Can you run it with --debug as the first option, capture the terminal output, and send it to me?
On 4/2/19 4:02 PM, Sims, Sara A (Campus) wrote: > > 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 > > 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: *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 > > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
