Freesurfer

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30099 discussions

Critical Issue?!!
by Alshikho, Mohamad J. 11 Nov '14

11 Nov '14

Hi Doug and Bruce, I posted this question before and I hope that you can help me to find an answer for this issue! I started recently using Tracula to do tractography for my DTI data. I did the analysis exactly as mentioned in wiki and every thing ran smoothly. The problem started when I was trying to repeat the third step (trac-all -path -c ) for the same subjects to generate the statistics; I surprised that Tracula updated all the information mentioned in the file "pathstats.overal.txt" regarding the tract's volume and the tract's metrics values. Every time the output is different i.e the statistics regarding the tracts volume and the tracts metrics are changing whenever I repeat the third step (trac-all -path -c ) of this analysis . This is weird??? Attached are three "pathstats.overal.txt" files for the same subject after three consecutive runs for the "trac-all -path -c" (the same subject) Looking forward for your support Thanks Mohamad

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Desikan-Killiany atlas - ideal for all age ranges?
by Martina Papmeyer 11 Nov '14

11 Nov '14

Dear FreeSurfer experts I have one question regarding the labeling of cortical structures using the Desikan-Killiany atlas and couldn't find any information in the archives. As far as I read, this atlas has been composed by including 40 subjects of broad age ranges (19-86 years of age), with 10 of them suffering from Alzheimer's disease. Since I am mainly working with data sets of much younger non-demented subjects (early twenties), I was wondering if it was more accurate to make use of a young subset of the Desikan-Killiany atlas to optimize the labeling of cortical parcellations and if that was possible at all? Thank you very much for your help! All best wishes Martina -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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FS vs. manual segmentation in HC
by Bernd Merkel 11 Nov '14

11 Nov '14

Dear all ! I know, this has been discussed a lot in the forum, however, I am still not sure, whether my analysis pipeline is correct. I simply want to compare volumes of FS vs. manual segmentation in the hippocampus and calculate the dice coefficient. So these are my steps: 1. mri_convert T1.mgz T1.nii 2. Register (e.g. with FLIRT) T1.nii to original_mprage.nii (where the manual segmentation was done), output: registration.matrix 3. mri_extract_label aseg.mgz 17 left_FreeSurfer_HC.nii mri_extract_label 53 right_FreeSurfer_HC.nii 4. Register left_ & right_FreeSurfer_HC.nii to original_mprage.nii by using registration.matrix 5. mri_compute_overlap left_Freesurfer_ HC left_manual_HC Now here are my questions: A) I've read that I should use mri_label2vol instead of mri_convert Is that correct and how would I process that afterwards ? B) The volumes form aseg.mgz are different (in my case: bigger) to the aseg.stats because of partial volume correction. Can I use partial volume corrected hippocampal masks ? C) Where can I find information about the segmentation method of the hippocampus, used in FreeSurfer, especially regarding the HC borders ? Because otherwise it might be difficult to calculate and interpret dice coefficients. Best regards and thanks for any help, Bernd

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inverted dicoms
by will brown 10 Nov '14

10 Nov '14

Hi all, I have files that are 2D axial slices that are left-right inverted, so the left side of the brain is on the right side of each slice. Do I need to do anything to the dicoms before importing them into freesurfer? Thanks, Will

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Re: [Freesurfer] freeview fault: PETSC Error ... PERSISTENT
by Krieger, Donald N. 10 Nov '14

