You should run the specific command that generates the .rot. file in 
PostFreeSurfer to get that file.  Starting with FreeSurfer for MSMAll is 
definitely not recommended as that will make the problem harder for MSMAll 
(having to try to undo the bad FreeSurfer distortions), and it might be better 
to rerun PostFreeSurfer before using MSMAll.

Peace,

Matt.

From: 
<[email protected]<mailto:[email protected]>>
 on behalf of Timothy Hendrickson <[email protected]<mailto:[email protected]>>
Date: Tuesday, July 10, 2018 at 10:24 AM
To: "[email protected]<mailto:[email protected]>" 
<[email protected]<mailto:[email protected]>>
Subject: [HCP-Users] Core Dump ${MSMBINDIR}/msm

Hello,

When I run msm within MSMAll I get a core dump because the --inmesh file could 
not be found: 
${NativeFolder}/${Subject}.${Hemisphere}.sphere.rot.native.surf.gii. I see that 
the file is generated within the PostFreeSurfer pipeline if the MSMSulc 
registration is specified. I've already run minimal preprocessing on this study 
with FS as registration name. While I will ultimately switch all of my 
processing to MSMSulc I would like to keep the preprocessing I have done with 
FS there. What file should I use then for inmesh?

-Tim


Timothy Hendrickson
Neuroimaging Analyst/Staff Scientist
University of Minnesota Informatics Institute
University of Minnesota
Bioinformatics M.S. Candidate
Office: 612-624-0783
Mobile: 507-259-3434 (texts okay)

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