Freesurfer October 2015

freesurfer@nmr.mgh.harvard.edu

142 participants
214 discussions

free surfer 6 beta freeview crash on mac os x 10.11.1
by Knut Jørgen Bjuland 30 Oct '15

30 Oct '15

Hi When I start freeview form command line on Mac OS X 11.10 it crash with this error message. Do I miss a file? freeview -f fsaverage/surf/lh.inflated fsaverage/surf/rh.inflated dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib dyld: Symbol not found: ___emutls_get_address Referenced from: /Applications/freesurfer/Freeview.app/Contents/MacOS/../Frameworks/libgomp.1.dylib Expected in: /usr/lib/libSystem.B.dylib [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 5 TRAP [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si… ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Unknown Name on a darwin12. named Knuts-MacBook-Pro.local by knutjorgenbjulan Fri Oct 30 09:42:53 2015 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 Knut Jørgen Bjuland NTNU

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error vcsf.config
by stdp82＠virgilio.it 30 Oct '15

30 Oct '15

Hi list, During fcseed-sess -s subj -cfg vcsf.config a subject produces the follow error.I have rerun recon-all, cheched aparc+aseg with tkmedit. They seem to be ok.Why this error is produced? Thanks Stefano Creating output directory /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm Loading y from /Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz Saving design matrix to /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm/Xg.dat Normalized matrix condition is 61.5872 Matrix condition is 1e+08 Pruning voxels by thr: 0.000000 Found 0 voxels in mask Saving mask to /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.39124/glm/mask.mgh search space = 0.000000 DOF = 297 Starting fit and test Fit completed in 0.0008 minutes Computing temporal AR1 Writing results Computing FSNR mean maxvox sig=0 F=0 at index 0 0 0 seed=1446518089 linear maxvox sig=0 F=0 at index 0 0 0 seed=1446518089 quad maxvox sig=0 F=0 at index 0 0 0 seed=1446518089 Computing PCA (300) ERROR: no voxels in mask

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How can I convert Martinos Center dicoms to the dicom format that dcm2niix recognizes?
by Emad Ahmadi 30 Oct '15

30 Oct '15

Hi Freesurfer experts, I hope you’re all enjoying your day! Working in Launchpad, I want to extract the bvals/bvecs from DTI dicoms obtained at Martinos Center. The dicoms have the following format: MR1.3.12.2.1107.5.2.32.35006.2010052613553219211129919 MR1.3.12.2.1107.5.2.32.35006.2010052613553736471330196 MR1.3.12.2.1107.5.2.32.35006.201005261355429098330464 ... I receive error when I run dcm2niix (to extract the b values and b vectors): Command: dcm2niix -f dti <folder of dicoms> The error I receive: Warning: output folder invalid MR1.3.12.2.1107.5.2.32.35006.2010052614044051320551992 will try Error: unable to find any DICOM images in Conversion required 0.000000 seconds. When I do the following steps to generate “treatable” dicoms, dcm2niix recognizes these dicoms: 1. copy Martinos Center dicoms to my local Mac 2. import dicoms into OsiriX 3. Export them as dicoms 4. copy the OsiriX-exported dicoms back to Launchpad 5. Run dcm2niix on the new dicoms Since this copying back and forth takes a lot of time, I need a better way to convert the “crazy” Martinos Center dicoms into the “treatable” ones! I would really appreciate your help. Best, Emad Emad Ahmadi, MD ----------------------------------------------- Research Fellow Department of Radiology Massachusetts General Hospital Harvard Medical School 25 New Chardon Street, Suite 400 Boston, MA 02114 Tel: 617 726 5237 Email: emad(a)nmr.mgh.harvard.edu

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License for a University HPC cluster
by Mike Croucher 29 Oct '15

29 Oct '15

Hi I am one of the sysadmins of a University HPC cluster. We've had a request to install Free Surfer and I note the need for a license. If I request one of these licenses, will we be permitted to install it such that all users of the cluster can access it or does each individual user need their own license? Best Wishes, Mike

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comparison of 4 groups: mri_glmfit or Qdec?
by Sandy Schramm 29 Oct '15

29 Oct '15

Dear Experts, we want to compare data (thickness) of 4 groups (3 morbid groups and 1 controll group). Both, Qdec and mri_glmfit, will do the same analyses. But we are not sure, if the usage of Qdec is statistically correct in our case. Because in Qdec we can only compare 2 of the 4 groups. But Qdec is much more comfortable to handle. Or do you advise the mri_glmfit for our data analyses? Thanks for some advice! Sandy Schramm

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R: Re: R: Re: R: import FS-FAST results in FSL
by stdp82＠virgilio.it 29 Oct '15