10 Nov '14

Hi Nick, I downloaded the most recent version of freeview.bin using wget as you suggested and ran it on two different machines. It appeared to load a volume file fully whereas before it was crashing when showing it had loaded only 1%. But it still crashes after that with the message below my signature. I tried a few different .mgz files including the original one with the same result. Both the machines on which I ran it have 8 GBytes of RAM. Any other thoughts would be welcome. Regards, Don [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find m emory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a linux-gnu named donHome1TB by kriegerd Mon Nov 10 13:48:15 2014 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-sha red=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > -----Original Message----- > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer- > bounces(a)nmr.mgh.harvard.edu] On Behalf Of Nick Schmansky, MGH > Sent: Tuesday, November 04, 2014 11:59 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] freeview fault: PETSC Error ... > > you can try downloading our nightly 'dev' build of freeview, from here: > > https://surfer.nmr.mgh.harvard.edu/fswiki/Download > > or here's a quicker way (this is a one-line command... wget <file>): > > wget > ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6…<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6…> > 86_64/freeview.bin<ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6…> > > and copy it to $FREESURFER_HOME/bin > then > chmod a+x $FREESURFER_HOME/bin/freeview.bin > > N. > > > On Tue, 2014-11-04 at 12:35 +0000, Krieger, Donald N. wrote: > > I recently downloaded and installed > > freesurfer-Linux-centos6_x86_64-table-pub-v5.3.0.tar.gz . > > > > I had been running this version previously but had to reload > > everything due to a disk crash. > > > > > > > > recon-all –all goes to completion with no errors. > > > > freeview starts up fine but fails on loading a volume file with the > > PETC error listed below. > > > > I found several references to this error in the archive but no > > resolution for my problem. > > > > Any thoughts would be welcome – thanks. > > > > > > > > [0]PETSC ERROR: > > ---------------------------------------------------------------------- > > -- > > > > [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, > > probably memory access out of range > > > > [0]PETSC ERROR: Try option -start_in_debugger or > > -on_error_attach_debugger > > > > [0]PETSC ERROR: or see > > http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.ht > > ml#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man > > libgmalloc on Apple to find memory corruption errors > > > > [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, > > and run > > > > [0]PETSC ERROR: to get more information on the crash. > > > > [0]PETSC ERROR: --------------------- Error Message > > ------------------------------------ > > > > [0]PETSC ERROR: Signal received! > > > > [0]PETSC ERROR: > > ---------------------------------------------------------------------- > > -- > > > > [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 > > 17:29:26 CDT 2008 HG revision: > > 4466c6289a0922df26e20626fd4a0b4dd03c8124 > > > > [0]PETSC ERROR: See docs/changes/index.html for recent updates. > > > > [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. > > > > [0]PETSC ERROR: See docs/index.html for manual pages. > > > > [0]PETSC ERROR: > > ---------------------------------------------------------------------- > > -- > > > > [0]PETSC ERROR: Unknown Name on a linux-gnu named BTRC-Server01 by > > kriegerd Tue Nov 4 06:55:17 2014 > > > > [0]PETSC ERROR: Libraries linked > > from > > /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p1 > > 3/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt > > > > [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 > > > > [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc > > --with-fc=g77 --download-f-blas-lapack=0 --download-mpich=1 > > --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 > > COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 > > > > [0]PETSC ERROR: > > ---------------------------------------------------------------------- > > -- > > > > [0]PETSC ERROR: User provided function() line 0 in unknown directory > > unknown file > > > > [unset]: aborting job: > > > > application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 > > > > > > > > Regards, > > > > > > > > Don > > > > > > > > Signature0001 > > > > Don Krieger, Ph.D. > > > > Department of Neurological Surgery > > > > University ofPittsburgh > > > > (412)648-9654 Office > > > > (412)521-4431 Cell/Text > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at http://www.partners.org/complianceline . If the e-mail was sent to you in > error but does not contain patient information, please contact the sender and > properly dispose of the e-mail.

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error with fast_selxavg3
by Francesca Strappini 10 Nov '14

10 Nov '14

Dear all, I'm trying to run a retinotopy analysis in several subjects but it crashed with an error in one subject. I ran this command line: selxavg3-sess -a rtopy.HS.rh -s SUBJ09 and this is the last part of the output with the error message. Any help would be much appreciated. Best Francesca < M A T L A B (R) > Copyright 1984-2013 The MathWorks, Inc. R2013b (8.2.0.701) 64-bit (glnxa64) August 13, 2013 ---------------------------------------------------- Your MATLAB license will expire in 56 days. Please contact your system administrator or MathWorks to renew this license. ---------------------------------------------------- To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> sxa3pwd = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed >> sxa3cmd = /usr/local/freesurfer/fsfast/bin/selxavg3-sess -a rtopy.HS.rh -s SUBJ09 >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# SUBJ09 ############################### /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09 ------------------------- $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m ------------------------- outtop = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed Extension format = nii.gz nruns = 4 autostimdur = outanadir = /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh Found 110059/126364 (87.1) voxels in mask Creating Design Matrix ... creation time = 0.005 sec DoMCFit = 1 ntptot = 960, nX = 36, DOF = 924 Saving X matrix to /usr/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 36) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strappini(a)weizmann.ac.il

