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
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