Freesurfer November 2014

freesurfer@nmr.mgh.harvard.edu

99 participants
144 discussions

Unpacking Siemens Functional Data: No DICOM files found
by Shady El Damaty 13 Nov '14

13 Nov '14

Hi freesurfers, I've been stuck on this problem for a while and couldn't find anything online to help me out so I've come to the mailing list as my last resort. I am trying to unpack my functional data into fsl format using the unpacksdcmdir command. However, I am not successful using this command and get the error message: "no dicom files found" This is the command I'm entering: unpacksdcmdir -src $DICOMDIR -targ ~/Ultimatum/sess01 -scanonly Ultimatum-01_Import.log When I list the contents of $DICOMDIR, I find that there are about 800 or so files with enumerated names ending in *.ACQ (e.g.: 1.ACQ, 2.ACQ... 800.ACQ). Does anyone have any ideas why unpacksdcmdir isn't reading these files? The output after running the command appears below. Thanks in advance for your help! Shady El Damaty unpacksdcmdir -src $DICOMDIR -targ ~/Ultimatum/sess01 -scanonly Ultimatum-01_Import.log $Id: unpacksdcmdir,v 1.23 2008/12/15 21:42:16 greve Exp $ /glusterfs/mirror/cfmi/home/se394 -src /raw/dicom/data/cfmi/MR/2014/10/21/1.3.12.2.1107.5.2.32.35052.30000014101416403831200000052.STU/1.3.12.2.1107.5.2.32.35052.2014102112462587284871374.0.0.0.SER -targ /exports/home/se394/Ultimatum/sess01 -scanonly Ultimatum-01_Import.log Thu Nov 13 12:59:20 EST 2014 mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2014/11/13-17:59:20-GMT BuildTimeStamp: May 13 2013 16:24:28 CVS: $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ User: se394 Machine: node020.cfmi.georgetown.edu Platform: Linux PlatformVersion: 3.10.0-123.9.2.el7.x86_64 CompilerName: GCC CompilerVersion: 40400 node020.cfmi.georgetown.edu Linux node020.cfmi.georgetown.edu 3.10.0-123.9.2.el7.x86_64 #1 SMP Tue Oct 28 18:05:26 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Thu Nov 13 12:59:20 EST 2014 Log File is /exports/home/se394/Ultimatum/sess01/unpack.log INFO: Logfile is /exports/home/se394/Ultimatum/sess01/unpack.log SkipMoCo 0 Scanning source directory ... INFO: summary file is /exports/home/se394/Ultimatum/sess01/dicomdir.sumfile INFO: status file is /exports/home/se394/Ultimatum/sess01/parse.status Scanning directory Thu Nov 13 12:59:20 EST 2014 mri_parse_sdcmdir --sortbyrun --d /raw/dicom/data/cfmi/MR/2014/10/21/1.3.12.2.1107.5.2.32.35052.30000014101416403831200000052.STU/1.3.12.2.1107.5.2.32.35052.2014102112462587284871374.0.0.0.SER --o /exports/home/se394/Ultimatum/sess01/dicomdir.sumfile --status /exports/home/se394/Ultimatum/sess01/parse.status 0 Done scanning Thu Nov 13 12:59:24 EST 2014 ------------------------------------------ ERROR: no dicom files found in /raw/dicom/data/cfmi/MR/2014/10/21/1.3.12.2.1107.5.2.32.35052.30000014101416403831200000052.STU/1.3.12.2.1107.5.2.32.35052.2014102112462587284871374.0.0.0.SER

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mri_cnr
by Jürgen Hänggi 13 Nov '14

13 Nov '14

Dear FS experts There is a reviewer question with respect to the voxels/vertices used to compute the SNR and CNR with FreeSurfer's mri_cnr function. Do we right that SNR/CNR computation is based only on the voxels that are located at the interface between the white and pial surface? Thanks in advance Regards Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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mritotal failed
by will brown 12 Nov '14

12 Nov '14

Hi there, I am receiving the following error during recon-all: mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.7573/src.mnc transforms/talairach.auto.xfm Can't locate shellwords.pl in @INC (@INC contains: /usr/local/freesurfer/mni/bin/../lib/mni_autoreg /usr/local/freesurfer/mni/lib/perl5/5.8.5 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /usr/local/freesurfer/mni/bin/mritotal line 460. ERROR: mritotal failed, see transforms/talairach.log Any ideas?

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Missing 'recon edit' button in Freeview
by Zhang, Kunyu 12 Nov '14

12 Nov '14

Hi all, I seem to be missing the ‘recon edit’ button that is supposed to be next to ‘voxel edit’ in Freeview. I am using version 1.0 on Mac OS X 10.10 from the latest version (v5.3.0) of FreeSurfer. According to the FreeSurferWiki, if I check ‘recon edit’ within ‘voxel edit,’ it just locks the brush value to 255 and eraser value to 1, but for extended editing, Recon edit mode is needed. If anyone can please help me with this issue, I would greatly appreciate it! Thanks, Kunyu

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FW: recon-all failure due to header
by Ashley Stillman 12 Nov '14

12 Nov '14

We are having issues running recon-all on our dicom files, as they are saved as a mosaic. When we open the original dicom file (attached) it lists out the rows, columns and slices. However, when we run mriparsesdcmdir, it just posts 0’s for the rows and columns (screen shot attached). We are able to recreate the output file necessary to run recon-all (basically fill in the missing 0’s). Is there a way to tell recon-all to call on this file to retrieve the missing data manually? Thank you, Ashley Ashley N. Stillman Clinical Psychology Graduate Research Assistant University of Tulsa, T.R.A.P.T. Lab Laureate Institute for Brain Research email: anstillman(a)laureateinstitute.org<mailto:anstillman@laureateinstitute.org> | ashley-stillman(a)utulsa.edu<mailto:ashley-stillman@utulsa.edu>

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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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Freesurfer November 2014