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Today's Topics:

   1. FreeSurfer Manual Edit Sequence (David S Lee)
   2. Using grad_unwarp (James Gullickson)


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Message: 1
Date: Fri, 22 Jun 2018 11:37:44 -0500
From: David S Lee <david.s.lee@wisc.edu>
Subject: [Freesurfer] FreeSurfer Manual Edit Sequence
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
        <CAGcZjx8px96eS=O64q5nivBObJP9cqDha3_R87G3GHdjkVQnqA@mail.gmail.com>
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Hello Experts,

When performing manual edits on brain masks, white matter, and gray matter,
do I have to strictly follow the sequences(process stages) listed here
<https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all>?

For instance, the link suggests that "autorecon2-pial is used after editing
brain volume *after running -autorecon2".

In other words, is it okay to perform "autorecon2-pial" before
"autorecon2-wm"?

Thank you for your time,
--
David S. Lee
Associate Research Specialist
Center for Healthy Minds
University of Wisconsin - Madison
(608) 890-1115
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Message: 2
Date: Fri, 22 Jun 2018 13:55:53 -0500
From: James Gullickson <jgullick@umn.edu>
Subject: [Freesurfer] Using grad_unwarp
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
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        <CAProeZLasNsVY0U78Xb5JCe6MsTnUG19iF_BGHZEH2eH8NJX+Q@mail.gmail.com>
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All,

I am interested in using grad_unwarp. I have been reading up on the
documentation a bit and from what I understand not all the necessary files
are distributed with the public version of Freesurfer, due to proprietary
information in the tables. However, there is a script called grad_unwarp in
 my $FREESURFER_HOME/bin directory. I have access to the .grad files
necessary for my project, so I was planning to just piece together the
environment manually. Based on:  https://surfer.nmr.mgh.
harvard.edu/fswiki/GradUnwarp there are a few pieces I'm missing:

   - create_displacement_tables script
   - grad_unwarp_converter.pl script
   -  matlab files

Is there somewhere I can locate these missing scripts/files?

Thanks,

James
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End of Freesurfer Digest, Vol 172, Issue 36
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