Re: [Freesurfer] mris_preproc not running
You need a new version of mri_concat. I've put one here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_concat Copy it to $FREESURFER_HOME/bin (after making a backup of the one there), then re-run On 4/2/2019 10:49 PM, Sims, Sara A (Campus) wrote: > External Email - Use Caution > > Here is the output file with debug on: > http://gate.nmr.mgh.harvard.edu/filedrop2/?p=bes7rp27gk0 > > Thanks, > Sara Sims > Graduate Research Fellow > University of Alabama at Birmingham > Department of Psychology > 205-975-4060 > sno...@uab.edu > > On 4/2/19, 3:34 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Greve, Douglas N.,Ph.D." dgr...@mgh.harvard.edu> wrote: > > 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: * on behalf of "Greve, > > Douglas N.,Ph.D." > > *Reply-To: *Freesurfer support list > > *Date: *Saturday, March 30, 2019 at 6:06 PM > > *To: *"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.> > > dgr...@mgh.harvard.edu> > <mailto:freesurf
Re: [Freesurfer] mris_preproc not running
External Email - Use Caution Here is the output file with debug on: http://gate.nmr.mgh.harvard.edu/filedrop2/?p=bes7rp27gk0 Thanks, Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 sno...@uab.edu On 4/2/19, 3:34 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D." wrote: 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: * on behalf of "Greve, > Douglas N.,Ph.D." > *Reply-To: *Freesurfer support list > *Date: *Saturday, March 30, 2019 at 6:06 PM > *To: *"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.> 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 comma
Re: [Freesurfer] mris_preproc not running
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: * on behalf of "Greve, > Douglas N.,Ph.D." > *Reply-To: *Freesurfer support list > *Date: *Saturday, March 30, 2019 at 6:06 PM > *To: *"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.> >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.> >dgr...@mgh.harvard.edu> > <mailto:freesurfer-boun...@nmr.mgh.harvard.eduonbehalfofdgr...@mgh.harvard.edu> > wrote: > > &
Re: [Freesurfer] mris_preproc not running
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: on behalf of "Greve, Douglas N.,Ph.D." Reply-To: Freesurfer support list Date: Saturday, March 30, 2019 at 6:06 PM To: "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.> <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.> <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 >
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.> <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.> <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: *<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Greve, > > Douglas N.,Ph.D." <mailto:dgr...@mgh.harvard.edu> > > *Reply-To: *Freesurfer support list <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> <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 > >
Re: [Freesurfer] mris_preproc not running
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." 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: * on behalf of "Greve,
> > Douglas N.,Ph.D."
> > *Reply-To: *Freesurfer support list
> > *Date: *Monday, March 18, 2019 at 10:24 AM
> > *To: *"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 S
Re: [Freesurfer] mris_preproc not running
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." 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: * on behalf of "Greve,
> Douglas N.,Ph.D."
> *Reply-To: *Freesurfer support list
> *Date: *Monday, March 18, 2019 at 10:24 AM
> *To: *"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
Re: [Freesurfer] mris_preproc not running
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: * on behalf of "Greve,
> Douglas N.,Ph.D."
> *Reply-To: *Freesurfer support list
> *Date: *Monday, March 18, 2019 at 10:24 AM
> *To: *"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
Re: [Freesurfer] mris_preproc not running
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: on behalf of "Greve, Douglas
N.,Ph.D."
Reply-To: Freesurfer support list
Date: Monday, March 18, 2019 at 10:24 AM
To: "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
___
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Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
___
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer@nmr.mgh.harvard.edu
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