Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Minc File Error
by MCLAREN, Donald 09 Dec '15

09 Dec '15

Zeke and others, I recently installed Freesurfer v6 ( freesurfer-Darwin-OSX-stable-v6-beta-20151015.dmg <ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-beta/freesurfer-…>, MacOS 10.9.5, XQuartz 2.7.8), and Freeview always closes whenever I try to open a mnc file. Below is the output from the terminal after Freeview closes. Please let me know what I need to resolve the issue. The file is in fact a valid minc file as it can be opened by register and display. Please let me know if additional details are needed. Best, Donald Output begins here: ================= ncopen: filename "XXX.mnc": Not a netCDF file miopen: MINC package entry point Error opening XXX.mnc mincRead(): error reading volume from file XXXX.mnc dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libstdc++.6.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libstdc++.6.dylib Expected in: /usr/lib/libSystem.B.dylib [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 5 TRAP [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 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 darwin12. named Belhavens-Best.local by mclaren Wed Dec 9 14:42:45 2015 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --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 [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 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 darwin12. named Belhavens-Best.local by mclaren Wed Dec 9 14:42:45 2015 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --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 Best Regards, Donald McLaren, PhD

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selxavg3-sess ERROR
by Christina Pressl 09 Dec '15

09 Dec '15

Dear Freesurfer Experts, I am having trouble with selxavg3-sess and was wondering if you could maybe help me resolving the issue (error log attached) I ran #preproc-sess –s Sess01 –surface fsaverage lhrh –mni305 –fwhm 5 –per-run and the following commands for lh, rh and mni305 #mkanalysis-sess –fsd bold –stc up -surface fsaverage lh -fwhm 5 -event-related -paradigm oddeven.par -nconditions 3 -spmhrf 0 -TR 2 -refeventdur 10.750 -nskip 4 –mcextreg -polyfit 2 -analysis oddeven.sm5.lh #mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-object –a 1 –c 2 –c 3 #mkcontrast-sess –analysis oddeven.sm5.lh –contrast face-vs-fix –a 1 –c 0 Thank you very much. Christina

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Question about Qdec
by levi solomyak 09 Dec '15

09 Dec '15

Dear experts, I've been attempting to generate a stats data table in qdec, but each time I get a "Index Error: list index is out of range" error. This is occurring when it is trying to parse the .stats file. I've made sure that the files all line up exactly with the qdec table and that SUBJECTS_DIR is properly sourced so I'm not sure how to fix this problem. Any help would be greatly appreciated! Thank you, L S --

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Re: [Freesurfer] Talairach_afd error (Bruce Fischl)
by Anna I. Garcia Diaz 09 Dec '15

