Freesurfer December 2011

freesurfer@nmr.mgh.harvard.edu

98 participants
157 discussions

trctrain/trainlist
by C. Paula de los Angeles 06 Dec '11

06 Dec '11

Hi, I am using TRACULA for the first time, and I am having trouble locating $FREESURFER/HOME/trctrain/trainlist.txt..of 33 normal subjects to enter in for set trainfile command. This is what my Freesurfer home directory looks like: cpdla@ba3:/software/Freesurfer/5.0.0$ ls ASegStatsLUT.txt FreeSurferColorLUT.txt SegmentNoLUT.txt AUTHORS FreeSurferEnv.csh sessions average FreeSurferEnv.sh SetUpFreeSurfer.csh bin fsafd SetUpFreeSurfer.sh build-stamp.txt fsfast Simple_surface_labels2009.txt DefectLUT.txt lib subjects diffusion matlab tkmeditParcColorsCMA docs mni WMParcStatsLUT.txt. Is there a way I can get this file? Thanks for the help in advance. Sorry for the confusion. -C. Paula

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Bad registration
by Antonella Kis 06 Dec '11

06 Dec '11

Dear All: I was using dtrecon on my DTI data and by default it will register my diffusion data (fa) on the TAL space so i got the fa-tal.nii file and the fa-tal-nii.reg the file which encodes the transformation while registering to the TAL space. Can you please advise me what is the best way to check if my registration is good or bad? Thank you. Antonella

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mri_annotation2label
by Klein, Holger 06 Dec '11

06 Dec '11

Dear freesurfers, I have created labels by using the command: mri_annotation2label command (aparc.a2009s): Are these new labels only for the subject I mentioned in the last command or can I use them for other subjects aswell (e.g. in order to measure Volumetry of the auditory Cortex)? THX, Greets, Holger

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List of midpoint talairach coordinates for each FreeSurfer cortical region?
by Carl Anderson 06 Dec '11

06 Dec '11

Dear FreeSurfers, Anyone out there know of a list of talairach coordinates for FreeSurfer cortical regions (MNI? I suppose)? Thanks! Carl -- <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>> Carl M. Anderson, Ph.D. (mail stop 204) Assistant Professor of Psychiatry, Harvard Medical School & The Neuroimaging Center, McLean Hospital 115 Mill St. Belmont, MA 02478 Ph: 617-855-2972; Fax: 617-855-2770 e-mail: remfract(a)gmail.com; carl_anderson(a)hms.harvard.edu <<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>~<>~<<•>>

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make a mask from an annotation file
by LAOUCHEDI MAKHLOUF 06 Dec '11

06 Dec '11

hi everyone i have made an annotation file from somme labels and i want to make a mask from the result (from the annotation file). i mean i want keep just the part of the brain covered by the annotation file in order to transform it by mri_convert to nifti format and make my mask. thank you for your help

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Problems with mri_watershed and creating the BEM geometry file
by Maria Felber 06 Dec '11

06 Dec '11

Dear all, I have successfully run the freesurfer-steps for my subject and completed it without errors. After that I started MNE to create my BEM meshes. The manual tells me, for MNE to do that, the mri_watershed routine from freesurfer is used. Also, this runs fine, as far as the four surfaces (brain, inner_skull, outer_skull and outer_skin) are produced. Here is the problem: when MNE wants to create the BEM geometry file, it checks whether the surfaces are overlapping or not. Apparently they do: outer skin CM is 0.20 -3.31 10.19 mm Going from 5th to 4th subdivision of an icosahedron (ntri: 20480 -> 5120) outer skin CM is 0.20 -3.31 10.19 mm outer skull CM is 0.20 -3.19 9.75 mm inner skull CM is 0.08 -5.38 17.14 mm Checking that outer skull surface is inside outer skin surface...[ok] Checking that inner skull surface is inside outer skull surface...[failed] Surface inner skull is not completely inside surface outer skull(sum of solid angles = -3.98566e-16 * 4*PI). Coulnd't create the geometry file Though I do not know what CM or these numbers in mm given mean, I can tell by using freeview, that the surfaces indeed overlap. My questions are now: which of all the files freesurfer created in the recon-all processes does the mri_watershed routine use? In other words, which of the surfs or transform do I have to check and manually edit to get rid of this problem? And which recon-processes do I have to run again? Is there an easier way around this problem? As always, help is very much appreciated. Thanks. Maria -- Maria J. Felber, PhD Student Max Planck Institute for Human Cognitive and Brain Sciences Stephanstraße 1A 04103 Leipzig, Germany Phone: +49 341 9940-2465/2522

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Auditory Cortex Labels missing
by Klein, Holger 05 Dec '11

