Re: [Freesurfer] possible to use multiple B value DTI in Tracula?
Hi, did you try specifying values in bvals file? (set bvalfile=... ) Riccardo Salil Soman salso...@stanford.edu ha scritto: Hi, I was wondering - is it possible to use DTI data of multiple B values in Tracula (acquired during the same session and same TE)? Best wishes, Sal Salil Soman, MD, MS ___ Freesurfer mailing list 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] error with fast_selxavg3
Hi, I am running into an error with fast_selxavg3 (NaN values in XtX). Other have people reported similar problems on the mailing list and I've tried implementing some of the suggestions (namely, using -nowhiten and checking that all events exist in my paradigm file), but I can't get rid of the error. I have an event-related design with very short events (duration of 1 screen refresh = 16.6ms) presented at random intervals. The error only occurs for the -gammafit and -spmhrf analyses and not for -fir. When I check the Xtmp.mat there are indeed NaNs in the first 2 columns of the X matrix. The commands I issue and the output of bugr are below.I attach the paradigm file from one run of the experiment (there are 5 runs in all but I started focusing on just one in order to troubleshoot). TR=2 and numTRs=172. Any help would be much appreciated. Thanks in advance, Leila mkanalysis-sess -fsd bold -surface fsaverage lh -fwhm 3 -event-related -paradigm VRpara.para -nconditions 1 -gammafit 2.25 1.25 -TR 2 -refeventdur 0.016 -polyfit 2 -mcextreg -analysis TargDist-gammafit-sm3.lh -per-run -rlf runlist -force -nowhiten mkcontrast-sess -analysis TargDist-gammafit-sm3.lh -contrast VR -a 1 selxavg3-sess -s $subj -analysis TargDist-gammafit-sm3.lh Error message: - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /APPLICATIONS/freesurfer/fsfast/toolbox/fast_selxavg3.m /APPLICATIONS/freesurfer/fsfast/toolbox/fast_ldanaflac.m /APPLICATIONS/freesurfer/matlab/MRIread.m - outtop = /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF Extension format = nii.gz 1 VR.mat nruns = 1 autostimdur = outanadir = /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF/BT/bold/TargDist-gammafit-sm3.lh Found 149786/163842 (91.4) voxels in mask Creating Design Matrix ... creation time = 0.005 sec DoMCFit = 1 ntptot = 172, nX = 7, DOF = 165 Saving X matrix to /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF/BT/bold/TargDist-gammafit-sm3.lh/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); -- ERROR: fast_selxavg3() failed\n Output of bugr: - FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.0.0 x86_64 - VRpara.para Description: Binary data ___ Freesurfer mailing list 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.
Re: [Freesurfer] bvecs error from Tracula
Dear Anastasia, I am trying to download the dmri_5.1_snow_leopard.tar.gzftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/macos-snow-leopard-intel/dmri_5.1_snow_leopard.tar.gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri a.h.manzo...@gmail.com wrote: The format of my bval file was wrong so I edited your file and tried and it worked, also bvec should be in three columns as you have mentioned before. On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Good to hear! Can you please share with all of us what was wrong with your original files? It may help others who have the same problem in the future. Thanks! On Wed, 17 Jul 2013, amirhossein manzouri wrote: Thanks Anastasia, IT HELPED! On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - I'm attaching sample files. a.y On Tue, 16 Jul 2013, amirhossein manzouri wrote: Hi Anastasia, I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 3-column format? http://surfer.nmr.mgh.harvard.** edu/fswiki/FsTutorial/Traculahttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri 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/**compliancelinehttp://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. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list 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] Average cortical diffusion
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. ___ Freesurfer mailing list 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.
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. ___ Freesurfer mailing list 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] freeview save error
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#Signal[0]PETSCERROR: 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 ___ Freesurfer mailing list 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.
Re: [Freesurfer] freeview save error
Hi Jason any chance you can figure out how to replicate this reliably? If so, we can track it down. Otherwise it's going to be hard thanks Bruce On Mon, 22 Jul 2013, Jason Tourville wrote: 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 seehttp://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si gnal[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 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 ___ Freesurfer mailing list 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] [Tracula] Run trac-all with 2 time points for DTI scan but 1 time point for T1 scan. How to?
Hi, I need to run trac-all on subjects scanned first time in T1 and DTI, second time DTI only. How to configure dmrirc? I've seen long.example but it seems that it require T1 second run too. Tnx, Riccardo ___ Freesurfer mailing list 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.
Re: [Freesurfer] Recon-all difficulties off-site
Hi Michelle is the MNI stuff installed? If seems like ti can't find MNI/Startup.pm. Mine is under: $MNI_PERL5LIB/MNI/Startup.pm cheers Bruce On Sun, 21 Jul 2013, Michelle W. Voss wrote: Hi, I seem to be having the same error, recon all is crashing out with the mri_nu_correct.mni command, e.g., if I run in the mri directory of a subject, I get what is pasted below. Any ideas for the fix? bash-3.2$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz /Users/mwvoss/Analysis/ChordLearning/Freesurfer/sub100/mri /Applications/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Darwin dhcp80ff9e7c.dynamic.uiowa.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 Sun Jul 21 09:25:15 CDT 2013 Can't locate MNI/Startup.pm in @INC (@INC contains: /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at /Applications/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line 37. tmpdir is ./tmp.mri_nu_correct.mni.30026 /Users/mwvoss/Analysis/ChordLearning/Freesurfer/sub100/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30026/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30026/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.30026/nu0.mnc... Iteration 1 Sun Jul 21 09:25:18 CDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.30026/nu0.mnc ./tmp.mri_nu_correct.mni.30026/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30026/0/ -iterations 1000 -distance 50 Can't locate MNI/Startup.pm in @INC (@INC contains: /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at /Applications/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line 37. ERROR: nu_correct On Tue, Jun 4, 2013 at 12:51 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It looks like it is not finding the MNI tools. Maybe Zeke can chime in. doug On 06/04/2013 01:48 PM, Nitenson, Adam wrote: 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 gr...@nmr.mgh.harvard.edu mailto:gr...@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,
Re: [Freesurfer] Skull stripped MNI305
Try $SUBJECTS_DIR/fsaverage/mri/brain.mgz doug On 07/19/2013 03:06 PM, Fotiadis, Panagiotis wrote: Hi, I was wondering if there is a skull stripped version of the file /usr/local/freesurfer/stable5_0_0/average/mni305.cor.mgz stored anywhere. I tried applying bet and mri_watershed on the mni305.cor.mgz file (with different frequencies as well) but there were still parts of the skull showing. Thank you for your time! Panos ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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.
Re: [Freesurfer] Average cortical diffusion
Many thanks From: Bruce Fischl [fis...@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-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: 22 July 2013 14:09 To: Afaf Elsarraj Cc: freesurfer@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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] rtview
Dear Freesurfer Users, I am running a retinotopic analysis in the 5.1.0 version of freesurfer. As tksurfer is not ideal for viewing the retinotopic data, I have been trying to find a download for rtview. I tried to go to the following link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview. However, this like will not work for me. Is there anywhere else that I can download rtview? Thanks, Nick ___ Freesurfer mailing list 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.
Re: [Freesurfer] autorecon2-wm without mri_fill in v4.5?
I guess the solution is -nofill... 2013/7/20 Caspar M. Schwiedrzik cschwie...@rockefeller.edu: 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 ___ Freesurfer mailing list 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.
Re: [Freesurfer] rtview
Sorry, try now On 07/22/2013 12:28 PM, Nicholas Paul Denisuk wrote: Dear Freesurfer Users, I am running a retinotopic analysis in the 5.1.0 version of freesurfer. As tksurfer is not ideal for viewing the retinotopic data, I have been trying to find a download for rtview. I tried to go to the following link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/rtview. However, this like will not work for me. Is there anywhere else that I can download rtview? Thanks, Nick ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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.
Re: [Freesurfer] error with fast_selxavg3
Hi Leila, does it work if you change the -refeventdur to something larger (eg, 2)? doug On 07/22/2013 06:11 AM, Leila Reddy wrote: Hi, I am running into an error with fast_selxavg3 (NaN values in XtX). Other have people reported similar problems on the mailing list and I've tried implementing some of the suggestions (namely, using -nowhiten and checking that all events exist in my paradigm file), but I can't get rid of the error. I have an event-related design with very short events (duration of 1 screen refresh = 16.6ms) presented at random intervals. The error only occurs for the -gammafit and -spmhrf analyses and not for -fir. When I check the Xtmp.mat there are indeed NaNs in the first 2 columns of the X matrix. The commands I issue and the output of bugr are below.I attach the paradigm file from one run of the experiment (there are 5 runs in all but I started focusing on just one in order to troubleshoot). TR=2 and numTRs=172. Any help would be much appreciated. Thanks in advance, Leila mkanalysis-sess -fsd bold -surface fsaverage lh -fwhm 3 -event-related -paradigm VRpara.para -nconditions 1 -gammafit 2.25 1.25 -TR 2 -refeventdur 0.016 -polyfit 2 -mcextreg -analysis TargDist-gammafit-sm3.lh -per-run -rlf runlist -force -nowhiten mkcontrast-sess -analysis TargDist-gammafit-sm3.lh -contrast VR -a 1 selxavg3-sess -s $subj -analysis TargDist-gammafit-sm3.lh Error message: - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /APPLICATIONS/freesurfer/fsfast/toolbox/fast_selxavg3.m /APPLICATIONS/freesurfer/fsfast/toolbox/fast_ldanaflac.m /APPLICATIONS/freesurfer/matlab/MRIread.m - outtop = /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF Extension format = nii.gz 1 VR.mat nruns = 1 autostimdur = outanadir = /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF/BT/bold/TargDist-gammafit-sm3.lh Found 149786/163842 (91.4) voxels in mask Creating Design Matrix ... creation time = 0.005 sec DoMCFit = 1 ntptot = 172, nX = 7, DOF = 165 Saving X matrix to /Volumes/LEILA_DATA/fMRI/Rodika/EEG_IRMF/BT/bold/TargDist-gammafit-sm3.lh/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); -- ERROR: fast_selxavg3() failed\n Output of bugr: - FREESURFER_HOME: /APPLICATIONS/freesurfer Build stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Kernel info: Darwin 12.0.0 x86_64 - ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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.
Re: [Freesurfer] possible to use multiple B value DTI in Tracula?
Thank you. I can concatenate the 3 acquisitions (I have 1 b2500, and 2 b1000) into a single nifti file, and then arrange the bval and bvec files to match. I will give it a try. Thank you for all your help. Best wishes, Sal On Mon, Jul 22, 2013 at 11:11 AM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Sal - Are these different scans that you want to merge? If they're all in one file, then you just define the b-value for each frame as usual in the bvalfile. There's no rule that all the b-values have to be the same. Hope this helps, a.y On Sun, 21 Jul 2013, Salil Soman wrote: Hi, I was wondering - is it possible to use DTI data of multiple B values in Tracula (acquired during the same session and same TE)? Best wishes, Sal Salil Soman, MD, MS 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/**compliancelinehttp://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. -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list 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.
Re: [Freesurfer] bvecs error from Tracula
Hi Amirhossein - That fix applied only to the 5.1 version. I'd recommend using the 5.3 version for tracula. Are you getting a memory error, and if so with which version? Thanks, a.y On Mon, 22 Jul 2013, amirhossein manzouri wrote: Dear Anastasia, I am trying to download the dmri_5.1_snow_leopard.tar.gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri a.h.manzo...@gmail.com wrote: The format of my bval file was wrong so I edited your file and tried and it worked, also bvec should be in three columns as you have mentioned before. On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Good to hear! Can you please share with all of us what was wrong with your original files? It may help others who have the same problem in the future. Thanks! On Wed, 17 Jul 2013, amirhossein manzouri wrote: Thanks Anastasia, IT HELPED! On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - I'm attaching sample files. a.y On Tue, 16 Jul 2013, amirhossein manzouri wrote: Hi Anastasia, I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 3-column format? http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri 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. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list 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.
Re: [Freesurfer] possible to use multiple B value DTI in Tracula?
Hi Sal - Are these different scans that you want to merge? If they're all in one file, then you just define the b-value for each frame as usual in the bvalfile. There's no rule that all the b-values have to be the same. Hope this helps, a.y On Sun, 21 Jul 2013, Salil Soman wrote: Hi, I was wondering - is it possible to use DTI data of multiple B values in Tracula (acquired during the same session and same TE)? Best wishes, Sal Salil Soman, MD, MS ___ Freesurfer mailing list 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.
Re: [Freesurfer] [Tracula] Run trac-all with 2 time points for DTI scan but 1 time point for T1 scan. How to?
Hi Riccardo - The way this is designed is that you have to have longitudinal T1 data and run the longitudinal stream of recon-all on it, before you run the longitudinal version of tracula on your DWI. You could fake this by simply creating a copy of the recon-all directory of your first T1 time point and name it as the 2nd time point, then run longitudinal recon-all on them to generate all the files that tracula expects to find. This of course may bias your study towards the first time point, and the whole point of the longitudinal stream is to make sure there is no bias. Hope this helps, a.y On Mon, 22 Jul 2013, r.nava...@itab.unich.it wrote: Hi, I need to run trac-all on subjects scanned first time in T1 and DTI, second time DTI only. How to configure dmrirc? I've seen long.example but it seems that it require T1 second run too. Tnx, Riccardo ___ Freesurfer mailing list 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] mri_label2label ERROR: srcvtxno=-1
Dear Freesurfer list, I was converting a surface label from 'fsaverage' space to individual subjects and got this error: ###-### Performing mapping from target back to the source label ERROR: srcvtxno = -1 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table ###-### The command I used was: mri_label2label --srclabel $fsaverage_brain_label --trg $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj --regmethod surface --hemi $hemi It's worth noting that this subject is from a patient population with lesion and we had to manually edit the white matter and re-run autorecon. This error only happens for one hemisphere of this patient, the other hemi is fine. Did anyone have this problem before or know how to resolve this? Thank you. BTW. I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.html in the archive but it was never followed up. Lingqiang -- Lingqiang Kong Auditory Neuroscience Laboratory Perceptual Neuroimaging Laboratory Boston University 677 Beacon St. Boston, MA 02215 http://www.cns.bu.edu/~shinn/ANL/index.html http://people.bu.edu/fmri/ ___ Freesurfer mailing list 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] recon-all error
Hi everyone, I'm quite new to FreeSurfer, my apologies for asking the obvious. I tried to run recon-all on multi echo T2* weighted data and got the following error: 'input(s) cannot have multiple frames' I was wondering how I should go about running recon-all on multi echo data. Any help would be appreciated! Thank you! ___ Freesurfer mailing list 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.
