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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

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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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I have attached them here.

Sara Sims Graduate Research Fellow University of Alabama at Birmingham Department of Psychology 205-975-4060 snolin@uab.edu

On 3/29/19, 10:05 AM, "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:

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 > 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 > > > _______________________________________________ > 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

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Sure! This is the job script: #!/bin/bash # #SBATCH --ntasks=1 #SBATCH --mem-per-cpu=50000 #SBATCH --partition=medium #SBATCH --time=48:00:00 #SBATCH --mail-type=FAIL #SBATCH --mail-user=snolin@uab.edu #SBATCH --job-name=DMNfclhmris_preproc #SBATCH --output=mris_preprocDMNfclh.txt export PATH=/home/snolin/Freesurfer_exec/:$PATH

#DMN fc# parentdir=/data/project/vislab/a/HCP_diff_Sara/V1stoFNtprob recon=/data/project/vislab/a/HCP_diff_Sara/subjects_reconall_postcheckcopy #make folder to populate with data files in=$parentdir/surface_analysis cd $in mkdir DMN

#copy fsaverage folder to analysis folder cp -R $recon/fsaverage $in/DMN

#set as Freesurfer subjects directory unset SUBJECTS_DIR SUBJECTS_DIR=$in/DMN export SUBJECTS_DIR

#make mris_preproc output folder out=$parentdir/surface_analysis cd $out mkdir preproc_DMN_fc

#location of participants you want to pull diff=/data/project/vislab/a/HCP_diff_Sara/subjects_reconall_postcheckcopy

#copy data into correct structure for mris_preproc to be happy for patient in `ls -1 $diff` do #copy newfar data cd $in/DMN mkdir $patient.newfar cp $parentdir/newfartoDMN_surf/newfartoDMNlhsurf_$patient.mgh $in/DMN/$patient.newfar/ mv $in/DMN/$patient.newfar/newfartoDMNlhsurf_$patient.mgh $in/DMN/$patient.newfar/lhsurf.mgh

#copy newcentral data cd $in/DMN mkdir $patient.newcentral cp $parentdir/newcentraltoDMN_surf/newcentraltoDMNlhsurf_$patient.mgh $in/DMN/$patient.newcentral/ mv $in/DMN/$patient.newcentral/newcentraltoDMNlhsurf_$patient.mgh $in/DMN/$patient.newcentral/lhsurf.mgh

#copy surf folder into both newfar and newcentral folders cp -R $recon/$patient/surf $in/DMN/$patient.newfar/ cp -R $recon/$patient/surf $in/DMN/$patient.newcentral/

#copy label folder into both newfar and newcentral folders cp -R $recon/$patient/label $in/DMN/$patient.newfar/ cp -R $recon/$patient/label $in/DMN/$patient.newcentral/ done

#actually finally run mris_preproc with isp flags in exact same order as subject file list #see makingsublist.m for generating sublist for mris_preproc sublist=$in/sublistfc.txt

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.newcentral/lhsurf.mgh --isp $in/DMN/103818.newfar/lhsurf.mgh --isp $in/DMN/103818.newcentral/lhsurf.mgh --isp $in/DMN/104012.newfar/lhsurf.mgh --isp $in/DMN/104012.newcentral/lhsurf.mgh --isp $in/DMN/104416.newfar/lhsurf.mgh --isp $in/DMN/104416.newcentral/lhsurf.mgh --isp $in/DMN/104820.newfar/lhsurf.mgh --isp $in/DMN/104820.newcentral/lhsurf.mgh --isp $in/DMN/105014.newfar/lhsurf.mgh --isp $in/DMN/105014.newcentral/lhsurf.mgh --isp $in/DMN/105115.newfar/lhsurf.mgh --isp $in/DMN/105115.newcentral/lhsurf.mgh --isp $in/DMN/105216.newfar/lhsurf.mgh --isp $in/DMN/105216.newcentral/lhsurf.mgh --isp $in/DMN/105923.newfar/lhsurf.mgh --isp $in/DMN/105923.newcentral/lhsurf.mgh --isp $in/DMN/106016.newfar/lhsurf.mgh --isp $in/DMN/106016.newcentral/lhsurf.mgh --isp $in/DMN/106319.newfar/lhsurf.mgh --isp $in/DMN/106319.newcentral/lhsurf.mgh --isp $in/DMN/106521.newfar/lhsurf.mgh --isp $in/DMN/106521.newcentral/lhsurf.mgh --isp $in/DMN/107018.newfar/lhsurf.mgh --isp $in/DMN/107018.newcentral/lhsurf.mgh --isp $in/DMN/107321.newfar/lhsurf.mgh --isp $in/DMN/107321.newcentral/lhsurf.mgh --isp $in/DMN/107422.newfar/lhsurf.mgh --isp $in/DMN/107422.newcentral/lhsurf.mgh --isp $in/DMN/107725.newfar/lhsurf.mgh --isp $in/DMN/107725.newcentral/lhsurf.mgh --isp $in/DMN/108121.newfar/lhsurf.mgh --isp $in/DMN/108121.newcentral/lhsurf.mgh --isp $in/DMN/108222.newfar/lhsurf.mgh --isp $in/DMN/108222.newcentral/lhsurf.mgh --isp $in/DMN/108323.newfar/lhsurf.mgh --isp $in/DMN/108323.newcentral/lhsurf.mgh --isp $in/DMN/108525.newfar/lhsurf.mgh --isp $in/DMN/108525.newcentral/lhsurf.mgh --isp $in/DMN/108828.newfar/lhsurf.mgh --isp $in/DMN/108828.newcentral/lhsurf.mgh --isp $in/DMN/109123.newfar/lhsurf.mgh --isp $in/DMN/109123.newcentral/lhsurf.mgh --isp $in/DMN/109830.newfar/lhsurf.mgh --isp $in/DMN/109830.newcentral/lhsurf.mgh --isp $in/DMN/110007.newfar/lhsurf.mgh --isp $in/DMN/110007.newcentral/lhsurf.mgh --isp $in/DMN/110411.newfar/lhsurf.mgh --isp $in/DMN/110411.newcentral/lhsurf.mgh --isp $in/DMN/111009.newfar/lhsurf.mgh --isp $in/DMN/111009.newcentral/lhsurf.mgh --isp $in/DMN/111413.newfar/lhsurf.mgh --isp $in/DMN/111413.newcentral/lhsurf.mgh --isp $in/DMN/111514.newfar/lhsurf.mgh --isp $in/DMN/111514.newcentral/lhsurf.mgh --isp $in/DMN/111716.newfar/lhsurf.mgh --isp $in/DMN/111716.newcentral/lhsurf.mgh --isp $in/DMN/112314.newfar/lhsurf.mgh --isp $in/DMN/112314.newcentral/lhsurf.mgh --isp $in/DMN/112516.newfar/lhsurf.mgh --isp $in/DMN/112516.newcentral/lhsurf.mgh --isp $in/DMN/112819.newfar/lhsurf.mgh --isp $in/DMN/112819.newcentral/lhsurf.mgh --isp $in/DMN/112920.newfar/lhsurf.mgh --isp $in/DMN/112920.newcentral/lhsurf.mgh --isp $in/DMN/113215.newfar/lhsurf.mgh --isp $in/DMN/113215.newcentral/lhsurf.mgh --isp $in/DMN/113619.newfar/lhsurf.mgh --isp $in/DMN/113619.newcentral/lhsurf.mgh --isp $in/DMN/113821.newfar/lhsurf.mgh --isp $in/DMN/113821.newcentral/lhsurf.mgh --isp $in/DMN/113922.newfar/lhsurf.mgh --isp $in/DMN/113922.newcentral/lhsurf.mgh --isp $in/DMN/114217.newfar/lhsurf.mgh --isp $in/DMN/114217.newcentral/lhsurf.mgh --isp $in/DMN/114318.newfar/lhsurf.mgh --isp $in/DMN/114318.newcentral/lhsurf.mgh --isp $in/DMN/114419.newfar/lhsurf.mgh --isp $in/DMN/114419.newcentral/lhsurf.mgh --isp $in/DMN/114621.newfar/lhsurf.mgh --isp $in/DMN/114621.newcentral/lhsurf.mgh --isp $in/DMN/114823.newfar/lhsurf.mgh --isp $in/DMN/114823.newcentral/lhsurf.mgh --isp $in/DMN/115017.newfar/lhsurf.mgh --isp $in/DMN/115017.newcentral/lhsurf.mgh --isp $in/DMN/115219.newfar/lhsurf.mgh --isp $in/DMN/115219.newcentral/lhsurf.mgh --isp $in/DMN/115320.newfar/lhsurf.mgh --isp 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$in/DMN/835657.newcentral/lhsurf.mgh --isp $in/DMN/837560.newfar/lhsurf.mgh --isp $in/DMN/837560.newcentral/lhsurf.mgh --isp $in/DMN/837964.newfar/lhsurf.mgh --isp $in/DMN/837964.newcentral/lhsurf.mgh --isp $in/DMN/841349.newfar/lhsurf.mgh --isp $in/DMN/841349.newcentral/lhsurf.mgh --isp $in/DMN/843151.newfar/lhsurf.mgh --isp $in/DMN/843151.newcentral/lhsurf.mgh --isp $in/DMN/844961.newfar/lhsurf.mgh --isp $in/DMN/844961.newcentral/lhsurf.mgh --isp $in/DMN/845458.newfar/lhsurf.mgh --isp $in/DMN/845458.newcentral/lhsurf.mgh --isp $in/DMN/849264.newfar/lhsurf.mgh --isp $in/DMN/849264.newcentral/lhsurf.mgh --isp $in/DMN/849971.newfar/lhsurf.mgh --isp $in/DMN/849971.newcentral/lhsurf.mgh --isp $in/DMN/852455.newfar/lhsurf.mgh --isp $in/DMN/852455.newcentral/lhsurf.mgh --isp $in/DMN/856463.newfar/lhsurf.mgh --isp $in/DMN/856463.newcentral/lhsurf.mgh --isp $in/DMN/856766.newfar/lhsurf.mgh --isp $in/DMN/856766.newcentral/lhsurf.mgh --isp $in/DMN/856968.newfar/lhsurf.mgh --isp $in/DMN/856968.newcentral/lhsurf.mgh --isp $in/DMN/859671.newfar/lhsurf.mgh --isp $in/DMN/859671.newcentral/lhsurf.mgh --isp $in/DMN/861456.newfar/lhsurf.mgh --isp $in/DMN/861456.newcentral/lhsurf.mgh --isp $in/DMN/865363.newfar/lhsurf.mgh --isp $in/DMN/865363.newcentral/lhsurf.mgh --isp $in/DMN/867468.newfar/lhsurf.mgh --isp $in/DMN/867468.newcentral/lhsurf.mgh --isp $in/DMN/870861.newfar/lhsurf.mgh --isp $in/DMN/870861.newcentral/lhsurf.mgh --isp $in/DMN/871762.newfar/lhsurf.mgh --isp $in/DMN/871762.newcentral/lhsurf.mgh --isp $in/DMN/871964.newfar/lhsurf.mgh --isp $in/DMN/871964.newcentral/lhsurf.mgh --isp $in/DMN/872158.newfar/lhsurf.mgh --isp $in/DMN/872158.newcentral/lhsurf.mgh --isp $in/DMN/872562.newfar/lhsurf.mgh --isp $in/DMN/872562.newcentral/lhsurf.mgh --isp $in/DMN/872764.newfar/lhsurf.mgh --isp $in/DMN/872764.newcentral/lhsurf.mgh --isp $in/DMN/873968.newfar/lhsurf.mgh --isp $in/DMN/873968.newcentral/lhsurf.mgh --isp $in/DMN/877168.newfar/lhsurf.mgh --isp $in/DMN/877168.newcentral/lhsurf.mgh --isp $in/DMN/877269.newfar/lhsurf.mgh --isp $in/DMN/877269.newcentral/lhsurf.mgh --isp $in/DMN/878776.newfar/lhsurf.mgh --isp $in/DMN/878776.newcentral/lhsurf.mgh --isp $in/DMN/880157.newfar/lhsurf.mgh --isp $in/DMN/880157.newcentral/lhsurf.mgh --isp $in/DMN/882161.newfar/lhsurf.mgh --isp $in/DMN/882161.newcentral/lhsurf.mgh --isp $in/DMN/885975.newfar/lhsurf.mgh --isp $in/DMN/885975.newcentral/lhsurf.mgh --isp $in/DMN/887373.newfar/lhsurf.mgh --isp $in/DMN/887373.newcentral/lhsurf.mgh --isp $in/DMN/889579.newfar/lhsurf.mgh --isp $in/DMN/889579.newcentral/lhsurf.mgh --isp $in/DMN/891667.newfar/lhsurf.mgh --isp $in/DMN/891667.newcentral/lhsurf.mgh --isp $in/DMN/894067.newfar/lhsurf.mgh --isp $in/DMN/894067.newcentral/lhsurf.mgh --isp $in/DMN/894673.newfar/lhsurf.mgh --isp $in/DMN/894673.newcentral/lhsurf.mgh --isp $in/DMN/894774.newfar/lhsurf.mgh --isp $in/DMN/894774.newcentral/lhsurf.mgh --isp $in/DMN/896879.newfar/lhsurf.mgh --isp $in/DMN/896879.newcentral/lhsurf.mgh --isp $in/DMN/898176.newfar/lhsurf.mgh --isp $in/DMN/898176.newcentral/lhsurf.mgh --isp $in/DMN/899885.newfar/lhsurf.mgh --isp $in/DMN/899885.newcentral/lhsurf.mgh --isp $in/DMN/901038.newfar/lhsurf.mgh --isp $in/DMN/901038.newcentral/lhsurf.mgh --isp $in/DMN/901139.newfar/lhsurf.mgh --isp $in/DMN/901139.newcentral/lhsurf.mgh --isp $in/DMN/901442.newfar/lhsurf.mgh --isp $in/DMN/901442.newcentral/lhsurf.mgh --isp $in/DMN/904044.newfar/lhsurf.mgh --isp $in/DMN/904044.newcentral/lhsurf.mgh --isp $in/DMN/907656.newfar/lhsurf.mgh --isp $in/DMN/907656.newcentral/lhsurf.mgh --isp $in/DMN/910241.newfar/lhsurf.mgh --isp $in/DMN/910241.newcentral/lhsurf.mgh --isp $in/DMN/910443.newfar/lhsurf.mgh --isp $in/DMN/910443.newcentral/lhsurf.mgh --isp $in/DMN/912447.newfar/lhsurf.mgh --isp $in/DMN/912447.newcentral/lhsurf.mgh --isp $in/DMN/917255.newfar/lhsurf.mgh --isp $in/DMN/917255.newcentral/lhsurf.mgh --isp $in/DMN/917558.newfar/lhsurf.mgh --isp $in/DMN/917558.newcentral/lhsurf.mgh --isp $in/DMN/919966.newfar/lhsurf.mgh --isp $in/DMN/919966.newcentral/lhsurf.mgh --isp $in/DMN/922854.newfar/lhsurf.mgh --isp $in/DMN/922854.newcentral/lhsurf.mgh --isp $in/DMN/923755.newfar/lhsurf.mgh --isp $in/DMN/923755.newcentral/lhsurf.mgh --isp $in/DMN/926862.newfar/lhsurf.mgh --isp $in/DMN/926862.newcentral/lhsurf.mgh --isp $in/DMN/927359.newfar/lhsurf.mgh --isp $in/DMN/927359.newcentral/lhsurf.mgh --isp $in/DMN/930449.newfar/lhsurf.mgh --isp $in/DMN/930449.newcentral/lhsurf.mgh --isp $in/DMN/932554.newfar/lhsurf.mgh --isp $in/DMN/932554.newcentral/lhsurf.mgh --isp $in/DMN/937160.newfar/lhsurf.mgh --isp $in/DMN/937160.newcentral/lhsurf.mgh --isp $in/DMN/942658.newfar/lhsurf.mgh --isp $in/DMN/942658.newcentral/lhsurf.mgh --isp $in/DMN/947668.newfar/lhsurf.mgh --isp $in/DMN/947668.newcentral/lhsurf.mgh --isp $in/DMN/951457.newfar/lhsurf.mgh --isp $in/DMN/951457.newcentral/lhsurf.mgh --isp $in/DMN/952863.newfar/lhsurf.mgh --isp $in/DMN/952863.newcentral/lhsurf.mgh --isp $in/DMN/955465.newfar/lhsurf.mgh --isp $in/DMN/955465.newcentral/lhsurf.mgh --isp $in/DMN/957974.newfar/lhsurf.mgh --isp $in/DMN/957974.newcentral/lhsurf.mgh --isp $in/DMN/959574.newfar/lhsurf.mgh --isp $in/DMN/959574.newcentral/lhsurf.mgh --isp $in/DMN/965367.newfar/lhsurf.mgh --isp $in/DMN/965367.newcentral/lhsurf.mgh --isp $in/DMN/965771.newfar/lhsurf.mgh --isp $in/DMN/965771.newcentral/lhsurf.mgh --isp $in/DMN/966975.newfar/lhsurf.mgh --isp $in/DMN/966975.newcentral/lhsurf.mgh --isp $in/DMN/972566.newfar/lhsurf.mgh --isp $in/DMN/972566.newcentral/lhsurf.mgh --isp $in/DMN/978578.newfar/lhsurf.mgh --isp $in/DMN/978578.newcentral/lhsurf.mgh --isp $in/DMN/979984.newfar/lhsurf.mgh --isp $in/DMN/979984.newcentral/lhsurf.mgh --isp $in/DMN/983773.newfar/lhsurf.mgh --isp $in/DMN/983773.newcentral/lhsurf.mgh --isp $in/DMN/984472.newfar/lhsurf.mgh --isp $in/DMN/984472.newcentral/lhsurf.mgh --isp $in/DMN/987983.newfar/lhsurf.mgh --isp $in/DMN/987983.newcentral/lhsurf.mgh --isp $in/DMN/990366.newfar/lhsurf.mgh --isp $in/DMN/990366.newcentral/lhsurf.mgh --isp $in/DMN/991267.newfar/lhsurf.mgh --isp $in/DMN/991267.newcentral/lhsurf.mgh --isp $in/DMN/992673.newfar/lhsurf.mgh --isp $in/DMN/992673.newcentral/lhsurf.mgh --isp $in/DMN/992774.newfar/lhsurf.mgh --isp $in/DMN/992774.newcentral/lhsurf.mgh --isp $in/DMN/993675.newfar/lhsurf.mgh --isp $in/DMN/993675.newcentral/lhsurf.mgh --isp $in/DMN/996782.newfar/lhsurf.mgh --isp $in/DMN/996782.newcentral/lhsurf.mgh --out $out/preproc_DMN_fc/lh.paired-diff.DMN_fc.mgh --f $sublist --no-cortex-only

