Freesurfer October 2010

freesurfer@nmr.mgh.harvard.edu

100 participants
129 discussions

Re: [Freesurfer] montecarlo
by Douglas N Greve 18 Oct '10

18 Oct '10

Hi Marco, I'm copying the list on this because this is a good question about an aspect that is not well documented. The answer to the question has to do with the sign of the test. By default, mri_glmfit produces p-values that are for unsigned tests. The p-value for a signed test if half that of the signed test (ie, it is more significant). When the p-value is expressed as -log10(p), then the signed test will be 0.301 higher than the unsigned test. Eg, if you have a p-value of .01, the value in the sig.mgh file will be 2.0, but for a signed test it would be .005, making the value in the sig.mgh file 2.3. When you run mri_glmfit-sim and specify a signed test (ie, --sim-sign pos or --sim-sign neg), it lowers the threshold to account for this. So below you specified 1.3 as the threshold and --sim-sign pos, so it lowered the threshold to 1.0. hope this is clear doug Marco Loggia, PhD wrote: > Sorry Doug, > > Below are directory and command line. Also attached is a screenshot showing > a vertex located on a significant cluster, but below threshold in the > sig.mgh. > > Thanks! > Marco > > dir=/autofs/cluster/randy/2/lbp/freesurfer/patients+controls/analyses/lh.lbp > +ctrl.session1.asl2-asl1_30sept10_sm7_03mm_masked_projfrac-max_P=0.05.glmdir > /lbp_only_24sept10 > > > pbsubmit -c "mri_glmfit-sim --glmdir > lh.lbp+ctrl.session1.asl2-asl1_30sept10_sm7_03mm_masked_projfrac-max_P=0.05. > glmdir > --sim perm 10000 1.30103 perm.positive --sim-sign pos --overwrite" > > > > -----Original Message----- > From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Monday, October 18, 2010 10:34 AM > To: Marco Loggia, PhD > Subject: Re: montecarlo > > Hi Marco, can you send the command-line and directory that you ran it > from? In general, it is always a good idea to send this ... > > doug > > Marco Loggia, PhD wrote: > >> Hello Doug, >> >> >> >> I have one question about the montecarlo simulation. >> >> >> >> When I compare the mc-z.positive.sig.cluster.mgh and the >> mc-z.positive.sig.masked.mgh, I notice that the significant clusters >> include also some vertices that are below the cluster forming >> threshold. Is this normal? Why is that? >> >> >> >> 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 >> >> >> >> > > > > ------------------------------------------------------------------------ > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] 答复: Problem with intensity normalization
by Douglas N Greve 18 Oct '10

18 Oct '10

Hi Jing, I'm reposting to the group in case someone else has any suggestions. I've answered some of your questions below 1) all of our outputs are "conformed" meaning that they are resampled to 1mm3 256^3. To convert back to native anatomical space search for "native" on our wiki. 2) Don't know 3) Don't know doug Huo, Jing wrote: > Hi Douglas, > > Thanks a lot for your reply!!! > I am doing brain tumor segmentation with voxel-based classification. We have images from all difference scanners. To have good performance in the training stage, I need to normalize the intensity into the same range... > And after segmentation, I need to compare the ground truth and the automated results. > I don't have a choice here...:( > > -Jing > ________________________________________ > 发件人: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] > 发送时间: 2010年10月14日 15:12 > 收件人: Huo, Jing > 抄送: freesurfer(a)nmr.mgh.harvard.edu > 主题: Re: [Freesurfer] Problem with intensity normalization > > Jing, why are you running these commands by hand instead of just running > recon-all? These are very complicated steps and don't lend themselves to > running by hand. > > doug > > Huo, Jing wrote: > >> 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. >> >> _______________________________________________ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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. > > > 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. > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Nifti data storage type 0?
by Luis Lafer-Sousa 18 Oct '10

18 Oct '10

We have anatomical NHP data that we unpack and preprocess using freesurfer and fsl (using Sebastian's scripts). An end product is a skull stripped brain in .mgz format, that I then convert to .nii using mri_convert. I am trying to use this to register to a McLaren template using jip-align, but always get an error: Error: the Nifti data storage type 0 is not supported. The only difference I have noticed between our files and files that successfully register are, when using mri_info: type: UCHAR (0) instead of type: FLOAT (3) Pulling up the .nii files in MatLab, I get the following: >> castor = load_nii('091017Castor_SkullStripped_unregistered.nii') castor = hdr: [1x1 struct] filetype: 2 fileprefix: '091017Castor_SkullStripped_unregistered' machine: 'ieee-le' img: [256x256x256 uint8] original: [1x1 struct] >> castor.filetype ans = 2 >> castor.hdr.hist ans = descrip: 'FreeSurfer Aug 11 2009' aux_file: '' qform_code: 0 sform_code: 0 quatern_b: 0 quatern_c: 0.7071 quatern_d: -0.7071 qoffset_x: 116.0951 qoffset_y: -115.1852 qoffset_z: 143.2094 srow_x: [-1 0 0 116.0951] srow_y: [0 0 1 -115.1852] srow_z: [0 -1 0 143.2094] intent_name: '' magic: 'n+1' originator: [139.9049 116.1852 112.7906 -3328 13572] rot_orient: [1 3 2] flip_orient: [3 0 3] >> castor.hdr ans = hk: [1x1 struct] dime: [1x1 struct] hist: [1x1 struct] Any ideas why we are getting this error? Or if I should be posting the problem in a differen't forum? Thanks, Luis

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ERROR: mpr2mni305 failed
by Maria Luisa Mandelli 18 Oct '10

18 Oct '10

Hi! I get this error running recon_all Applications/freesurfer/bin/talairach_avi --i nu.mgz --xfm transforms/talairach.auto.xfm ERROR: mpr2mni305 failed, see transforms/talairach_avi.log parameter 1 1.219086 -> -0.500000 qaram 1.5209 imgrege: no voxels in register ERROR: 'imgreg_4dfp /data/henry4/Applications/freesurfer/average/711-2C_as_mni_average_305 /data/henry4/Applications/freesurfer/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254 ERROR: mpr2mni305 execution aborted Have someone some ideas about this error? thank you! -- Maria Luisa Mandelli Postdoctoral Fellow Center for Functional and Molecular Imaging UCSF Department of Radiology and Biomedical Imaging China Basin Landing 185 Berry Street, Suite 350 San Francisco, CA 94107 phone (415) 353-9419

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qdec plots
by Khalid Hamandi 17 Oct '10

17 Oct '10

(How) Can I modify the plots produced using the Ctrl click on a vertex of interest in the brain map on the qdec GUI? I have two groups, 12 subjects each, currently using the Ctrl Click I get the measure of interest on the y-axis, and my subjects along the x-axis. I would like just two abcissae - patients and controls (with means shown for each!?) on my x-axis instead? if not easily modified, where are these values found? many thanks Khalid

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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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Freesurfer October 2010