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 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: 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
snolin@uab.edumailto:snolin@uab.edu
On 3/29/19, 10:05 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D."mailto:freesurfer-bounces@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D. <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of DGREVE@mgh.harvard.edu>mailto:freesurfer-bounces@nmr.mgh.harvard.eduonbehalfofDGREVE@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.edumailto:snolin@uab.edu
>
> On 3/19/19, 3:30 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D."mailto:freesurfer-bounces@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D. <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of DGREVE@mgh.harvard.edu>mailto:freesurfer-bounces@nmr.mgh.harvard.eduonbehalfofDGREVE@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.edumailto:snolin@uab.edu
> >
> > *From: *freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Greve,
> > Douglas N.,Ph.D." DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu
> > *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
> >
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer