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
>
>
>
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> Freesurfer@nmr.mgh.harvard.edu
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--
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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