My reply was not posted, most likely because the email is too large so here is the script:
….. --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.
Hi Sara, can you just cut and paste them into the email. And are you sure you're running the new command?
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
> >
> >
> >
> > _______________________________________________
> >
> > 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
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer