Freesurfer July 2013

freesurfer@nmr.mgh.harvard.edu

165 participants
332 discussions

autorecon2-wm without mri_fill in v4.5?
by Caspar M. Schwiedrzik 22 Jul '13

22 Jul '13

Hi Freesurfer Experts, I am working on a primate anatomy and I am having problems with the white matter filling in the temporal lobe in version 4.5. I manually edited wm.mgz and recreated filled.mgz using mri_fill. I then manually edited filled.mgz. However, when I then run autorecon-all -autorecon2-wm, all my manual edits in filled.mgz are overwritten. Is there a way to autorecon2-wm without mri_fill in v4.5? Thank you very much, Caspar

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Re: [Freesurfer] Average cortical diffusion
by Afaf Elsarraj 22 Jul '13

22 Jul '13

Many thanks ________________________________________ From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] Sent: 22 July 2013 16:31 To: Afaf Elsarraj Subject: RE: [Freesurfer] Average cortical diffusion can you cc the list so that others can answer and learn from the responses? Put -t <MD sampled to surface> before the mandatory argument On Mon, 22 Jul 2013, Afaf Elsarraj wrote: > > > Thank you for your reply I appreciate it. So when I use the command line: mris_anatomical_stats [options] <subjectname> <hemi> [<surfacename>]. Do I need to use (-t) as an option or shall I just put the file name. > > Regards, > Afaf > > > > __________________ > From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: 22 July 2013 14:09 > To: Afaf Elsarraj > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Average cortical diffusion > > use mri_vol2surf to sample it onto the surface, then give > mris_anatomical_stats the file that it created instead of thickness (-t > <file name>). Everthing it reports as thickness will actually be MD values > instead > > On Mon, 22 Jul 2013, Afaf Elsarraj wrote: > >> >> Hi, >> >> >> >> I’ve registered the mean diffusivity (MD) values on the cortical surface. >> Can you please tell me how to get the average cortical MD of the whole >> hemisphere for each subject, rather than the regional cortical MD. >> >> >> >> Kind regards, >> >> Afaf >> >> >> This message and any attachment are intended solely for the addressee and >> may contain confidential information. If you have received this message in >> error, please send it back to me, and immediately delete it. Please do not >> use, copy or disclose the information contained in this message or in any >> attachment. Any views or opinions expressed by the author of this email do >> not necessarily reflect the views of the University of Nottingham. >> >> This message has been checked for viruses but the contents of an attachment >> may still contain software viruses which could damage your computer system, >> you are advised to perform your own checks. Email communications with the >> University of Nottingham may be monitored as permitted by UK legislation. >> >> >> >> This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. > > This message has been checked for viruses but the contents of an attachment > may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation. > > > > > > > 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. This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system, you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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freeview save error
by Jason Tourville 22 Jul '13

22 Jul '13

Hi there, Occassionally when using the "save volume" function from the gui to save edits made to the wm.mgz, freeview crashes (see command line error report below) and the wm.mgz being deleted from subject's 'mri' directory (the temp wm.mgz~ is still present...but all edits are lost). I am running freeview from freesurfer v5.3 on Mac OSX 10.8.4. Any thoughts on the cause? Thanks, Jason 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…: 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 JayMac.local by jaytour Mon Jul 22 10:40:30 2013 [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 -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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Re: [Freesurfer] Recon-all difficulties off-site
by Nitenson, Adam 22 Jul '13

22 Jul '13

> > Hi Doug, > > The command runs a bit further now but then exits with errors. > Unfortunately this time there is no specific stated error. The last few > lines of the log are: > > INFO: extension is mgz > #-------------------------------------------- > #@# Talairach Tue Jun 4 13:22:08 EDT 2013 > /gpfs/data/twhite/anitenso/FreesurferPractice/unpack4/mri > > mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale > --i orig.mgz --o orig_nu.mgz > > Linux node271 2.6.32-279.2.1.el6.x86_64 #1 SMP Fri Jul 20 01:55:29 UTC > 2012 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s unpack4 exited with ERRORS at Tue Jun 4 13:22:10 EDT 2013 > > > > The only other section of the log that seems like it could be related to > an error is: > > Can't locate MNI/Startup.pm in @INC (@INC contains: > /gpfs/runtime/opt/perl/5.16.0/lib > /gpfs/runtime/opt/perl/5.16.0/lib/site_perl /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 > /gpfs/runtime/opt/freesurfer/5.2.0/mni/bin/nu_correct line 37. > BEGIN failed--compilation aborted at > /gpfs/runtime/opt/freesurfer/5.2.0/mni/bin/nu_correct line 37. > > So, I'm not sure what it's not liking here. > > Thanks again, > Adam > > > On Tue, Jun 4, 2013 at 11:44 AM, Douglas N Greve < > greve(a)nmr.mgh.harvard.edu> wrote: > >> That dcmunpack command will put the data into a file called >> unpack3/MPRAGE/002/struct.nii >> It needs to be put into upack3/mri/orig/002.mgz >> doug >> >> >> >> >> On 06/04/2013 11:22 AM, Nitenson, Adam wrote: >> >>> Hi Doug, >>> >>> When I try the command as you suggested: >>> recon-all -all -s unpack3 >>> I get the following error: >>> >>> ERROR: no run data found in /gpfs/data/twhite/anitenso/** >>> FreesurferPractice/unpack3/**mri. Make sure to >>> have a volume called 001.mgz in /gpfs/data/twhite/anitenso/** >>> FreesurferPractice/unpack3/**mri/orig >>> >>> Do you know why I might be lacking that volume? This was not usually an >>> issue after running the two unpacksdcmdir commands (for MPRAGE and bold >>> runs). >>> >>> Thanks, >>> Adam >>> >>> >>> On Mon, Jun 3, 2013 at 3:44 PM, Douglas N Greve < >>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu>>> >>> wrote: >>> >>> Hi Adam, if the subject folder exists and you pass recon-all a -i >>> flag, >>> then it will exit with error saying that the data exist (otherwise it >>> would overwrite what is there). However, just because the subject >>> folder >>> exists does not mean that there is any data sitting in >>> subject/mri/orig. >>> Then it will tell you that it cannot find any data. >>> >>> Note that when you run recon-all, you need to tell it to do something >>> (eg, add the "-all" flag to do everything) >>> >>> doug >>> >>> >>> On 06/03/2013 03:21 PM, Nitenson, Adam wrote: >>> > Hello users, >>> > >>> > I am trying to get Freesurfer (5.2) working properly off-site and >>> am >>> > encountering errors I did not have while working at the Martinos >>> > center. We use the same Siemens 3T Tim Trio scanner at Brown, so I >>> > would hope the data is similar to work with. >>> > >>> > I have been using dcmunpack since unpacksdcmdir is not >>> identifying the >>> > DICOM files properly. I have successfully unpacked the >>> structural and >>> > bold scans using the command (entered from the raw scan data >>> folder: >>> > >>> > dcmunpack -src DICOM -targ (path)/FreesurferPractice/**unpack3 >>> -run 2 >>> > MPRAGE nii struct (I also tried using mgz instead of nii, >>> and also >>> > changed struct to other things as it appears to be a naming >>> argument) >>> > >>> > dcmunpack -src DICOM -targ (path)/FreesurferPractice/**unpack3 >>> -fsfast >>> > -run 3 bold nii f.nii -run 4 bold nii f.nii -run 5 bold nii >>> f.nii -run >>> > 6 bold nii f.nii -run 7 bold nii f.nii -run 8 bold nii f.nii -run 9 >>> > bold nii f.nii >>> > >>> > (path) just being an abbreviate piece of the relevant pathway >>> > >>> > These generate the MPRAGE and bold folders in the subject folder as >>> > expected. I have difficulties with the next commands >>> (environment has >>> > been set). >>> > >>> > I try: >>> > recon-all -i <path to structural data> -s <subject name> -force >>> > recon-all -i (path)/FreesurferPractice/**unpack/MPRAGE/002 -s >>> unpack3 >>> > (I got an error about using -force so I omitted that from my >>> command) >>> > >>> > and get the following Error >>> > ERROR: You are trying to re-run an existing subject with (possibly) >>> > new input data (-i). If this is truly new input data, you >>> should delete >>> > the subject folder and re-run, or specify a different subject >>> name. >>> > If you are just continuing an analysis of an existing subject, >>> then >>> > omit all -i flags. >>> > >>> > Yet when I omit -i and just use "recon-all -s unpack3", I get >>> "ERROR: >>> > nothing to do" >>> > >>> > I tried a different tactic and used >>> > >>> > "recon-all -s unpack3 -autorecon1" as well as "recon-all >>> > -autorecon-all -s unpack3" >>> > >>> > which both created the various folders (bem, label, mri, surf, etc) >>> > but failed with >>> > "ERROR: no run data found in (path)/FreesurferPractice/** >>> unpack3/mri. >>> > Make sure to have a volume called 001.mgz in >>> > (path)/FreesurferPractice/**unpack3/mri/orig. If you have a >>> second run >>> > of data call it 002.mgz, etc." >>> > >>> > I have tried these commands in both bash and tcsh shells with >>> the same >>> > effect. So the problem, it seems, is that my "mri" file is >>> blank, and >>> > this was not a problem I had running these commands at Martinos. >>> Any >>> > idea what the issue might be? >>> > >>> > Best, >>> > >>> > Adam Nitenson >>> > Neuroscience Graduate Program >>> > Laboratory of Affective Neuroscience >>> > Brown University >>> > >>> > >>> > >>> > ______________________________**_________________ >>> > Freesurfer mailing list >>> > Freesurfer(a)nmr.mgh.harvard.edu >>> <mailto:Freesurfer@nmr.mgh.**harvard.edu<Freesurfer(a)nmr.mgh.harvard.edu> >>> > >>> >>> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.**edu<greve(a)nmr.mgh.harvard.edu> >>> > >>> Phone Number: 617-724-2358 <tel:617-724-2358> >>> Fax: 617-726-7422 <tel:617-726-7422> >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> > >>> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >>> > >>> >>> Outgoing: >>> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >>> >>> ______________________________**_________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.** >>> harvard.edu <Freesurfer(a)nmr.mgh.harvard.edu>> >>> >>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >>> >>> >>> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >

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[Tracula] ERRORS in Tracula Preprocessing
by r.navarra＠itab.unich.it 21 Jul '13

21 Jul '13

Hi Vivian, did you solve your issue? I got (almost) same error, not "Too many )'s." but "ERROR: flag ; unrecognized" and the final "trac-preproc exited with ERRORS ... IsRunningFile: Undefined variable." Thank you. Riccardo ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ [Freesurfer] ERRORS in Tracula Preprocessing Vivian Roger Steiger Sat, 25 May 2013 03:43:14 -0700 Dear Freesurfer experts I am trying to process the data of a Longitudinal DTI Study with 2 Timepoints I have encountered the following error while running the tracula pre-processing: ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer/ FSFAST_HOME /Applications/freesurfer//fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Users/zenso/Subjects/structural_23VPs FSL_DIR /Applications/fsl MNI_DIR /Applications/freesurfer//mni FSL_DIR /Applications/fsl [iMac:Subjects] zenso% trac-all -prep -c /Users/zenso/Subjects/Tracula/dmrirc.long.sad Too many )'s. INFO: SUBJECTS_DIR is /Users/zenso/Subjects/structural_23VPs INFO: Diffusion root is /Users/zenso/Subjects/Tracula Actual FREESURFER_HOME /Applications/freesurfer trac-preproc -c /Users/zenso/Subjects/Tracula/1Pre_VP3/scripts/dmrirc.local -log /Users/zenso/Subjects/Tracula/1Pre_VP3/scripts/trac-all.log -cmd /Users/zenso/Subjects/Tracula/2Post_VP3/scripts/trac-all.log -cmd /Users/zenso/Subjects/Tracula/2Post_VP3/scripts/trac-all.cmd ; trac-preproc -c /Users/zenso/Subjects/Tracula/VP3_Base/scripts/dmrirc.local -log /Users/zenso/Subjects/Tracula/VP3_Base/scripts/trac-all.log -cmd /Users/zenso/UZH/MSc/FS2013/Psychologie/Masterarbeit/Subjects/Tracula/VP3_Base/scripts/trac-all.cmd ; ERROR: flag ; unrecognized -c /Users/zenso/Subjects/Tracula/1Pre_VP3/scripts/dmrirc.local -log /Users/zenso/Subjects/Tracula/1Pre_VP3/scripts/trac-all.log -cmd /Users/zenso/Subjects/Tracula/1Pre_VP3/scripts/trac-all.cmd ; trac-preproc -c /Users/zenso/Subjects/Tracula/2Post_VP3/scripts/dmrirc.local -log /Users/zenso/Subjects/Tracula/2Post_VP3/scripts/trac-all.log -cmd /Users/zenso/Subjects/Tracula/2Post_VP3/scripts/trac-all.cmd ; trac-preproc -c /Users/zenso/Subjects/Tracula/VP3_Base/scripts/dmrirc.local -log /Users/zenso/Subjects/Tracula/VP3_Base/scripts/trac-all.log -cmd /Users/zenso/Subjects/Tracula/VP3_Base/scripts/trac-all.cmd ; Darwin iMac.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 trac-preproc exited with ERRORS at Sa 25 Mai 2013 11:28:57 CEST IsRunningFile: Undefined variable. ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Please let me know if this is not enough information. Thanks a lot for your support. Vivian

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SOLVED? recon on all subjects error: on "CA Reg Inv" but "CA Reg" fails cause "CUDA Error in file '../include/ctfactory.hpp' on line 76 : out of memory."
by r.navarra＠itab.unich.it 21 Jul '13

