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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
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