Re: [Freesurfer] Recon-all difficulties off-site
The MNI directory directly under freesurfer is there, but the MNI_PERL5 directory is not. e.g, bash-3.2$ echo $MNI_PERL5LIB /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 bash-3.2$ cd $MNI_PERL5LIB bash: cd: /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6: No such file or directory Is there a patch to fix? thanks Michelle On Mon, Jul 22, 2013 at 9:25 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Michelle is the MNI stuff installed? If seems like ti can't find MNI/Startup.pm. Mine is under: $MNI_PERL5LIB/MNI/Startup.pm cheers Bruce On Sun, 21 Jul 2013, Michelle W. Voss wrote: Hi, I seem to be having the same error, recon all is crashing out with the mri_nu_correct.mni command, e.g., if I run in the mri directory of a subject, I get what is pasted below. Any ideas for the fix? bash-3.2$ mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz /Users/mwvoss/Analysis/ChordLearning/Freesurfer/sub100/mri /Applications/freesurfer/bin/mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz nIters 1 $Id: mri_nu_correct.mni,v 1.18.2.1 2013/01/09 21:23:42 nicks Exp $ Darwin dhcp80ff9e7c.dynamic.uiowa.edu 11.4.2 Darwin Kernel Version 11.4.2: Thu Aug 23 16:25:48 PDT 2012; root:xnu-1699.32.7~1/RELEASE_X86_64 x86_64 Sun Jul 21 09:25:15 CDT 2013 Can't locate MNI/Startup.pm in @INC (@INC contains: /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at /Applications/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line 37. tmpdir is ./tmp.mri_nu_correct.mni.30026 /Users/mwvoss/Analysis/ChordLearning/Freesurfer/sub100/mri mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30026/nu0.mnc -odt float mri_convert orig.mgz ./tmp.mri_nu_correct.mni.30026/nu0.mnc -odt float $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from orig.mgz... TR=2530.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) changing data type from uchar to float (noscale = 0)... writing to ./tmp.mri_nu_correct.mni.30026/nu0.mnc... Iteration 1 Sun Jul 21 09:25:18 CDT 2013 nu_correct -clobber ./tmp.mri_nu_correct.mni.30026/nu0.mnc ./tmp.mri_nu_correct.mni.30026/nu1.mnc -tmpdir ./tmp.mri_nu_correct.mni.30026/0/ -iterations 1000 -distance 50 Can't locate MNI/Startup.pm in @INC (@INC contains: /Applications/freesurfer/mni/lib/../System/Library/Perl/5.8.6 /Library/Perl/5.12/darwin-thread-multi-2level /Library/Perl/5.12 /Network/Library/Perl/5.12/darwin-thread-multi-2level /Network/Library/Perl/5.12 /Library/Perl/Updates/5.12.3 /System/Library/Perl/5.12/darwin-thread-multi-2level /System/Library/Perl/5.12 /System/Library/Perl/Extras/5.12/darwin-thread-multi-2level /System/Library/Perl/Extras/5.12 .) at /Applications/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /Applications/freesurfer/mni/bin/nu_correct line 37. ERROR: nu_correct On Tue, Jun 4, 2013 at 12:51 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It looks like it is not finding the MNI tools. Maybe Zeke can chime in. doug On 06/04/2013 01:48 PM, Nitenson, Adam wrote: 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
Re: [Freesurfer] recon-all error
we need a T1-weighted input, such as FLASH (with flip angle =20deg) or mprage cheers Bruce On Mon, 22 Jul 2013, Smian wrote: Hi everyone, I'm quite new to FreeSurfer, my apologies for asking the obvious. I tried to run recon-all on multi echo T2* weighted data and got the following error: 'input(s) cannot have multiple frames' I was wondering how I should go about running recon-all on multi echo data. Any help would be appreciated! Thank you! ___ 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 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.