05 Dec '11

Dear Freesurfers, I'm looking for a suitable solution for Volumetry of the auditory Cortex. As a proxy for Heschl Gyrus I tried the Gyrus temporalis transversus label - as it is posted in the Color LUT. After typing: asegstats2table --subjects WD \ --segno 1034 \ --tablefile aseg.vol.table I proved the output file: But the label 1034 ctx-lh-transversetemporal was not diplayed. Only the general volumetry of the whole cortex etc. was displayed. How is this possible? By taking a look to the subject's label directory, there are only a few, e.g. BA1 etc. How can I find the other labels displayed in the COLOR LUT (> 1000)? For segmenting the auditory cortex more precisely (like A1, A2 etc.), are there any newer methods you could recommend to me? I'd be glad if you could help me. Thank you so much in advance, Holger

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mri_cvs_register error on Mac
by Peter J. Molfese 05 Dec '11

05 Dec '11

All, I've been trying to use mri_cvs_register on a 64-bit mac and received the following error (below). Google found a couple of hits that others are having this problem but no solution. I'm running the most recent version from version 5.1 with the patch on the release notes page ($Id: mri_cvs_register,v 1.15.2.9 2011/05/26 14:03:26 lzollei Exp $). Running the process on a Mac Pro running 10.6.7 with 40GB of RAM (10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:32:41 PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64). I've tried the process on several different Macs. Previous emails thought it was because the Mac wasn't running a 64-bit version of freesurfer, but there don't appear to be 64-bit binaries available for Mac yet. Any help would be appreciated. Peter surf2vol(98451) malloc: *** mmap(size=295714816) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Out of memory. This could be due to allocating [0]PETSC ERROR: too large an object or bleeding by not properly [0]PETSC ERROR: destroying unneeded objects. [0]PETSC ERROR: Memory allocated 0 Memory used by process 0 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 295714444! [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: surf2vol on a darwin9.8 named duke.haskins.lab by pete Mon Dec 5 13:21:35 2011 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt [0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: PetscMallocAlign() line 61 in src/sys/memory/mal.c [0]PETSC ERROR: MatSeqAIJSetPreallocation_SeqAIJ() line 2818 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: MatCreateSeqAIJ() line 2703 in src/mat/impls/aij/seq/aij.c [0]PETSC ERROR: TSolver::setup_matrix() line 658 in unknowndirectory/solver.h [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Caught signal number 10 BUS: Bus Error, possibly illegal memory access [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: surf2vol on a darwin9.8 named duke.haskins.lab by pete Mon Dec 5 13:21:35 2011 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/current/src/petsc-2.3.3-p13/lib/darwin9.8.0-c-opt [0]PETSC ERROR: Configure run at Thu Feb 17 18:27:43 2011 [0]PETSC ERROR: Configure options --with-mpi-dir=/usr/pubsw/packages/petsc/current/src/mpilatestbuild/ --with-shared=0 --with-debugging=0 --with-fc=gfortran --with-cc=gcc [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

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DTI analysis and mri_glmfit-sim \
by Antonella Kis 05 Dec '11

05 Dec '11

Dear all: I am doing an FA group study (controls vs. patients without any covariant so my C = +1.00000 -1.00000) and I want to see if there are any clusters that survives by multiple comparison so I ran: mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\ --fsgd DTI_group_analysis.fsgd --C contrast.mtx --glmdir group_analysis.glmdir and then: mri_glmfit-sim \ --glmdir group_analysis.glmdir \ --grf 2 neg \ --cwpvalthresh .025 \ --overwrite One of the output files is group_analysis.glmdir /contrast/sig.mgh which by my understanding is the significant uncorrected map which I can visualize it using freeview: freeview -v /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group-fa-tal.nii \ /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/sig.mgh:colormap=heat The significant and corrected map containing the surviving clusters by multiple comparison should be the grf.th2.neg.sig.cluster.mgh file but unfortunately when I try to visualize this clusters with Freeview I cannot see anything. Can you please give me an advise on how I can see this clusters over the group-fa-tal.nii? This is what I was trying and the only thing I can see is a white mask: freeview -v /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group-fa-tal.nii \ /media/1Tra/Antonella_2011/DTI_FS/dtrecon/group_analysis.glmdir/contrast/grf.th2.neg.sig.cluster.mgh:colormap=heat Am I doing something wrong? Thank you for your time and help. Antonella

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resampled image of the diffusion data to structural data
by Antonella Kis 05 Dec '11

05 Dec '11

Dear FS experts, 1) From dt_recon --help I found that: Registration of lowb to same-subject anatomical using FSLs flirt creates mask.nii and register.dat I would appreciate if you can let me know if mask.nii is theresampled image of any of my diffusion related files in the structural space. If not what is the name of this resampled image after I ran dt_recon? Do I need to have the resampled image of my diffusion data to the structural space before I run the GLM group analysis in TAL space? 2) How can I get the TAL_to_avg35 template? 3) How can I analyze my GLM group analysis, or how can I find if there are clusters that survived after multiple comparison. What I see on the dt_recon webpage is: mri_concat */mask-tal.nii --o group-masksum-tal.nii --mean mri_binarize --i group-masksum-tal.nii --min .999 --o group-mask-tal.nii mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\ --fsgd your.fsgd --C contrast --glmdir groupanadir What is the meaning of the 0.99n value? Can you please advise me how to do my data analysis for this GLM group study of my DTI data? THANK YOU! Antonella

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Freesurfer December 2011