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edit failure
by Octavian Lie 10 Nov '14

10 Nov '14

Dear all, 1. in the attached there is a gyrus that does not incorporated into surfaces, whatever I do (wm edits/topological defects-cloning voxels from brainmask.mgz or T1.mgz into wm.mgz, save volume then run recon-all autorecon2-wm autorecon 3), or control points addition to wm in brainmask.mgz, then run the -cp flag. Is there any other solution left to clone the white matter (and pial voxels) left out? is brain.finalsurfs.manedit.mgz a solution? 2. Unrelated, after manual pial edits and reruning the recon-all autorecon-pial command, the pial surface generated is mostly OK, however where there have been heavy dura editing the surface looks granular. Is there a workaround (along with better hands), such as smoothing the final pia a bit more (preferably in the recon-all pipeline as to be convergent with other segmentation results). I appreciate your help, Octavian

2 4

Infinite loop in mri_convert
by Nooshin Zadeh 10 Nov '14

10 Nov '14

Dear FreeSurfer experts, I get a new message when I use "mri_convert" command to convert dicom to mgz. I used to apply this command before and there was no problem. I wonder what is the reason that I receive the following message. In addition, it does not create mgz file, and goes to infinite loop. *mri_convert "/M1/t1_se_ax_5/IM-0004-0001.dcm" "/FS/M1/mri/orig/001.mgz"* mri_convert /M1/t1_se_ax_5/IM-0004-0001.dcm /FS/M1/mri/orig/001.mgz $Id: mri_convert.c,v 1.166.2.2 2010/08/10 19:11:50 greve Exp $ reading from /M1/t1_se_ax_5/IM-0004-0001.dcm... Getting Series No Scanning Directory INFO: Found 39 files in /Users/christine/Raw_Data/M226/t1_se_ax_5 INFO: Scanning for Series Number 5INFO: found 37 files in series INFO: loading series header info. I appreciate if you can advise me. Regards, Nooshin PhD Candidate Departments of Electrical & Computer Engineering University of Miami Email: n.zadeh(a)miami.edu

3 2

mri_surfcluster and "sub-clustering"
by Sophie Maingault 10 Nov '14

10 Nov '14

Dear FS experst, I used the command mri_surfcluster. For one analysis, I obtained 6 clusters with one huge of 473 cm2 which corresponds to several "sub-clusters" because it was expanded through a large part of the cortex (covering several anatomical regions). Is there a way to separate one apparent cluster in several sub clusters by extracting several maximum vertices and not only one per cluster ? Best, Sophie Maingault – Doctorante/PhD student GIN (Groupe d'Imagerie Neurofonctionnelle) UMR 5296 – Université de Bordeaux – CNRS/CEA 146, rue Léo Saignat – Case 71 33076 Bordeaux cedex

2 1

Pial edits and wm control points.
by Octavian Lie 08 Nov '14

08 Nov '14

Dear all, I am editing recon-all segmentation results in freeview using the recon edit function. 1. Is there a way to complement the toggle between the brainmask.mgz and T1.mgz, especially at the end of pial editing, before resubmitting the saved brainmask volume to recon-all? It would be nice to be able to see the edited voxels (the final ones remaining edited, after successive deletions/clones) as a mask over the T1.mgz in freeview as the final check before sending brainmask back to segmentation. 2. As far as control points go, the FS tutorial mentions that there is a certain trial and error as to the no or density of control points to be used. Still, the example fig in the tutorial shows control points spaced about 2-5-voxels. Is this a good starting point in general? 3. Some of the segmentations need bit corrections in wm edits (filling holes), missing wm in brainmask (control points with T1.mgz as reference), and pial edits. It is OK if all of these corrections are done in a single step on brainmask.mgz with aux T1.mgz, then do recon-all -autorecon2-cp -autorecon3 -subjid? Thank you for your tips, Octavian

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