09 Dec '15

Hi Bruce, Were you able to take a look at the error we discussed previously? We are very concerned about this problem, because our study depends on the preprocessing of these images. The previous e-mail with logs from the error is copied below. Any help would be very much appreciated. Thanks in advance and kind regards, Anna Garcia The recon-all.log file from the tailaraich processes on reads as follows: #@# Talairach Tue Sep 22 13:07:35 CEST 2015 /psiquiatria/home/anna/subjects/prova/mri talairach --i orig.mgz --xfm transforms/talairach.auto.xfm /psiquiatria/home/anna/subjects/prova/mri /psiquiatria/software/freesurfer/bin/talairach --i orig.mgz --xfm transforms/talairach.auto.xfm $Id: talairach,v 1.7 2011/03/02 20:16:40 nicks Exp $ Linux blade01 2.6.32.12-0.7-default #1 SMP 2010-05-20 11:14:20 +0200 x86_64 x86_64 x86_64 GNU/Linux Tue Sep 22 13:07:36 CEST 2015 tmpdir is transforms/tmp.talairach.22322 /psiquiatria/home/anna/subjects/prova/mri mri_convert orig.mgz transforms/tmp.talairach.22322/src.mnc mri_convert orig.mgz transforms/tmp.talairach.22322/src.mnc input_transform(): error reading transform elem [1,1] input_transform: error reading transform. error loading transform from /psiquiatria/home/anna/subjects/prova/mri/transforms/talairach.xfm $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from orig.mgz... TR=2300.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 5.40604e-09, 3.72529e-09) j_ras = (0, 0, -1) k_ras = (-6.90488e-09, 1, 4.65661e-10) writing to transforms/tmp.talairach.22322/src.mnc... -------------------------------------------- mritotal -verbose -debug -clobber -modeldir /psiquiatria/software/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.22322/src.mnc transforms/talairach.auto.xfm Tue Sep 22 13:08:01 CEST 2015 talairach done INFO: transforms/talairach.xfm already exists! The new transforms/talairach.auto.xfm will not be copied to transforms/talairach.xfm This is done to retain any edits made to transforms/talairach.xfm Add the -clean-tal flag to recon-all to overwrite transforms/talairach.xfm #-------------------------------------------- #@# Talairach Failure Detection Tue Sep 22 13:08:02 CEST 2015 /psiquiatria/home/anna/subjects/prova/mri talairach_afd -T 0.005 -xfm transforms/talairach.xfm ltMNIreadEx: could not read row 1 from transforms/talairach.xfm (Linear_Transform = ) ERROR: talairach_afd::Load_xfm(): could not parse transforms/talairach.xfm Manual Talairach alignment may be necessary, or include the -notal-check flag to skip this test, making sure the -notal-check flag follows -all or -autorecon1 in the command string. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach Linux blade01 2.6.32.12-0.7-default #1 SMP 2010-05-20 11:14:20 +0200 x86_64 x86_64 x86_64 GNU/Linux recon-all -s prova exited with ERRORS at Tue Sep 22 13:08:04 CEST 2015 For more details, see the log file /psiquiatria/home/anna/subjects/prova/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Also, a recon-all.error file was created, and says the following: SUBJECT prova DATE Mon Sep 28 18:56:32 CEST 2015 USER anna HOST blade07 PROCESSOR x86_64 OS Linux Linux blade07 2.6.32.12-0.7-default #1 SMP 2010-05-20 11:14:20 +0200 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.379.2.17 2011/05/20 22:48:18 nicks Exp $ /psiquiatria/software/freesurfer/bin/recon-all PWD /psiquiatria/home/anna/subjects/prova/mri CMD mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 (The same exact recon-all.error file appears when using the -notal-check flag) Kind regards, Anna Garcia On Wed, Oct 28, 2015 at 2:36 PM, <freesurfer-request(a)nmr.mgh.harvard.edu> wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. mri_parse_sdcmdir splitting a single series into two? > (Oliver Hinds) > 2. Postdoc Positions for the Adolescent Brain Cognitive > Development (ABCD) study (Don Hagler) > 3. Re: FreeSurfer pve correction tool (Mohamed Ali Bahri) > 4. Re: A mixed effect model approach in within subject dataset > {Disarmed} (Martin Reuter) > 5. Re: FreeSurfer pve correction tool (Douglas N Greve) > 6. Understanding the brainstem AtlasMesh file structure format > (Jonathan Plasencia) > 7. Re: comparison of 4 groups: mri_glmfit or Qdec? (Sandy Schramm) > 8. Re: Talairach_afd error (Bruce Fischl) (Bruce Fischl) > 9. error finding Matlab (Jason Haberman) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 27 Oct 2015 15:14:25 -0400 (EDT) > From: Oliver Hinds <ohinds(a)nmr.mgh.harvard.edu> > Subject: [Freesurfer] mri_parse_sdcmdir splitting a single series into > two? > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: > <alpine.LRH.2.20.1510271455210.6558(a)gate.nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=US-ASCII > > Hi, > > I'm running into an issue where the slices from one DICOM series are being > parsed by mri_parse_sdcmdir (and mri_info and mri_convert) as two separate > series. > > A few example lines from a scan.out: > > 6 AR_t.s40.c0 ok 64 64 41 1 <long file name> > 7 AR_t.s40.c0 ok 64 64 23 1 <different long file name> > > The scan AR_t.s40.c0 was run as a single series on the scanner, with 64 > slices. Inspection of the dicom header shows that the series UID is the > same for the DICOM files in each, except there is an extra string '.0.0.0' > at the end of series UID in the DICOMS that are parsed into the second > series. > > Has anyone else experienced this behavior? If so, is there a workaround? > > Thanks, > Oliver > > > > > ------------------------------ > > Message: 2 > Date: Tue, 27 Oct 2015 13:41:36 -0700 > From: Don Hagler <dhaglerjr(a)hotmail.com> > Subject: [Freesurfer] Postdoc Positions for the Adolescent Brain > Cognitive Development (ABCD) study > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <BLU436-SMTP65024FB31221FBD3A8E848A6220(a)phx.gbl> > Content-Type: text/plain; charset="us-ascii" > > Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) > study > > > > University of California, San Diego > > > > Several funded postdoctoral positions are available in image analysis > method development, including automated cortical- and subcortical > segmentation, advanced diffusion tractography, and fMRI mapping and time > series analysis. We are looking to build a team to help build the next > generation of analysis pipelines and visualization tools for a newly funded > study to follow 10,000 children with longitudinal structural and functional > imaging across 19 sites across the US. The study will use a cross-platform > Harmonized Human Connectome Protocol, optimized for quantitative accuracy > and consistency of imaging biomarkers across scanners and time. To learn > more about the ABCD study, please see > http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-lan… > < > http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-lan… > >. > > > > Requirements: Applicants should have research experience in any of the > above fields, with a Ph.D. or equivalent degree. They should be comfortable > working in a distributed team environment, and should have a track record > of quality scientific publications. Candidates are expected to be > experienced in programming with Matlab, Python, and/or <> C/C++. Experience > with FreeSurfer, FSL, and the Human Connectome analysis pipelines is > strongly preferred. > > > > To formally apply, submit a current CV, a personal statement describing > your research experience and interests, and contact information for 2-3 > references to abcd(a)ucsd.edu <mailto:abcd@ucsd.edu>. Or feel free to email > Dr. Donald Hagler (dhagler(a)ucsd.edu <mailto:dhagler@ucsd.edu>) or Anders > M. Dale (amdale(a)ucsd.edu <mailto:amdale@ucsd.edu>) for more information. > > > > The University of California, San Diego is an Equal > Opportunity/Affirmative Action Employer advancing inclusive excellence. All > qualified applicants will receive consideration for employment without > regard to race, color, religion, sex, sexual orientation, gender identity, > national origin, disability, age, protected veteran status, or other > protected categories covered by the UC nondiscrimination policy. >

