
This means that the template is asymmetric, not symmetric, correct? Thanks, Xavier. On Fri, Apr 5, 2019 at 5:48 PM Glasser, Matthew wrote: > FSL’s MNI152. > > Matt. > > From: on behalf of Xavier Guell > Paradis > Date: Friday, April 5, 2019 at 4:46 PM > To: "hcp-users@humanconnectome.org" > Subject: [HCP-Users] Volumetric subcortical group-averaged data: what is > the exact MNI template you used? > > Dear HCP experts, > I am interested in analyzing your group-averaged subcortical volumetric > data. My understanding is that your volumetric data is registered to MNI > space. I was wondering if you could let me know what specific MNI template > you used. I am especially interested in knowing whether it is a symmetric > or an asymmetric MNI template. > Thank you, > Xavier. > > ___ > HCP-Users mailing list > 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
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 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 > 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 > 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 "$0" is a symlink first.
>>
>> Tim
>>
>>
>> On Mon, Apr 1, 2019 at 9:31 AM Harms, Michael > > wrote:
>> Tim will have to comment on the ‘readlink -f’ issue, since I think he
>> introduced that particular syntax.
>>
>>
>>
>> Please keep posts cc’ed to the HCP-User list, so that we can archive the
>> discussion, and other users can benefit from it.
>>
>>
>>
>> --
>>
>> Michael Harms, Ph.D.
>>
>> ---
>>
>> Associate Professor of Psychiatry
>>
>> Washington University School of Medicine
>>
>> Department of Psychiatry, Box 8134
>>
>> 660 South Euclid Ave.Tel: 314-747-6173
>>
>> St. Louis, MO 63110 Email: mha...@wustl.edu
>>
>>
>>
>> From: Marta Moreno > >
>> Date: Monday, April 1, 2019 at 9:21 AM
>> To: "Harms, Michael" mailto:mha...@wustl.edu>>
>> Subject: Re: [HCP-Users] ICA+FIX error
>>
>>
>>
>> Thanks for your response, Michael. The issue with single ICA+ FIX is solved
>> after running fMRISurface again.
>>
>>
>>
>> The problem is now with MR ICA+FIX. I am copying the error below for your
>> convenience. Matt said is probably related to the fact that I am using a MAC.
>>
>>
>>
>> bash-3.2$ 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 > > 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
>>
>>
>>
>> From: > > on behalf of Marta Moreno
>> mailto:mmorenoort...@icloud.com>>
>> Date: Sunday, March 31, 2019 at 6:44 PM
>> To: HCP Users >
Re: [HCP-Users] MR ICA+FIX error
I would use mode=1
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Marta Moreno
mailto:mmorenoort...@icloud.com>>
Date: Saturday, April 6, 2019 at 2:46 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: HCP Users
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
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
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
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 "$0" is a symlink first.
Tim
On Mon, Apr 1, 2019 at 9:31 AM Harms, Michael
mailto:mha...@wustl.edu>> wrote:
Tim will have to comment on the ‘readlink -f’ issue, since I think he
introduced that particular syntax.
Please keep posts cc’ed to the HCP-User list, so that we can archive the
discussion, and other users can benefit from it.
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email:
mha...@wustl.edu
From: Marta Moreno mailto:mmorenoort...@icloud.com>>
Date: Monday, April 1, 2019 at 9:21 AM
To: "Harms, Michael" mailto:mha...@wustl.edu>>
Subject: Re: [HCP-Users] ICA+FIX error
Thanks for your response, Michael. The issue with single ICA+ FIX is solved
after running fMRISurface again.
The problem is now with MR ICA+FIX. I am copying the error below for your
convenience. Matt said is probably related to the fact that I am using a MAC.
bash-3.2$ 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
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
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Marta Moreno
mailto:mmorenoort...@icloud.com>>
Date: Sunday, March 31, 2019 at 6:44 PM
To: HCP Users
mailto:hcp-users@humanconnectome.org>>
Re: [HCP-Users] MR ICA+FIX error
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
From: on behalf of "Glasser, Matthew"
Date: Saturday, April 6, 2019 at 2:57 PM
To: Marta Moreno , NEUROSCIENCE tim
Cc: HCP Users
Subject: Re: [HCP-Users] MR ICA+FIX error
I would use mode=1
Matt.
From:
mailto:hcp-users-boun...@humanconnectome.org>>
on behalf of Marta Moreno
mailto:mmorenoort...@icloud.com>>
Date: Saturday, April 6, 2019 at 2:46 PM
To: Timothy Coalson mailto:tsc...@mst.edu>>
Cc: HCP Users
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
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
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
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 "$0" is a symlink first.
Tim
On Mon, Apr 1, 2019 at 9:31 AM Harms, Michael
mailto:mha...@wustl.edu>> wrote:
Tim will have to comment on the ‘readlink -f’ issue, since I think he
introduced that particular syntax.
Please keep posts cc’ed to the HCP-User list, so that we can archive the
discussion, and other users can benefit from it.
--
Michael Harms, Ph.D.
---
Associate Professor of Psychiatry
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO 63110 Email:
mha...@wustl.edu
From: Marta Moreno mailto:mmorenoort...@icloud.com>>
Date: Monday, April 1, 2019 at 9:21 AM
To: "Harms, Michael" mailto:mha...@wustl.edu>>
Subject: Re: [HCP-Users] ICA+FIX error
Thanks for your response, Michael. The issue with single ICA+ FIX is solved
after running fMRISurface again.
The problem is now with MR ICA+FIX. I am copying the error below for your
convenience. Matt said is probably related to the fact that I am using a MAC.
bash-3.2$ 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
mailto:mha...@wustl.edu>> wrote:
Check