Re: [Freesurfer] bvecs error from Tracula
Hi, Yes I am getting the memory error with version 5.3, exactly the one that is reported in this link: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-July/019392.html Thanks, On Mon, Jul 22, 2013 at 8:15 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - That fix applied only to the 5.1 version. I'd recommend using the 5.3 version for tracula. Are you getting a memory error, and if so with which version? Thanks, a.y On Mon, 22 Jul 2013, amirhossein manzouri wrote: Dear Anastasia, I am trying to download the dmri_5.1_snow_leopard.tar.**gz from FreeSurfer website to solve memory problem but it is not available. Would you please check the source to the link? On Wed, Jul 17, 2013 at 5:51 PM, amirhossein manzouri a.h.manzo...@gmail.com wrote: The format of my bval file was wrong so I edited your file and tried and it worked, also bvec should be in three columns as you have mentioned before. On Wed, Jul 17, 2013 at 5:11 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Good to hear! Can you please share with all of us what was wrong with your original files? It may help others who have the same problem in the future. Thanks! On Wed, 17 Jul 2013, amirhossein manzouri wrote: Thanks Anastasia, IT HELPED! On Tue, Jul 16, 2013 at 5:25 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - I'm attaching sample files. a.y On Tue, 16 Jul 2013, amirhossein manzouri wrote: Hi Anastasia, I have tried both , 3-row and 3-column format and still wrong bvecc and bval from flip4fsl. Could you please send me a sample of your original files so I can compare? On Mon, Jul 15, 2013 at 7:44 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Amirhossein - Are your original bvecs/bvals in 3-row format instead of 3-column format? http://surfer.nmr.mgh.harvard.**edu/fswiki/FsTutorial/Traculahttp://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula Thanks, a.y On Mon, 15 Jul 2013, amirhossein manzouri wrote: Dear Experts, I am running trac-all -prep -c dmrirc on my DWI data. After flip4fsl step I get the attached bval and bvec file which the bvec one is wrong so the process exits with error in dtifit. I have also attached original bvec and bval. -- Best regards, Amirhossein Manzouri 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/**compliancelinehttp://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. -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri -- Best regards, Amirhossein Manzouri ___ Freesurfer mailing list 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
Re: [Freesurfer] Skull stripped MNI305
Thanks Doug, that looks great! In addition, is the specific fsaverage brain in the MNI space? Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, July 22, 2013 12:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Skull stripped MNI305 Try $SUBJECTS_DIR/fsaverage/mri/brain.mgz doug On 07/19/2013 03:06 PM, Fotiadis, Panagiotis wrote: Hi, I was wondering if there is a skull stripped version of the file /usr/local/freesurfer/stable5_0_0/average/mni305.cor.mgz stored anywhere. I tried applying bet and mri_watershed on the mni305.cor.mgz file (with different frequencies as well) but there were still parts of the skull showing. Thank you for your time! Panos ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 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.
Re: [Freesurfer] Skull stripped MNI305
yes, mni305 doug On 07/22/2013 04:28 PM, Fotiadis, Panagiotis wrote: Thanks Doug, that looks great! In addition, is the specific fsaverage brain in the MNI space? Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, July 22, 2013 12:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Skull stripped MNI305 Try $SUBJECTS_DIR/fsaverage/mri/brain.mgz doug On 07/19/2013 03:06 PM, Fotiadis, Panagiotis wrote: Hi, I was wondering if there is a skull stripped version of the file /usr/local/freesurfer/stable5_0_0/average/mni305.cor.mgz stored anywhere. I tried applying bet and mri_watershed on the mni305.cor.mgz file (with different frequencies as well) but there were still parts of the skull showing. Thank you for your time! Panos ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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.
Re: [Freesurfer] Skull stripped MNI305
Great, thanks! From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, July 22, 2013 4:46 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Skull stripped MNI305 yes, mni305 doug On 07/22/2013 04:28 PM, Fotiadis, Panagiotis wrote: Thanks Doug, that looks great! In addition, is the specific fsaverage brain in the MNI space? Panos From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, July 22, 2013 12:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Skull stripped MNI305 Try $SUBJECTS_DIR/fsaverage/mri/brain.mgz doug On 07/19/2013 03:06 PM, Fotiadis, Panagiotis wrote: Hi, I was wondering if there is a skull stripped version of the file /usr/local/freesurfer/stable5_0_0/average/mni305.cor.mgz stored anywhere. I tried applying bet and mri_watershed on the mni305.cor.mgz file (with different frequencies as well) but there were still parts of the skull showing. Thank you for your time! Panos ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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 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.
Re: [Freesurfer] mri_label2label ERROR: srcvtxno=-1
what is the input label? How was it created? Does it have -1 as the first number on any line? On 07/22/2013 03:54 PM, Lingqiang Kong wrote: Dear Freesurfer list, I was converting a surface label from 'fsaverage' space to individual subjects and got this error: ###-### Performing mapping from target back to the source label ERROR: srcvtxno = -1 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table ###-### The command I used was: mri_label2label --srclabel $fsaverage_brain_label --trg $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj --regmethod surface --hemi $hemi It's worth noting that this subject is from a patient population with lesion and we had to manually edit the white matter and re-run autorecon. This error only happens for one hemisphere of this patient, the other hemi is fine. Did anyone have this problem before or know how to resolve this? Thank you. BTW. I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.html in the archive but it was never followed up. Lingqiang -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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.
