External Email - Use Caution
Here is the output file with debug on:
http://gate.nmr.mgh.harvard.edu/filedrop2/?p=bes7rp27gk0
Thanks,
Sara Sims
Graduate Research Fellow
University of Alabama at Birmingham
Department of Psychology
205-975-4060
sno...@uab.edu
On 4/2/19, 3:34 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Greve, Douglas N.,Ph.D." <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
dgr...@mgh.harvard.edu> wrote:
Can you run it with --debug as the first option, capture the terminal
output, and send it to me?
On 4/2/19 4:02 PM, Sims, Sara A (Campus) wrote:
>
> External Email - Use Caution
>
> My reply was not posted, most likely because the email is too large so
> here is the script:
>
> mris_preproc --target fsaverage --hemi lh --no-prune --isp
> $in/DMN/100206.newfar/lhsurf.mgh --isp
> $in/DMN/100206.newcentral/lhsurf.mgh --isp
> $in/DMN/100307.newfar/lhsurf.mgh --isp
> $in/DMN/100307.newcentral/lhsurf.mgh --isp
> $in/DMN/100408.newfar/lhsurf.mgh --isp
> $in/DMN/100408.newcentral/lhsurf.mgh --isp
> $in/DMN/100610.newfar/lhsurf.mgh --isp
> $in/DMN/100610.newcentral/lhsurf.mgh --isp
> $in/DMN/101006.newfar/lhsurf.mgh --isp
> $in/DMN/101006.newcentral/lhsurf.mgh --isp
> $in/DMN/101107.newfar/lhsurf.mgh --isp
> $in/DMN/101107.newcentral/lhsurf.mgh --isp
> $in/DMN/101309.newfar/lhsurf.mgh --isp
> $in/DMN/101309.newcentral/lhsurf.mgh --isp
> $in/DMN/101410.newfar/lhsurf.mgh --isp
> $in/DMN/101410.newcentral/lhsurf.mgh --isp
> $in/DMN/101915.newfar/lhsurf.mgh --isp
> $in/DMN/101915.newcentral/lhsurf.mgh --isp
> $in/DMN/102008.newfar/lhsurf.mgh --isp
> $in/DMN/102008.newcentral/lhsurf.mgh --isp
> $in/DMN/102311.newfar/lhsurf.mgh --isp
> $in/DMN/102311.newcentral/lhsurf.mgh --isp
> $in/DMN/102513.newfar/lhsurf.mgh --isp
> $in/DMN/102513.newcentral/lhsurf.mgh --isp
> $in/DMN/102816.newfar/lhsurf.mgh --isp
> $in/DMN/102816.newcentral/lhsurf.mgh --isp
> $in/DMN/103111.newfar/lhsurf.mgh --isp
> $in/DMN/103111.newcentral/lhsurf.mgh --isp
> $in/DMN/103414.newfar/lhsurf.mgh --isp
> $in/DMN/103414.newcentral/lhsurf.mgh --isp
> $in/DMN/103515.newfar/lhsurf.mgh --isp $in/DMN/103515.n
>
> ….. --out $out/preproc_DMN_fc/lh.paired-diff.DMN_fc.mgh --f $sublist
> --no-cortex-only
>
> I also double checked with our research computing department to make
> sure I was referencing the command you sent me previously.
>
> Sara Sims
>
> Graduate Research Fellow
>
> University of Alabama at Birmingham
>
> Department of Psychology
>
> 205-975-4060
>
> sno...@uab.edu
>
> *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Greve,
> Douglas N.,Ph.D." <dgr...@mgh.harvard.edu>
> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Date: *Saturday, March 30, 2019 at 6:06 PM
> *To: *"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> *Subject: *Re: [Freesurfer] mris_preproc not running
>
> Hi Sara, can you just cut and paste them into the email. And are you
> sure you're running the new command?
>
> On 3/29/19 6:59 PM, Sims, Sara A (Campus) wrote:
>
> 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
>
> sno...@uab.edu <mailto:sno...@uab.edu>
>
> On 3/29/19, 10:05 AM,"freesurfer-boun...@nmr.mgh.harvard.edu on
behalf of Greve,
> Douglas N.,Ph.D."
<mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D.>
<freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> dgr...@mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofdgr...@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
>
> >sno...@uab.edu <mailto:sno...@uab.edu>
>
> >
>
> > On 3/19/19, 3:30 PM,"freesurfer-boun...@nmr.mgh.harvard.edu on
behalf of Greve,
> Douglas N.,Ph.D."
<mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D.>
<freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> dgr...@mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofdgr...@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
>
> > >
>
> > >sno...@uab.edu <mailto:sno...@uab.edu>
>
> > >
>
> > > *From: *<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Greve,
>
> > > Douglas N.,Ph.D."<dgr...@mgh.harvard.edu>
<mailto:dgr...@mgh.harvard.edu>
>
> > > *Reply-To: *Freesurfer support
list<freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu>
>
> > > *Date: *Monday, March 18, 2019 at 10:24 AM
>
> > > *To: *"freesurfer@nmr.mgh.harvard.edu"
<mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu>
<mailto: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
>
> > >
>
> > >
>
> > >
>
> > > _______________________________________________
>
> > >
>
> > > Freesurfer mailing list
>
> > >
>
> > >Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
<mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>
> > >
>
> >
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> > >
>
> > >
>
> > >
>
> > >
>
> > > _______________________________________________
>
> > > Freesurfer mailing list
>
> > >Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>
> >
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> >
>
> >
>
> > _______________________________________________
>
> > Freesurfer mailing list
>
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<mailto:Freesurfer@nmr.mgh.harvard.edu>
>
> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> >
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> >
>
> > _______________________________________________
>
> > Freesurfer mailing list
>
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<mailto:Freesurfer@nmr.mgh.harvard.edu>
>
> >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
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>
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>
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