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30086 discussions

Talairach coordinates for gyral regions
by Robustelli, Briana (NIH/NIMH) [F] 15 Oct '10

15 Oct '10

Hi all, How can I get the Talairach coordinates for the center of each of the gyral regions? Is this information listed somewhere or do I need to calculate it, if so how would I do that? Thank you. Briana

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Missing files in the average folder
by Linda Shuster 15 Oct '10

15 Oct '10

Hi, I just upgraded to v5.0.0 (Leopard (10.5/6.x) Intel). When I run recon-all I receive the following message and FreeSurfer stops: ERROR: cannot find /Applications/freesurfer/average/lh.curvature.buckner40.filled.desikan_killiany.2009-03-04.gcs When I look in that folder, that file is not there, nor are any of the other older gcs files that recon-all seems to want (based on looking at the code). Can you please advise? Thanks! Linda

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cluster including vertices below cluster-forming threshold
by Marco Loggia, PhD 15 Oct '10

15 Oct '10

Dear all, I have some questions about the outputs of mri_glmfit-sim (which I used to perform permutation tests on my surface analyses). When I compare *.sig.clusters.mgh and *.sig.masked.mgh surfaces, I notice that the clusters reported as statistically significant also include some vertices that are slightly below the cluster-forming threshold (especially at the borders of the clusters). It would appear as if some spatial smoothing has occurred on the clusters themselves. Why is it so? Is there a way to perform clustering on the data that are above cluster-forming threshold? Thanks, Marco _____________________ Marco L. Loggia, PhD Postdoctoral Fellow, Mass General Hospital & Brigham and Women's Hospital Harvard Medical School CNY Building 120, suite 101E Charlestown, Massachusetts 02129 Phone: (617) 643-7267 Fax: (617) 643-7340 marco(a)nmr.mgh.harvard.edu

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Potential memory leak in mri_cvs_register
by Martin Kavec 15 Oct '10