Re: [Freesurfer] infant atlas segmentation
Hi Mark, I have no idea what you are doing. Can you send a command line? Are either of the images generated by FS? doug On 07/22/2013 03:56 PM, Mark Plantz wrote: Hello FreeSurfers, I recently obtained a set of infant templates. Out of curiousity, I decided to view one of the input brains with the provided segmented volume file. It appears that there is some misalignment. I wouldn't expect the alignment to be perfect, since I am basically overlaying an average of multiple brains onto one. However, it looks like this misalignment may be caused by either: 1.) the segmentation volume file being shifted down or 2.) the slices not lining up properly (i.e. one file starts before the other). Any ideas what could cause a problem like this? Could it be that the segmented files are simply not compatible with FreeSurfer? Thanks for the help, Mark ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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.
Re: [Freesurfer] mri_label2label ERROR: srcvtxno=-1
The input label is one from a set published 1000 brain functional connectivity label from the Buckner lab (Yeo Krienen, et al., 2011). No. The first number of all lines are integers ranging from 5 to 132000. Just adding some details: 1) when we first ran recon did the same label conversion and mri_label2label worked fine. Later we edited the white matter and added control points, and re-ran autorecon2-cp and autorecon2-wm. The surface looked better after the editing, but we have this label conversion problem now. 2) the label conversion ERROR: srcvtno=-1 happens only on one hemi, and mri_label2label haults. However, on the other hemi, although mri_label2label runs through without reporting error, the converted labels on subject surface looks like gibberish and out of place. So it's likely there are problem with both hemis, but with different severity. Thank you. Lingqiang what is the input label? How was it created? Does it have -1 as the first number on any line? On 07/22/2013 03:54 PM, Lingqiang Kong wrote: Dear Freesurfer list, I was converting a surface label from 'fsaverage' space to individual subjects and got this error: ###-### Performing mapping from target back to the source label ERROR: srcvtxno = -1 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table ###-### The command I used was: mri_label2label --srclabel $fsaverage_brain_label --trg $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj --regmethod surface --hemi $hemi It's worth noting that this subject is from a patient population with lesion and we had to manually edit the white matter and re-run autorecon. This error only happens for one hemisphere of this patient, the other hemi is fine. Did anyone have this problem before or know how to resolve this? Thank you. BTW. I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.html in the archive but it was never followed up. Lingqiang -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Lingqiang Kong Ph.D candidate Auditory Neuroscience Laboratory Perceptual Neuroimaging Laboratory Boston University 677 Beacon St. Boston, MA 02215 http://www.cns.bu.edu/~shinn/ANL/index.html http://people.bu.edu/fmri/ ___ Freesurfer mailing list 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.
Re: [Freesurfer] mri_label2label ERROR: srcvtxno=-1
Can you send the first 100 lines (or point me to the label on the file system)? doug On 07/22/2013 05:01 PM, Lingqiang Kong wrote: The input label is one from a set published 1000 brain functional connectivity label from the Buckner lab (Yeo Krienen, et al., 2011). No. The first number of all lines are integers ranging from 5 to 132000. Just adding some details: 1) when we first ran recon did the same label conversion and mri_label2label worked fine. Later we edited the white matter and added control points, and re-ran autorecon2-cp and autorecon2-wm. The surface looked better after the editing, but we have this label conversion problem now. 2) the label conversion ERROR: srcvtno=-1 happens only on one hemi, and mri_label2label haults. However, on the other hemi, although mri_label2label runs through without reporting error, the converted labels on subject surface looks like gibberish and out of place. So it's likely there are problem with both hemis, but with different severity. Thank you. Lingqiang what is the input label? How was it created? Does it have -1 as the first number on any line? On 07/22/2013 03:54 PM, Lingqiang Kong wrote: Dear Freesurfer list, I was converting a surface label from 'fsaverage' space to individual subjects and got this error: ###-### Performing mapping from target back to the source label ERROR: srcvtxno = -1 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table ###-### The command I used was: mri_label2label --srclabel $fsaverage_brain_label --trg $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj --regmethod surface --hemi $hemi It's worth noting that this subject is from a patient population with lesion and we had to manually edit the white matter and re-run autorecon. This error only happens for one hemisphere of this patient, the other hemi is fine. Did anyone have this problem before or know how to resolve this? Thank you. BTW. I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.html in the archive but it was never followed up. Lingqiang -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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.
