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 > > On 3/19/19, 3:30 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Greve, Douglas N.,Ph.D." <freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > dgr...@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 > > > > *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Greve, > > Douglas N.,Ph.D." <dgr...@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
