        External Email - Use Caution        

I have attached them here. 

Sara Sims 
Graduate Research Fellow
University of Alabama at Birmingham
Department of Psychology
205-975-4060
snolin@uab.edu

On 3/29/19, 10:05 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D." <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of DGREVE@mgh.harvard.edu> wrote:

    Can you send your full command line and the full terminal output? Are 
    you sure you're using the new command?

    On 3/27/19 10:33 PM, Sims, Sara A (Campus) wrote:
    >          External Email - Use Caution
    >
    > Doug,
    > I have implemented the new version of the command. I am getting this error when I add the no-prune flag to my script.
    > ERROR: could not find volume --no-prune.  Does it exist?
    > ERROR: reading --no-prune
    > Are there specifics with where in the command line it should go? I have tried it near the beginning and near the end and still get this error.
    >
    > Sara Sims
    > Graduate Research Fellow
    > University of Alabama at Birmingham
    > Department of Psychology
    > 205-975-4060
    > snolin@uab.edu
    >
    > On 3/19/19, 3:30 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D." <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of DGREVE@mgh.harvard.edu> wrote:
    >
    >      I think the problem is that one or more of the subjects has all 0s. The
    >      way mris_preproc works is that if any subject has a 0 in a vertex, that
    >      vertex is set to 0 for all subjects. So, if one subject has all 0s or if
    >      tp1=tp2, then everything can get set to 0. At the end of the terminal
    >      output you'll see "Found 0 voxels in prune mask" indicating that this is
    >      the case. I've created a version of mris_preproc that allows you to turn
    >      this function off using --no-prune. You can get it from here:
    >      https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_preproc
    >      I would run it with --no-prune and without --paired-diff to give you a
    >      stack of all data. You can load this as an overlay in freeview. At the
    >      top of the freeview window is a little box with waveform in it. If you
    >      click on that and then click on a point in the surface, you should be
    >      able to see a waveform of the measurements for all inputs. See if there
    >      is one that is always 0. If you don't find any, then repeat with
    >      --paired-diff
    >      
    >      
    >      
    >      
    >      On 3/19/19 3:30 PM, Sims, Sara A (Campus) wrote:
    >      >
    >      >         External Email - Use Caution
    >      >
    >      > I uploaded them to the Filedrop here:
    >      > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=65zt2jk45ll
    >      >
    >      > Thanks!
    >      >
    >      > Sara Sims
    >      >
    >      > Graduate Research Fellow
    >      >
    >      > University of Alabama at Birmingham
    >      >
    >      > Department of Psychology
    >      >
    >      > 205-975-4060
    >      >
    >      > snolin@uab.edu
    >      >
    >      > *From: *<freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Greve,
    >      > Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu>
    >      > *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
    >      > *Date: *Monday, March 18, 2019 at 10:24 AM
    >      > *To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
    >      > *Subject: *Re: [Freesurfer] mris_preproc not running
    >      >
    >      >
    >      > can you send the terminal output? I realize it might be quite big. You
    >      > can ftp it to here: /autofs/space/nihilus_001/CICS/ACRsoftware/ACRcurrent
    >      >
    >      >
    >      > On 3/18/19 11:12 AM, Sims, Sara A (Campus) wrote:
    >      >
    >      >     *        External Email - Use Caution *
    >      >
    >      >     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
    >      >
    >      >
    >      >
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