Re: [Freesurfer] mri_label2label ERROR: srcvtxno=-1
Yes. The label file is attached. Although since this error did not happen with the old surface of the same subject, I suspect editing it and running autorecon2-wm created a new surface that had some unknown issues. Lingqiang Can you send the first 100 lines (or point me to the label on the file system)? doug On 07/22/2013 05:01 PM, Lingqiang Kong wrote: The input label is one from a set published 1000 brain functional connectivity label from the Buckner lab (Yeo Krienen, et al., 2011). No. The first number of all lines are integers ranging from 5 to 132000. Just adding some details: 1) when we first ran recon did the same label conversion and mri_label2label worked fine. Later we edited the white matter and added control points, and re-ran autorecon2-cp and autorecon2-wm. The surface looked better after the editing, but we have this label conversion problem now. 2) the label conversion ERROR: srcvtno=-1 happens only on one hemi, and mri_label2label haults. However, on the other hemi, although mri_label2label runs through without reporting error, the converted labels on subject surface looks like gibberish and out of place. So it's likely there are problem with both hemis, but with different severity. Thank you. Lingqiang what is the input label? How was it created? Does it have -1 as the first number on any line? On 07/22/2013 03:54 PM, Lingqiang Kong wrote: Dear Freesurfer list, I was converting a surface label from 'fsaverage' space to individual subjects and got this error: ###-### Performing mapping from target back to the source label ERROR: srcvtxno = -1 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table ###-### The command I used was: mri_label2label --srclabel $fsaverage_brain_label --trg $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj --regmethod surface --hemi $hemi It's worth noting that this subject is from a patient population with lesion and we had to manually edit the white matter and re-run autorecon. This error only happens for one hemisphere of this patient, the other hemi is fine. Did anyone have this problem before or know how to resolve this? Thank you. BTW. I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.html in the archive but it was never followed up. Lingqiang -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Lingqiang Kong Ph.D candidate Auditory Neuroscience Laboratory Perceptual Neuroimaging Laboratory Boston University 677 Beacon St. Boston, MA 02215 http://www.cns.bu.edu/~shinn/ANL/index.html http://people.bu.edu/fmri/ lh.7Networks_1.first110.label Description: Binary data ___ Freesurfer mailing list 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.
Re: [Freesurfer] mri_label2label ERROR: srcvtxno=-1
Are you sure the label was generated on fsaverage? Does it look ok if you run tksurfer fsaverage lh inflated -label lh.7Networks_1.first110.label On 07/22/2013 05:13 PM, Lingqiang Kong wrote: Yes. The label file is attached. Although since this error did not happen with the old surface of the same subject, I suspect editing it and running autorecon2-wm created a new surface that had some unknown issues. Lingqiang Can you send the first 100 lines (or point me to the label on the file system)? doug On 07/22/2013 05:01 PM, Lingqiang Kong wrote: The input label is one from a set published 1000 brain functional connectivity label from the Buckner lab (Yeo Krienen, et al., 2011). No. The first number of all lines are integers ranging from 5 to 132000. Just adding some details: 1) when we first ran recon did the same label conversion and mri_label2label worked fine. Later we edited the white matter and added control points, and re-ran autorecon2-cp and autorecon2-wm. The surface looked better after the editing, but we have this label conversion problem now. 2) the label conversion ERROR: srcvtno=-1 happens only on one hemi, and mri_label2label haults. However, on the other hemi, although mri_label2label runs through without reporting error, the converted labels on subject surface looks like gibberish and out of place. So it's likely there are problem with both hemis, but with different severity. Thank you. Lingqiang what is the input label? How was it created? Does it have -1 as the first number on any line? On 07/22/2013 03:54 PM, Lingqiang Kong wrote: Dear Freesurfer list, I was converting a surface label from 'fsaverage' space to individual subjects and got this error: ###-### Performing mapping from target back to the source label ERROR: srcvtxno = -1 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table ###-### The command I used was: mri_label2label --srclabel $fsaverage_brain_label --trg $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj --regmethod surface --hemi $hemi It's worth noting that this subject is from a patient population with lesion and we had to manually edit the white matter and re-run autorecon. This error only happens for one hemisphere of this patient, the other hemi is fine. Did anyone have this problem before or know how to resolve this? Thank you. BTW. I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.html in the archive but it was never followed up. Lingqiang -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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.
