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Re: [Freesurfer] Total GM and WM volumes
by Ed Gronenschild 27 Oct '10

27 Oct '10

Dear Bruce/Allison, Could you please try to give response to my question which wm and gm volumes I shoud use, see my today's submission below. Ed On 27 Oct 2010, at 14:41, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Dear Christian, > > Thanks for your suggestion. I followed the instructions to derive the > GM and WM volumes. Here are the (rounded-off) results for one example: > > mris_volume lh.pial: 532767 > mris_volume rh.pial: 536127 > > mris_wm_volume lh: 251139 > mris_wm_volume rh: 254730 > > Accordingly: > gm lh = 532767 - 251139 = 281628 > gm rh = 536127 - 254730 = 281397 > > Left + right: > total = 1068894 > wm = 505869 > gm = 563025 > > ------------ > > The aseg.stats file lists the following results: > > cortical wm lh: 251139 > cortical wm rh: 254730 > total wm: 505869 > > cortical gm lh: 263888 > cortical gm rh: 265231 > total cortical gm: 529119 > subcortical gm: 181270 > total gm: 710389 > > -------------- > > For wm both results are equal but for gm they are not. > > So now my question still exists: which wm and gm volumes should I > take? > > Ed > > > On 26 Oct 2010, at 20:40, freesurfer-request(a)nmr.mgh.harvard.edu > wrote: > >> Dear Ed, >> >> to my knowledge, "mris_wm_volume" is the best option to determine the >> white matter volume. >> >> See this wiki page for usage: >> http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats >> >> Best wishes, >> Christian >> >> >> --- >> Christian Scheel >> Department of Psychiatry >> University of Cologne >> >> >> >> >> Am 26.10.2010 15:22, schrieb Ed Gronenschild: >>> Hi, >>> >>> I post this once again because I didn't get any response. >>> >>> In the v5.0.0 aseg.stats file I can find the following volumes: >>> >>> - left/right cortical gray matter >>> - subcortical gray matter >>> - total cortical gray matter >>> - total gray matter volume >>> and >>> - left/right cortical white matter >>> - total cortical white matter >>> >>> How can I derive the total white matter volume? >>> >>> Ed >> >

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problems with labels in tkmedit
by swoodman＠nmr.mgh.harvard.edu 26 Oct '10

26 Oct '10

Hi all, We have been drawing some labels in tkmedit recently, but when we reload the labels, only a very small proportion of the label actually shows up, or appears to be contained in the file at all, given the number of voxels in the label file. We originally made a label, I believe, in the stable 4 environment (when it was the std environment), which was quite large, and most of it appears to be gone when uploaded in the stable 4 environment now. At first, I thought this was the wrong file, but then I started recreating the label file, and after reloading that one, this one also lost the majority of its voxels. We are doing the labeling in the stable 4 environment since tkmedit does not appear to open in the current std environment. The original file is: /space/amaebi/35/users/ablood/FSLanalysis/fnirt_data/ptx_trans2MNI/AL_trans/Left-antAL/session_1/brainstemlabel.label and the new one created today is: /space/amaebi/35/users/ablood/FSLanalysis/fnirt_data/ptx_trans2MNI/AL_trans/Left-antAL/session_1/brainstemsegforcorrect.label The original one, made in February, 2010, covered the majority of the brainstem and cerebellum, while the one started today was mostly regions just below the basal ganglia across 8-10 slices (when re-uploaded, the label now only shows up in one slice, 138). Can anyone help us figure out what is going wrong here? Thank you!! Anne ------------------------------- Anne J. Blood, Ph.D. Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital CNY 149-2301, 13th St. Charlestown, MA 02129 phone: (617) 643-2297 fax: (617) 726-7422 email: ablood(a)nmr.mgh.harvard.edu

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Total GM and WM volumes
by Ed Gronenschild 26 Oct '10

26 Oct '10

Hi, In the v5.0.0 aseg.stats file I can find the following volumes: - left/right cortical gray matter - subcortical gray matter - total cortical gray matter - total gray matter volume and - left/right cortical white matter - total cortical white matter How can I derive the total white matter volume? Ed