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: 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

snolin@uab.edumailto:snolin@uab.edu

On 3/29/19, 10:05 AM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D."mailto:freesurfer-bounces@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D. <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of DGREVE@mgh.harvard.edu>mailto:freesurfer-bounces@nmr.mgh.harvard.eduonbehalfofDGREVE@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

> snolin@uab.edumailto:snolin@uab.edu

>

> On 3/19/19, 3:30 PM, "freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D."mailto:freesurfer-bounces@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D. <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of DGREVE@mgh.harvard.edu>mailto:freesurfer-bounces@nmr.mgh.harvard.eduonbehalfofDGREVE@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.edumailto:snolin@uab.edu

> >

> > *From: *freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of "Greve,

> > Douglas N.,Ph.D." DGREVE@mgh.harvard.edumailto:DGREVE@mgh.harvard.edu

> > *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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.edumailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

> >

> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

> >

> >

> >

> >

> > _______________________________________________

> > Freesurfer mailing list

> > Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

>

>

> _______________________________________________

> Freesurfer mailing list

> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

>

>

> _______________________________________________

> Freesurfer mailing list

> Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________

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Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu

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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

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: *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

snolin@uab.edu  <mailto:snolin@uab.edu>

On 3/29/19, 10:05 AM,"freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve,
Douglas N.,Ph.D."  <mailto:freesurfer-bounces@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D.>  <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
DGREVE@mgh.harvard.edu>  <mailto:freesurfer-bounces@nmr.mgh.harvard.eduonbehalfofDGREVE@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

     >snolin@uab.edu  <mailto:snolin@uab.edu>

     >

     > On 3/19/19, 3:30 PM,"freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve,
Douglas N.,Ph.D."  <mailto:freesurfer-bounces@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D.>  <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
DGREVE@mgh.harvard.edu>  <mailto:freesurfer-bounces@nmr.mgh.harvard.eduonbehalfofDGREVE@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  <mailto:snolin@uab.edu>

     >      >

     >      > *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>  <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>  on behalf of "Greve,

     >      > Douglas N.,Ph.D."<DGREVE@mgh.harvard.edu>  <mailto:DGREVE@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

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 snolin@uab.edu

On 4/2/19, 3:34 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:

 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
 >
 > 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: *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
 >
 >     snolin@uab.edu  <mailto:snolin@uab.edu>
 >
 >     On 3/29/19, 10:05 AM,"freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve,
 >     Douglas N.,Ph.D."  <mailto:freesurfer-bounces@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D.>  <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
 >     DGREVE@mgh.harvard.edu>  <mailto:freesurfer-bounces@nmr.mgh.harvard.eduonbehalfofDGREVE@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
 >
 >          >snolin@uab.edu  <mailto:snolin@uab.edu>
 >
 >          >
 >
 >          > On 3/19/19, 3:30 PM,"freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Greve,
 >     Douglas N.,Ph.D."  <mailto:freesurfer-bounces@nmr.mgh.harvard.eduonbehalfofGreve,DouglasN.,Ph.D.>  <freesurfer-bounces@nmr.mgh.harvard.edu on behalf of
 >     DGREVE@mgh.harvard.edu>  <mailto:freesurfer-bounces@nmr.mgh.harvard.eduonbehalfofDGREVE@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  <mailto:snolin@uab.edu>
 >
 >          >      >
 >
 >          >      > *From: *<freesurfer-bounces@nmr.mgh.harvard.edu>  <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>  on behalf of "Greve,
 >
 >          >      > Douglas N.,Ph.D."<DGREVE@mgh.harvard.edu>  <mailto:DGREVE@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>
 >
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