Insula Parcelation - Freesurfer

19 Mar 2019


      Dear Freesurfer team,
I was wondering if you are aware of an extensive label for insula parcellation (LH and RH), something more advanced then the DK atlas. I've been struggling to find one.
Thank you!
Kind regards
Eduard Vasile
On 3/18/19, 12:01 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu" <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu> wrote:
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Today's Topics:
1. mris_preproc not running (Sims, Sara A (Campus))
       2. Longitudinal QDEC (AKUDJEDU, THEOPHILUS)
       3. Re: mris_preproc not running (Greve, Douglas N.,Ph.D.)
       4. Re: Longitudinal QDEC (Greve, Douglas N.,Ph.D.)
       5. Re: Cortical thickness values extraction issue
          (Giuliana Klencklen)
       6. Re: Cortical thickness values extraction issue
          (Greve, Douglas N.,Ph.D.)
       7. Re: Cortical thickness values extraction issue
          (Giuliana Klencklen)
       8. skip subjects already processed (Akshay Patel)
       9. tkregister-sess (Nasiriavanaki, Zahra)
----------------------------------------------------------------------
Message: 1
    Date: Mon, 18 Mar 2019 15:12:39 +0000
    From: "Sims, Sara A (Campus)" snolin@uab.edu
    Subject: [Freesurfer] mris_preproc not running
    To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
    Message-ID: 24C66DC0-853A-4C52-943B-0AB3E731FA7C@uab.edu
    Content-Type: text/plain; charset="utf-8"
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Hello!
    I have 786 subjects that I am trying to do a paired difference analysis using mri_glm. I am getting stuck at the mris_preproc stage. I have tried running it on a handful of subjects and it works wonderfully. However, when I run it on all the subjects it outputs an empty file.
    I think part of my problem is that I am having to do 1572 flags to enter all the subjects files (which I made a script to create, I did not hand type them). Is there a better way to do this? Do I just have too many subjects?
This is what I have that isn?t working:
    mris_preproc --target fsaverage --hemi lh --isp $in/${network}/100206.${run1}/lhsurf.mgh --isp $in/${network}/100206.${run2}/lhsurf.mgh --isp $in/${network}/100307.${run1}/lhsurf.mgh --isp $in/${network}/100307.${run2}/lhsurf.mgh ??. --out $out/preproc_${network}_${pair}/lh.paired-diff.${network}_${pair}.mgh --f $sublist --paired-diff --no-cortex-only
Thanks for the help!
Sara Sims