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Re: [Freesurfer] Edit the number of segments in the segmentation of the corpus callosum
by UQAM 09 Dec '15

09 Dec '15

Hi Zeke, We tried the new version of mri_cc and we still do not get 12 segments of the corpus callosum when we open the aseg.12segmentsCC.mgz in a viewer. Could you send us the script you launch after the recon_all to get aseg.mgz files with 12 segments? basically the mri_cc Could you also please explain how to edit the ColorLut.txt file Finally, what is the precise script of the mri_segstats to generate stats tables. Thanks again, Cheers, Genevieve On Tue, Nov 24, 2015 at 11:20 PM, Z K <zkaufman(a)nmr.mgh.harvard.edu> wrote: > Hello Genevieve, > > Below is a link to the newest version of mri_cc. Please copy it to your > FREESURFER_HOME directory and backup the original. > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/mri_cc > > Hope this help. > > -Zeke > > > On 11/24/2015 05:56 AM, UQAM wrote: > >> Hi Bruce, >> >> DELL R910 >> Intel(R) Xeon(R) CPU E7520 @ 1.87GHz (16 cores) >> 32 Go RAM >> CentOS release 5.10 (Final) >> kernel 2.6.18-371.3.1.el5 >> >> On Mon, Nov 23, 2015 at 7:32 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: >> >> Hi Genevieve >> >> I just tracked this down and it is a bug in mri_cc. If you tell Zeke >> your hardware/software environment he can get you a new version that >> should work >> >> cheers >> Bruce >> >> >> On Mon, 23 Nov 2015, UQAM wrote: >> >> Hi Bruce, >> Please find the two files attached. >> >> Genevieve >> >> >> >> On Mon, Nov 23, 2015 at 2:39 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >> >> wrote: >> Hi Geneviève >> >> if you send us the $SUBJECTS_DIR/CColorLUT.txt and >> $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz and we will take a >> look >> >> cheers >> Bruce >> On Mon, 23 Nov 2015, UQAM wrote: >> >> Hi, >> This a a "re-posting" of a question I've raised >> last week ; ) >> >> I would like to segment the corpus callosum >> into twelve even lenght segments >> instead of the five segments that freesurfer >> includes by default. >> >> - First I ran a mri_cc on subject e0070: >> >> mri_cc -aseg aseg.auto_noCCseg.mgz -o >> aseg.12segmentsCC.mgz -d 12 e0070 >> >> - Then I edited the ColorLUT.txt file and renamed >> it CColorLUT.txt (see >> attachment, segments 251 to 262). >> >> - Finally I ran a mri_segstats to compute the >> statistics on segmented >> volumes. >> >> mri_segstats seg >> $SUBJECTS_DIR/e0070/mri/aseg.12segmentsCC.mgz --ctab >> $SUBJECTS_DIR/CColorLUT.txt --nonempty --excludeid >> 0 sum >> --e0070_CC12.aseg.stats >> >> The e0070_CC12.aseg.stats file still displays only >> five segments of the >> corpus callosum. >> >> Any tips or clues on how I could do things >> differently to get 12 segments? >> >> Thanks in advance, >> >> Geneviève >> >> >> _______________________________________________ >> 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. >> >> >> >> >> _______________________________________________ >> 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. >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >>