15 Oct '10

Hi, I am trying to do a mri_cvs_register two subjects analyzed with FS-5.0.0 on a 64-bit Gentoo linux with 4GB memory and another 4GB of swap space. I am running a signle mri_cvs_register and after certain time the PC starts using swap intensively and finally the process terminates. My commandline is: mri_cvs_register --mov S2 --template S1 --outdir /home/me/CVS/S2 --nocleanup Thanks, Martin I am pasting the last couple of tens of lines of the trace_el_reg_to_S1_S2.txt below: *************************************************************************************************** compressing morph dcds mesh direct image = 0 0 0 dir img for computed transform = 2.08004e-317 2.122e-314 2.122e-314 dir img for compressed = 2.08004e-317 2.122e-314 2.122e-314 dcds total image for source point = 2.08004e-317 2.122e-314 2.122e-314 name = compressed_step_3 Initial transform name = compressed_step_4 Initial transform name = compressed_step_5 Initial transform name = compressed_step_6 Initial transform name = compressed_step_7 Initial transform name = compressed_step_8 Initial transform name = compressed_step_9 Initial transform name = compressed_step_10 Initial transform name = compressed_step_11 Initial transform name = compressed_step_12 Initial transform name = compressed_step_13 Initial transform name = compressed_step_14 Initial transform name = compressed_step_15 Initial transform name = compressed_step_16 Initial transform name = compressed_step_17 Initial transform name = FEM error Initial displacement = 7.25836 Final displacement = 1.36008 Max after displacement = 24.2243 Error points = 0 ====================== step = 2 =============== elt_vol= 5.3125 Constructing Delaunay tetrahedralization. Delaunay seconds: 0.33 Creating surface mesh. Perturbing vertices. Delaunizing segments. Constraining facets. Segment and facet seconds: 4.17 Removing unwanted tetrahedra. Hole seconds: 0.2 Repairing mesh. Repair seconds: 0.09 Adding Steiner points to enforce quality. Quality seconds: 38.28 Smoothing mesh. Smooth seconds: 2.6 Writing nodes. Writing elements. Writing faces. Output seconds: 0.22 Total running seconds: 46.58 Statistics: Input points: 8 Input facets: 6 Input holes: 0 Input regions: 0 Mesh points: 216665 Mesh tetrahedra: 1330756 Mesh faces: 2685486 Mesh subfaces: 47948 Mesh subsegments: 733 Saving nodes to iteration.node Saving elements to iteration.ele Saving faces to iteration.face mesh nodes = 216665 mesh elts = 1330756 building index src done building the list count inserted = 0 elapsed = 0.026 seconds element count = 1 count inserted = 100000 elapsed = 61.096 seconds element count = 554226 count inserted = 200000 elapsed = 4.754 seconds element count = 1587360 count inserted = 300000 elapsed = 40.398 seconds element count = 2754998 count inserted = 400000 elapsed = 20.41 seconds element count = 3851406 count inserted = 500000 elapsed = 1.861 seconds element count = 4890326 count inserted = 600000 elapsed = 1.384 seconds element count = 5917866 count inserted = 700000 elapsed = 1.302 seconds element count = 6942363 count inserted = 800000 elapsed = 0.495 seconds element count = 7957496 count inserted = 900000 elapsed = 0.377 seconds element count = 8967778 count inserted = 1000000 elapsed = 0.45 seconds element count = 9982380 count inserted = 1100000 elapsed = 0.175 seconds element count = 11004521 count inserted = 1200000 elapsed = 0.813 seconds element count = 12022297 count inserted = 1300000 elapsed = 0.176 seconds element count = 13050507 done building octree - total elements = 13367338 penalty_weight = 1000 setting bc 206.321 180.221 209.482 -> 0 0 0 instead 206.311 180.211 209.472 -> norm = 0.0173205 setting bc 206.321 180.221 15.2289 -> 0 0 0 instead 206.311 180.211 15.2389 -> norm = 0.0173205 setting bc 206.321 46.9577 209.482 -> 0 0 0 instead 206.311 46.9677 209.472 -> norm = 0.0173205 setting bc 206.321 46.9577 15.2289 -> 0 0 0 instead 206.311 46.9677 15.2389 -> norm = 0.0173205 setting bc 48.9912 180.221 209.482 -> 0 0 0 instead 49.0012 180.211 209.472 -> norm = 0.0173205 setting bc 48.9912 180.221 15.2289 -> 0 0 0 instead 49.0012 180.211 15.2389 -> norm = 0.0173205 setting bc 48.9912 46.9577 209.482 -> 0 0 0 instead 49.0012 46.9677 209.472 -> norm = 0.0173205 setting bc 48.9912 46.9577 15.2289 -> 0 0 0 instead 49.0012 46.9677 15.2389 -> norm = 0.0173205 computing statistics for the displacement application error average norm of error in placement = 0.0173205 iterating done with candidates Active BCs = 179269 Total BCs = 563742 no-eqs = 649995 [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 -2147483648 [0]PETSC ERROR: Try running with -malloc_dump or -malloc_log for info. [0]PETSC ERROR: Memory requested 782593984! [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 linux-gnu named k2 by kavec Sat Sep 25 17:52:24 2010 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --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: 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 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Si…: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: --------------------- Error Message ------------------------------------ [0]PETSC ERROR: Signal received! [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: ------------------------------------------------------------------------ [0]PETSC ERROR: surf2vol on a linux-gnu named k2 by kavec Sat Sep 25 17:52:24 2010 [0]PETSC ERROR: Libraries linked from /autofs/space/lyon_006/pubsw/Linux2-2.3-x86_64/packages/petsc/2.3.3-p13/src/petsc-2.3.3-p13/lib/linux-gnu-c-opt [0]PETSC ERROR: Configure run at Tue Aug 10 15:01:59 2010 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=g77 --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

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re-calculating stats based on an updated ?h.pial surface
by Dominic Brendon Dwyer 15 Oct '10

15 Oct '10

Hi all, We're using a tool which allows direct alteration of the pial surface (http://sites.google.com/site/vxxsoftware/) resulting in another ?h.pial file being created. We've found that it is a good way to both decrease and increase the pial boundary where there are errors. The current procedure is to use mris_fill once the surfaces are created and then apply this to the brainmask.mgz before re-running recon2. I was wondering if it was possible to recalculate the surface stats based on an altered ?h.pial file without running recon2 again? The reason being is that if the surface is extended rather than reduced then it will not necessarily appear in the updated pial surface. Any help would be greatly appreciated. Many thanks, Dominic Melbourne Neuropsychiatry Centre