29 Oct '15

Thank you very much, How can I export a conjunction maps from surf to volume? I need to make it to perform the DCM analysis by SPM. Stefano >----Messaggio originale---- >Da: fischl(a)nmr.mgh.harvard.edu >Data: 27-ott-2015 13.21 >A: <stdp82(a)virgilio.it>, "Freesurfer support list"<freesurfer(a)nmr.mgh. harvard.edu> >Ogg: Re: [Freesurfer] R: Re: R: import FS-FAST results in FSL > >Hi Stefano > >mri_vol2surf samples the volume onto the surface and saves it as a 1D >list of values, one per surface vertex. You can't view that in fslview >AFAIK - you need to load a surface in freeview/tksurfer and visualize it >as an overlay on the surface. > >cheers >Bruce >On Tue, 27 Oct 2015, stdp82(a)virgilio.it wrote: > >> Yes I would like to open with fslview (FSL) the sig.nii.gz of each >> subject which is computed by seed-based analysis by FS-FAST. >> I have mask the sig.nii.gz by fslmaths -div >> I have run: >> mri_vol2surf --src sig_mask.nii.gz --src_type nii.gz --srcreg >> subj/rest/001/register.dof6.dat --hemi rh --o prova.nii.gz >> >> but when I open the prova.nii.gz with fslview the windows is empty >> with a line. >> >> Thanks >> >> >> Stefano >> >>> ----Messaggio originale---- >>> Da: greve(a)nmr.mgh.harvard.edu >>> Data: 29-set-2015 22.09 >>> A: <freesurfer(a)nmr.mgh.harvard.edu> >>> Ogg: Re: [Freesurfer] R: import FS-FAST results in FSL >>> >>> Do you mean surface-based analysis? You'd have to put them back into >> the >>> volume using mri_surf2vol, write them out as nifti and then run >> fslview >>> on them >>> >>> On 09/29/2015 11:17 AM, stdp82(a)virgilio.it wrote: >>>> >>>> Hi list, >>>> >>>> I would like to import FS-FAST results (conjunction maps) in >> FSL, >>>> opening them by fslview. >>>> Could you provide me any suggestion? >>>> >>>> Thank you very much >>>> Best regards, >>>> >>>> >>>> Stefano >>>> >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)nmr.mgh.harvard.edu >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> -- >>> 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 >>> 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(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> The information in this e-mail is intended only for the person to >> whom it is >>> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >>> contains patient information, please contact the Partners Compliance >> HelpLine at >>> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >>> but does not contain patient information, please contact the sender >> and properly >>> dispose of the e-mail. >>> >>> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >_______________________________________________ >Freesurfer mailing list >Freesurfer(a)nmr.mgh.harvard.edu >https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >

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How to realign a surface in matlab to a realigned parent volume
by Octavian Lie 29 Oct '15

29 Oct '15

Dear All, I ran recon-all and generated a brain.mgz and say, lh.pial. I converted brain.mgz to brain.nii, imported the latter to matlab/spm and realigned it to rbrain.nii, generating a transform matrix M=rbrain.reorient.mat. if MM is the header for rbrain.nii, the header O for the original brain.nii can be calculated with O=inv(M) *MM. How do I reorient the lh.pial to the rbrain.nii? I suppose I need a reader for the pial header in matlab. Many thanks, Octavian

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z-value from a cluster
by stdp82＠virgilio.it 29 Oct '15

29 Oct '15

HI list, how can I extract the z-value from a cluster ?I'm referring to subject-level analysis and to resting-state fMRi data analyzed by using FS-FAST. Stefano

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no voxels in mask vcsf.config
by stdp82＠virgilio.it 29 Oct '15

29 Oct '15

Hi list, I'm using FS-FAST. For a subject I have the error reported below after fcseed-sess -s subj -cfg vcsf.config.The segmentation of the structural image is fine. $Id: mri_glmfit.c,v 1.196.2.8 2012/11/01 18:51:41 greve Exp $ cwd /Applications/freesurfer/subjects/fMRI cmdline mri_glmfit --y /Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz --mask /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/mask.nii.gz --qa --glmdir /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/glm --pca --no-est-fwhm sysname Darwin hostname iMac-di-Stefano.local machine x86_64 user Stefano FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz logyflag 0 usedti 0 mask /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/mask.nii.gz maskinv 0 glmdir /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/glm IllCondOK 0 ReScaleX 1 DoFFx 0 Creating output directory /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/glm Loading y from /Applications/freesurfer/subjects/fMRI/subj/rest/001/fmcpr.nii.gz Saving design matrix to /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/glm/Xg.dat Normalized matrix condition is 61.5872 Matrix condition is 1e+08 Pruning voxels by thr: 0.000000 Found 0 voxels in mask Saving mask to /Applications/freesurfer/subjects/fMRI/subj/rest/001/tmp.fcseed-sess.44153/glm/mask.mgh search space = 0.000000 DOF = 297 Starting fit and test Fit completed in 0.00075 minutes Computing temporal AR1 Writing results Computing FSNR mean maxvox sig=0 F=0 at index 0 0 0 seed=1446346479 linear maxvox sig=0 F=0 at index 0 0 0 seed=1446346479 quad maxvox sig=0 F=0 at index 0 0 0 seed=1446346479 Computing PCA (300) ERROR: no voxels in mask

1 0

remove label from aseg
by Jacobs H (NP) 28 Oct '15

28 Oct '15

Hi, I am trying to generate a segmentation file containing the aseg+aparc but replacing the hippocampus with the hippocampal subfields. With mergeseg I was able to merge the segmentations, but unfortunately parts of the “old” hippocampus (labeled as 17 and 53) are still in there (as the area covered by the subfields is not 100% equal to the hippocampus of the aseg). How can I remove the remains of the old hippocampal labels? Many thanks! Best Heidi

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Freesurfer October 2015