Re: [Freesurfer] mri_label2label ERROR: srcvtxno=-1
yes, spherical registration is part of autorecon3, so that makes sense On Mon, 22 Jul 2013, Lingqiang Kong wrote: Yes. The input label looks fine on fsaverage. But I just realized something. After editing the surface, I re-ran autorecon2-wm and autorecon2-cp. But never autorecon3. For it to do the spherical mapping correctly, I also have to re-run autorecon3 right? I did not realize that. So I'm running autorecon3 now, and hopefully this will resolve the problem. Lingqiang Are you sure the label was generated on fsaverage? Does it look ok if you run tksurfer fsaverage lh inflated -label lh.7Networks_1.first110.label On 07/22/2013 05:13 PM, Lingqiang Kong wrote: Yes. The label file is attached. Although since this error did not happen with the old surface of the same subject, I suspect editing it and running autorecon2-wm created a new surface that had some unknown issues. Lingqiang Can you send the first 100 lines (or point me to the label on the file system)? doug On 07/22/2013 05:01 PM, Lingqiang Kong wrote: The input label is one from a set published 1000 brain functional connectivity label from the Buckner lab (Yeo Krienen, et al., 2011). No. The first number of all lines are integers ranging from 5 to 132000. Just adding some details: 1) when we first ran recon did the same label conversion and mri_label2label worked fine. Later we edited the white matter and added control points, and re-ran autorecon2-cp and autorecon2-wm. The surface looked better after the editing, but we have this label conversion problem now. 2) the label conversion ERROR: srcvtno=-1 happens only on one hemi, and mri_label2label haults. However, on the other hemi, although mri_label2label runs through without reporting error, the converted labels on subject surface looks like gibberish and out of place. So it's likely there are problem with both hemis, but with different severity. Thank you. Lingqiang what is the input label? How was it created? Does it have -1 as the first number on any line? On 07/22/2013 03:54 PM, Lingqiang Kong wrote: Dear Freesurfer list, I was converting a surface label from 'fsaverage' space to individual subjects and got this error: ###-### Performing mapping from target back to the source label ERROR: srcvtxno = -1 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table ###-### The command I used was: mri_label2label --srclabel $fsaverage_brain_label --trg $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj --regmethod surface --hemi $hemi It's worth noting that this subject is from a patient population with lesion and we had to manually edit the white matter and re-run autorecon. This error only happens for one hemisphere of this patient, the other hemi is fine. Did anyone have this problem before or know how to resolve this? Thank you. BTW. I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.html in the archive but it was never followed up. Lingqiang -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list 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
Re: [Freesurfer] mri_label2label ERROR: srcvtxno=-1
Yes. The input label looks fine on fsaverage. But I just realized something. After editing the surface, I re-ran autorecon2-wm and autorecon2-cp. But never autorecon3. For it to do the spherical mapping correctly, I also have to re-run autorecon3 right? I did not realize that. So I'm running autorecon3 now, and hopefully this will resolve the problem. Lingqiang Are you sure the label was generated on fsaverage? Does it look ok if you run tksurfer fsaverage lh inflated -label lh.7Networks_1.first110.label On 07/22/2013 05:13 PM, Lingqiang Kong wrote: Yes. The label file is attached. Although since this error did not happen with the old surface of the same subject, I suspect editing it and running autorecon2-wm created a new surface that had some unknown issues. Lingqiang Can you send the first 100 lines (or point me to the label on the file system)? doug On 07/22/2013 05:01 PM, Lingqiang Kong wrote: The input label is one from a set published 1000 brain functional connectivity label from the Buckner lab (Yeo Krienen, et al., 2011). No. The first number of all lines are integers ranging from 5 to 132000. Just adding some details: 1) when we first ran recon did the same label conversion and mri_label2label worked fine. Later we edited the white matter and added control points, and re-ran autorecon2-cp and autorecon2-wm. The surface looked better after the editing, but we have this label conversion problem now. 2) the label conversion ERROR: srcvtno=-1 happens only on one hemi, and mri_label2label haults. However, on the other hemi, although mri_label2label runs through without reporting error, the converted labels on subject surface looks like gibberish and out of place. So it's likely there are problem with both hemis, but with different severity. Thank you. Lingqiang what is the input label? How was it created? Does it have -1 as the first number on any line? On 07/22/2013 03:54 PM, Lingqiang Kong wrote: Dear Freesurfer list, I was converting a surface label from 'fsaverage' space to individual subjects and got this error: ###-### Performing mapping from target back to the source label ERROR: srcvtxno = -1 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table ###-### The command I used was: mri_label2label --srclabel $fsaverage_brain_label --trg $my_subject_brain_label --srcsubject fsaverage --trgsubject $mysubj --regmethod surface --hemi $hemi It's worth noting that this subject is from a patient population with lesion and we had to manually edit the white matter and re-run autorecon. This error only happens for one hemisphere of this patient, the other hemi is fine. Did anyone have this problem before or know how to resolve this? Thank you. BTW. I found this https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-January/016835.html in the archive but it was never followed up. Lingqiang -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ -- Lingqiang Kong Ph.D candidate Auditory Neuroscience Laboratory Perceptual Neuroimaging Laboratory Boston University 677 Beacon St. Boston, MA 02215 http://www.cns.bu.edu/~shinn/ANL/index.html http://people.bu.edu/fmri/ ___ Freesurfer mailing list 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
