Dear all,
I've been following the instructions for building a custom registration template as written here ( http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) and here ( https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018345.html ).
I'm now at the mris_preproc stage and according to the instructions, the command should be:
# Get thickness values in the newtemplate space for GLM analysis mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 ...
I put my subject list into a text file and replaced --s with --f [subjlist] but kept everything else the same. I got two errors for no source hemi specified and no output specified, so I added --hemi lh and --out lh.surfreg.newtemplate.thick --meas thickness. Am I supposed to do this, and will the output file be used for anything else down the line, i.e., should it be named something more specific? I see that the next step is to rerun the make_average_subject, but I don't see where the output from the mris_preproc step would figure in.
On a (maybe) separate issue, when I finally ran my command line:
mris_preproc --surfreg sphere.reg.newtemplate --f subjlist --hemi lh --out lh.surfreg.newtemplate.thick --meas thickness
I got the following error:
nsubjects=100 tmpdir is ./tmp.mris_preproc.25619 /home/fsuser/data set: Variable name must contain alphanumeric characters.
I'm not sure where the problem might be here. I'm running FreeSurfer v.5.3 in Virtualbox, and I haven't had any problems while running recon-all on the subjects previously.
Any insight would be greatly appreciated, thank you!
Cheers, Linda
1. The "..." means to include the other options needed for the command to run. Looks like you figured it out. Using -f as you have is correct.
2. can you send the full terminal output?
On 04/06/2017 08:55 AM, Linda Zhang wrote:
Dear all,
I've been following the instructions for building a custom registration template as written here (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) and here (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018345.html).
I'm now at the mris_preproc stage and according to the instructions, the command should be:
# Get thickness values in the newtemplate space for GLM analysis mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 ...
I put my subject list into a text file and replaced --s with --f [subjlist] but kept everything else the same. I got two errors for no source hemi specified and no output specified, so I added --hemi lh and --out lh.surfreg.newtemplate.thick --meas thickness. Am I supposed to do this, and will the output file be used for anything else down the line, i.e., should it be named something more specific? I see that the next step is to rerun the make_average_subject, but I don't see where the output from the mris_preproc step would figure in.
On a (maybe) separate issue, when I finally ran my command line:
mris_preproc --surfreg sphere.reg.newtemplate --f subjlist --hemi lh --out lh.surfreg.newtemplate.thick --meas thickness
I got the following error:
nsubjects=100 tmpdir is ./tmp.mris_preproc.25619 /home/fsuser/data set: Variable name must contain alphanumeric characters.
I'm not sure where the problem might be here. I'm running FreeSurfer v.5.3 in Virtualbox, and I haven't had any problems while running recon-all on the subjects previously.
Any insight would be greatly appreciated, thank you!
Cheers, Linda
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Douglas,
Thanks, good to know! That was the full terminal output after I ran mris_preproc, though.
Cheers, Linda
On Thu, 6 Apr 2017 at 22:07 Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
- The "..." means to include the other options needed for the command
to run. Looks like you figured it out. Using -f as you have is correct.
- can you send the full terminal output?
On 04/06/2017 08:55 AM, Linda Zhang wrote:
Dear all,
I've been following the instructions for building a custom registration template as written here (http://surfer.nmr.mgh.harvard.edu/fswiki/SurfaceRegAndTemplates) and here (
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-May/018345.html ).
I'm now at the mris_preproc stage and according to the instructions, the command should be:
# Get thickness values in the newtemplate space for GLM analysis mris_preproc --surfreg sphere.reg.newtemplate --s subj1 --s subj2 --s subj3 ...
I put my subject list into a text file and replaced --s with --f [subjlist] but kept everything else the same. I got two errors for no source hemi specified and no output specified, so I added --hemi lh and --out lh.surfreg.newtemplate.thick --meas thickness. Am I supposed to do this, and will the output file be used for anything else down the line, i.e., should it be named something more specific? I see that the next step is to rerun the make_average_subject, but I don't see where the output from the mris_preproc step would figure in.
On a (maybe) separate issue, when I finally ran my command line:
mris_preproc --surfreg sphere.reg.newtemplate --f subjlist --hemi lh --out lh.surfreg.newtemplate.thick --meas thickness
I got the following error:
nsubjects=100 tmpdir is ./tmp.mris_preproc.25619 /home/fsuser/data set: Variable name must contain alphanumeric characters.
I'm not sure where the problem might be here. I'm running FreeSurfer v.5.3 in Virtualbox, and I haven't had any problems while running recon-all on the subjects previously.
Any insight would be greatly appreciated, thank you!
Cheers, Linda
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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