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