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
> 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
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
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