21 Jul '13

Hi. only to notify that witout -use_gpu it worked :) Riccardo ----- Messaggio inoltrato da r.navarra(a)itab.unich.it ----- Data: Sat, 20 Jul 2013 11:59:47 +0200 Da: r.navarra(a)itab.unich.it Oggetto: recon on all subjects error: on "CA Reg Inv" but "CA Reg" fails cause "CUDA Error in file '../include/ctfactory.hpp' on line 76 : out of memory." A: freesurfer(a)nmr.mgh.harvard.edu Hi list, I have seven subject named 101 to 107 with a couple of T1 each one. I ran for i in $(seq 101 107) ; do \ recon-all \ -i DATA/WHOLE/10${i}_1_T1.nii.gz \ -i DATA/WHOLE/10${i}_2_T1.nii.gz \ -subject $ii -all -use_gpu & done but I got error on "#@# CA Reg Inv ..." because "#@# CA Reg" fails (cuda out of memory). An extract of recon-all-status.log and recon-all.log: ############################################################################### #-------------------------------------- #@# CA Reg Sat Jul 20 03:24:55 CEST 2013 /FS/101/mri mri_ca_register_cuda -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /DATA/grid/share/freesurfer53/average/RB_all_2008-03-26.gca transforms/talairach.m3z nvcc ... CUDA Error in file '../include/ctfactory.hpp' on line 76 : out of memory. ... Abort ERROR: mri_ca_register with non-zero status 134 but continuing despite the error #-------------------------------------- #@# CA Reg Inv Sat Jul 20 11:05:26 CEST 2013 /FS/101/mri mri_ca_register -invert-and-save transforms/talairach.m3z Loading, Inverting, Saving, Exiting ... Reading transforms/talairach.m3z ERROR: cannot find or read transforms/talairach.m3z ERROR: mri_ca_register with non-zero status 0 Linux FSLSERVER02 2.6.32-48-generic #110-Ubuntu SMP Fri May 31 18:32:53 UTC 2013 x86_64 GNU/Linux recon-all -s 101 exited with ERRORS at Sat Jul 20 11:05:28 CEST 2013 ############################################################################### bugr: ############################################################################### FREESURFER_HOME: /DATA/grid/share/freesurfer53 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Debian version: squeeze/sid Kernel info: Linux 2.6.32-48-generic x86_64 ############################################################################### full files attached. Please help! Thank you. Now I'm going to try without -use_gpu options... Riccardo ----- Fine messaggio inoltrato. -----

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Angel Wong
by Angel Wong 21 Jul '13

21 Jul '13

http://newrichplayground.com/gwwqp/aavwqsexk.wbczvtznbedv

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Not white matter
by ye tian 19 Jul '13

19 Jul '13

Dear freesurfers, I would like to confirm that the circled region in whitematter.png is not white matter. I initially manually deleted the white matter in wm.mgz for a few subjects. Now I see that it is such a common problem and I start to loose confidence in my editing. Would anyone please give me a second opinion? Thank you very much! Sincerely, Ye

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isxconcat ERROR:cannot find ERROR
by Emily Levin 19 Jul '13

19 Jul '13

Hello, I've been running into a problem when using isxconcat to run a group analysis. The command I've been using is: isxconcat-sess -analysis <name> -contrast <name> -sf sessidfile -o group.ffx.lh -df sesspar -hemi lh I am trying to concatenate data from 8 sessions, and whenever I run the isxconcat command I get this output/error: controls_meditators.group.ffx. lh/between_group.attendpassive.sm3.lh/log/isxconcat.log ERROR: cannot find ERROR:/bold_nopace/between_group.attendpassive.sm3.lh/dof I have a sessid file with all the sessions in it, and whenever I type sf -sessidfile it seems freesurfer cannot see which sessions to use, and instead looks for a file named error. When I run isxconcat with just one subject it works, but if I switch the subject isxconcat will continue to only run for the first subject I ran. I ran isxconcat on two groups (with 4 sessions each) and am now combining the groups to run all 8 sessions together. When I ran each group separately isxconcat worked just fine. The only difference now is that I symlinked the 8 sessions to a new project directory to run everything together. Any idea of what this error means and how I can fix it? Thank you, Emily

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WM and pial surfaces problem
by LAOUCHEDI MAKHLOUF 19 Jul '13

19 Jul '13

Hi i run recon-all on a subject and when checking the surfaces, i noticed that a big part of the temporal part is badly segmented; this concerned WM as well as the grey matter. on the RecommendedReconstruction page, it is explained how to remove parts of non-pial structures considered as so, but not how to move the red surface to include missed wm and grey matter. thank you for help

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Freesurfer July 2013