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Qdec - cluster labels
by sabin khadka 09 Dec '15

09 Dec '15

Hi all - When you get a significant cluster after doing monte-carlo simulation, we get peak vertex/Talairach coordinates and also saved in *summary files. Is there a way to find all the parcellated regions (Desikan, or, Destriuex) in the significant clusters? Thanks,Sabin

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file error
by LIEWALD David 09 Dec '15

09 Dec '15

OS Opensuse 13.2 Freesurfer 6 Dev Logfile Attached I have had no luck trying to get freesurfer to run. It is failing at the same point each time ( Please see log). I have tried with multiple datasets in multiple locations both on the local machine and across the network. I have also verified that the permissions of the dir are correct and I can manually read and write to the. I'm at a loss? Dave Liewald The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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ASCII Error
by Marc Callison 08 Dec '15

08 Dec '15

Good day, I'm getting the following error when I try to convert my DICOM files. Some of the files do not have the issue, but others do. The error is below. WARNING: file /Users/marc/Desktop/brainscan/DICOM/PA000000/ST000000/SE000001/IM000000 does not contain a Siemens ASCII header has this file been anonymized? ERROR: cannot unpack mosiacs without ASCII header Darwin Marcs-MacBook-Air.local 15.0.0 Darwin Kernel Version 15.0.0: Sat Sep 19 15:53:46 PDT 2015; root:xnu-3247.10.11~1/RELEASE_X86_64 x86_64 recon-all -s my_brain exited with ERRORS at Fri Dec 4 20:02:27 CST 2015 For more details, see the log file /Applications/freesurfer/subjects/my_brain/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I need help figuring out how to solve this if anyone can. I'd really appreciate it. Thanks, Marc

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3dClustSim and Gaussian filter width
by Emma Thompson 08 Dec '15

08 Dec '15

Dear Freesurfers, I am trying to use 3dclustsim in AFNI to determine the minimum number of voxel in a cluster to reach significance, my understanding is that in the command line the -fwhm s flag refers to the gaussian filter width and NOT the Gaussian Kernel, can anyone point me to how I might be able to obtain this for each hemisphere in freesurfer? I am using my own average brain that I created, but it would help to know how to do this for the fsaverage as well. Many thanks for your help! http://afni.nimh.nih.gov/pub../pub/dist/doc/program_help/3dClustSim.html

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edits in a subjects
by angela.favaro＠unipd.it 08 Dec '15

08 Dec '15

Hi Freesurfer experts, I am checking quality of recon of some new scan and I need some advice about the needed edits. I attached two snapshots showing the problems: 1. a problem with white matter recon (surface seems good, but volume not) 2. a problem in the right medial subcortical wall (a lot of confusion in sufaces). My questions are whether I have to discard this subjects or try to edit and which type of edits do you suggest Thank you! Angela

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