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Potential memory leak in mri_cvs_register (fwd)
by Lilla Zollei 26 Oct '10

26 Oct '10

Hi Martin, I thought we fixed this problem with the latest release. I am checking into this. --Lilla ---------- Forwarded message ---------- Date: Fri, 15 Oct 2010 14:38:29 +0200 From: Martin Kavec <martin.kavec(a)gmail.com> To: Freesurfer mailing list <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Potential memory leak in mri_cvs_register 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 _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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corpus callosum coordinates
by Lars M. Rimol 26 Oct '10

26 Oct '10

Hi, We are planning to do shape analysis of the corpus callosum. In order to do that we need the coordinates (x,y,z) of the voxels comprising the cc in the subcortical segmentation. We are using FS v. 3.0.2. The corpus callosum info in the aseg.stats shows all zeros for all subjects, does that mean that cc is not identified in 'aseg.mgz' in FS v. 3.0.2? There is corpus callosum info in the aparc.stats files but we assume that's from the cortical surface reconstruction and therefore not appropriate. Do any of the later versions of FS have the information we need in order to identify the corpus callosum in the volumetric segmentation? We know that v. 4.0.0 (and up) have a corpus callosum segmentation with five labels in 'aseg.mgz'. Does that mean that if we redid the recons with this version we would be able to obtain the coordinates of the cc? Is there any way to get this info from the data recon'ed with v3.0.2? Thank you! yours, Dr. Lars M. Rimol

1 0

How to transform the thickness per vertex to another space?
by Mohammed el Morabit 25 Oct '10

25 Oct '10

Dear FS experts, I 've question concerning the thickness per vertex. Here is what I want to do: I have a data series which entered the FS pipeline. Afterwards, I transformed the aparc+aseg file to another space. Is it somehow possible to transform the thickness per vertex to this space using the same transformation matrix? Thanks, Mo

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Error with mri_segstats
by Ed Gronenschild 25 Oct '10

25 Oct '10

Hi, I'm trying to use mri_segstats and get the following error: ERROR: could not open stats/aseg1.stats for writing The full command I gave was: mri_segstats --seg mri/aseg.mgz --sum stats/aseg1.stats --pv mri/ norm.mgz --empty --excludeid 0 --excl-ctxgmwm --supratent -- subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity- units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --ctab / Applications/freesurfer/ASegStatsLUT.txt --subject C001 The SUBJECTS_DIR was set to the directory containing the subject C001. I have full privileges to read/write to all folders. If I try to write to just aseg1.stats (so using option --sum aseg1.stats) I get the error message that aseg.mgz could not be opened. I'm on a Mac using FreeSurfer v5.0.0. Ed

2 1

average p-value from an ROI
by Agnieszka Burzynska 25 Oct '10

25 Oct '10

Dear all, I have a follow-up question to the previous discussion ("correction for behavioral varialbles in qdec" Tue, 04 Aug 2009. Is there an option to extract the average p-value from a ROI? After a group analysis I specified ROIs at p < 0.001 and extracted the mean cortical thickness, the peak p-value, and mean ROI size. Now, I would like to report not the peak, but the average p-value of an ROI in the fsaverage space. Is there any flag to obtain this information? I did not use the mri_surfcluster command, but a matlab script to extract the information form the output of the mri_segstats command. Thanks for help! Cheers, Aga

3 2

mni coordinates to volume index
by Yigal Agam 25 Oct '10

25 Oct '10

Hi, Is it possible in matlab to get the volume index coordinates corresponding to specific MNI coordiates? Thanks, Yigal

2 1

data not Surving FDR
by Mira Michelle Raman 25 Oct '10

25 Oct '10

Hi, I have a dataset that seems to have some very nice group differences (please see the graph and qdec image), but they never seem to survive FDR. I noticed when I run the "Set Using FDR", it generates a very high threshold above 5; where as, with some of my other datasets FDR is set much lower (often in the 2's and 3's). Can you please give me some insight into why the threshold is being set so high? Is it solely linked to the small sample size, or is there something additional we can do in the processing, so that regions with such large group differences will survive correction? Thank you, Mira

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