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Cannot allocate memory
by Pradeep 14 Oct '10

14 Oct '10

Hello All, I get the following error while running mri_glmfit. I am using freesurfer V5.0. But qdce seem to run well with the similar settings. ---------log------- [pthiyyagura@ fsgd]$ mri_glmfit --glmdir g2v0 --y fsgd_input.mgh --fsgd g2v0.fsgd --C group.diff.mtx gdfReadHeader: reading g2v0.fsgd INFO: gd2mtx_method is dods $Id: mri_glmfit.c,v 1.187.2.1 2010/07/26 15:54:39 greve Exp $ cwd /data/rawdata/API/FS_MPRAGE/fsgd cmdline mri_glmfit --glmdir g2v0 --y fsgd_input.mgh --fsgd g2v0.fsgd --C group.diff.mtx sysname Linux hostname machine x86_64 user pthiyyagura FixVertexAreaFlag = 1 UseMaskWithSmoothing 1 OneSampleGroupMean 0 y /data/rawdata/API/FS_MPRAGE/fsgd/fsgd_input.mgh logyflag 0 usedti 0 FSGD g2v0.fsgd glmdir g2v0 IllCondOK 0 DoFFx 0 Creating output directory g2v0 Loading y from /data/rawdata/API/FS_MPRAGE/fsgd/fsgd_input.mgh MRIalloc: could not allocate 1378828612 slices Cannot allocate memory --------end------- Any suggestion on this would be greatly appreciated. Thanks, Pradeep

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MNI152
by Yigal Agam 14 Oct '10

14 Oct '10

Hi, Is it possible to export a functional volume from individual brain space to mni152, so it can be overlaid on the standard mni152 brain in fslview? Thanks, Yigal

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Problem with intensity normalization
by Huo, Jing 14 Oct '10

14 Oct '10

Hi, I have a problem with using mri_normalize for intensity normalization for T1w+contrast 3D volumes. What I ran: mri_convert t1.hdr t1.mgz mri_normalize -g 1 t1.mgz t1_norm.mgz mri_convert t1_norm.mgz t1_norm.hdr (1) The first problem is that all volumes are 256*256*256 as output. Why are there dummy slices? Is there an automatic way to get rid of the dummy slices? (2) For 1/3 of the 50 cases, I observed a spatial shift for some voxels. I was wondering whether this comes from the spatial registration, but it is wierd coz the rest 2/3 of the cases are pretty OK visually. Anyone has similar experience before? That would be very helpful. Thanks. (3) For 4 cases, the brain white matter was normalized to 59 instead of 110. I dunno why... Thanks! I will really appreciate if anyone could help here! Best, Jing IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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FDR in gray matter
by Yigal Agam 14 Oct '10

14 Oct '10

Hi, Is it possible to restrict FDR correction to gray matter in tkmedit? Thanks

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postdoctoral fellow position for dementia research
by Anqi Qiu 14 Oct '10

14 Oct '10

Postdoctoral Fellow Position on Dementia NeuroImaging Job description: National University of Singapore (NUS) is a leading global university centred in Asia. It offers a global approach to education and research, with a focus on Asian perspectives and expertise. Computation functional anatomy laboratory at NUS (http://www.bioeng.nus.edu.sg/cfa) focuses on brain and cognition studies using neuroimaging techniques. Our group is leading the dementia neuroimaging project in Singapore. The project involves multi-modal MRI techniques, including resting fMRI, HARDI, and ASL. We are looking for a research fellow who is interested in multi-modal MRI studies in dementia, especially, who is interested in developing anatomical and functional connectivity methods or investigating anatomical and functional connectivity in dementia. We offer high salary with medical and other benefits. Requirements: Ph. D or MD Background on Alzheimers disease or vascular disease research is preferable but necessary Knowledge in statistical analysis is necessary Good communication and writing skills in English language If you are interested in the jobs listed below, please send your CV to Dr. Anqi QIU Division of Bioengineering National University of Singapore Email: bieqa(a)nus.edu.sg Phone: +(65) 6516 7002

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