Freesurfer April 2012

freesurfer@nmr.mgh.harvard.edu

123 participants
192 discussions

aseg.mgz
by Steven Thomas Korycinski 12 Apr '12

12 Apr '12

Freesurfer users, Can anyone tell me if the subcortical segmentation shown in TkMedit (aseg.mgz) is subject-specific or a general outline of structure labels in Talairach space for all subjects? Also, are the statistics provided in aseg.stats based directly on the aseg.mgz or something else? Thanks, Steve

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changing data structure
by Anthony Dick 12 Apr '12

12 Apr '12

Hello, I am running the rebuild_gca_atlas.csh program and got the following error for seg_edited.mgz, which is the manually defined file imported from a different program outside of freesurfer. mri_ca_train: segmentation file <path>/seg_edited.mgz is not type UCHAR or FLOAT Is there a way to redefine the data structure? Anthony -- Anthony Steven Dick, Ph.D. Assistant Professor Department of Psychology Florida International University Modesto A. Maidique Campus DM 296B 11200 S.W. 8th Street Miami, FL 33199 Phone: 305-348-4202 (try this first) Lab Phone: 305-348-9057 or 305-348-9055 Fax: 305-348-3879 Email: adick(a)fiu.edu Webpage: http://www.fiu.edu/~adick Lab Webpage: http://dcn.fiu.edu

3 2

FreeView doesn't load surfaces
by Domenico M. Mezzapesa 12 Apr '12

12 Apr '12

Dear FreeSurfer experts, I have a problem using FreeView: it can load volume without problems, but when I try to load surface it crash. The error is: MatrixMultiply: m2 is null! No such file or directory Best regards Domenico M Mezzapesa Invita i tuoi amici e Tiscali ti premia! Il consiglio di un amico vale più di uno spot in TV. Per ogni nuovo abbonato 30 € di premio per te e per lui! Un amico al mese e parli e navighi sempre gratis: http://freelosophy.tiscali.it/

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perplex
by 传玺 12 Apr '12

12 Apr '12

Dear FS experts I could not understand fully the Program Name: tkregister2_cmdl and Program Name: mri_make_uchar and Program Name: mri_ca_label and Program Name: mri_gcut and Program Name: mri_concatenate_lta and Program Name: mri_normalize_tp2 and Program Name: mris_topo_fixer and Program Name: mris_volmask and Program Name: mris_calc and Program Name: mri_fuse_segmentations Could you tell me what is the meaning of that program? Thanks for your help! haochuanxi peking university

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Re: [Freesurfer] Stylus Input for Cortical Edits
by Alan Francis 11 Apr '12

11 Apr '12

Hi Wil: The model we use for manual morphometry is the Wacom BAMBOO (pen) : Model CTL-460. best, Alan On Mon, Apr 9, 2012 at 12:22 PM, Irwin, William <WIrwin(a)memory.ucsf.edu>wrote: > Hi-**** > > ** ** > > I have been considering this option, and these comments pretty much make > it a given.**** > > ** ** > > Could you provide a bit more details: Which models? Are you using tablets > with Linux (RH or Ubuntu) and/or MAC OS?**** > > ** ** > > Thanks,**** > > Wil**** > > ____________________________________ > William Irwin | Imaging Core Supervisor > UCSF | Memory and Aging Center > 350 Parnassus Avenue, Suite 905 > San Francisco CA 94143-1207 > wirwin(a)memory.ucsf.edu | memory.ucsf.edu > p: 415.476.1680 | f: 415.476.1816**** > > ** ** > > ** ** > > ** ** > > *From:* Alan Francis [mailto:alandarkenergy@gmail.com] > *Sent:* Thursday, April 05, 2012 6:53 AM > *To:* Jeff Stout > *Cc:* freesurfer(a)nmr.mgh.harvard.edu > > *Subject:* Re: [Freesurfer] Stylus Input for Cortical Edits**** > > ** ** > > Hi Jeff:**** > > ** ** > > We too have found Wacom tablets are great for editing and also these are > easy on the back and eyes.**** > > ** ** > > best,**** > > ** ** > > Alan**** > > On Wed, Apr 4, 2012 at 6:46 PM, Emily Rogalski <erogalski(a)gmail.com> > wrote:**** > > We have found Wacom tablets are excellent for editing.**** > > On Apr 4, 2012 4:40 PM, "Jeff Stout" <jstout211(a)yahoo.com> wrote:**** > > Hi All,**** > > ** ** > > We have a large number of subjects that need minor edits (orbital frontal > cortex/eye issues subcortical parcellation etc.). To speed up the process > I was wondering if a stylus input would help with the editing.**** > > ** ** > > Do the graphics tablets (stylus input) work with freesurfer editing? Do > they end up being useful or is it not worth investing in? And if so, could > someone recommend a brand (wacom?) that would work with Ubuntu 10.04 (or > just linux in general).**** > > ** ** > > ** ** > > Thank you, > Jeff Stout**** > > ** ** > > _______________________________________________ > 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 > > > 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.**** > > ** ** >

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freeview command line generic overlay colormap question
by Heath Pardoe 11 Apr '12

11 Apr '12

Hi all, I have a question about controlling freeview from the command line. I would like to overlay some z-score maps for individual subjects on the fsaverage inflated surface. I would like to use the 'color wheel' color scale setting and threshold the images between -1 and 1 standard deviations (for example). Because I have a number of subjects, I was hoping to make this a bit easier using the command line. So far I use the command: freeview --surface /opt/freesurfer/subjects/fsaverage/surf/lh.inflated:overlay=lh.overlay.mgh:edgethickness=0 --screenshot lh.overlay.png But I can't figure out from 'freeview --help' how to control the color of the overlay and the thresholding levels. Does anyone know if it is possible to control these options from the command line? Or an alternative approach, maybe using tksurfer or even slicer? Best wishes Heath

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mri_segstats memory corruption error
by Jeff Sadino 11 Apr '12

11 Apr '12

Hello FreeSurfers, I ran the following command: mri_glmfit-sim --glmdir rhFwhm12Sig13 --sim mc-z 10000 1.3 mc-z.abs.13.jls --sim-sign abs --overwrite When it gets to the part to do mri_segstats, it throws this error: 0 1*** glibc detected *** mri_segstats: malloc(): memory corruption: 0x2f302488 *** I see this person had a similar problem: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15423.html All of my other mri_glmfit-sim commands have worked fine. Is this a bug in mri_segstats? I am rerunning it again to see if it is duplicatable. The rest of the error log looks like this: $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $ cwd cmdline mri_segstats --seg rhFwhm12Sig13/rh-Diff-M-F-Intercept-volume/mc-z.abs.13.jls.sig.ocn.mgh --exclude 0 --i rhFwhm12Sig13/y.mgh --avgwf rhFwhm12Sig13/rh-Diff-M-F-Intercept-volume/mc-z.abs.13.jls.y.ocn.dat --sum /tmp/mri_glmfit-sim.junk.20258 sysname Linux hostname calypso machine i686 user ash Loading rhFwhm12Sig13/rh-Diff-M-F-Intercept-volume/mc-z.abs.13.jls.sig.ocn.mgh Loading rhFwhm12Sig13/y.mgh Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 3 segmentations Computing statistics for each segmentation 1 1 1327 1327 2 2 1403 1403 Reporting on 2 segmentations Computing spatial average of each frame 0 1*** glibc detected *** mri_segstats: malloc(): memory corruption: 0x2f302488 *** ======= Backtrace: ========= /lib/i386-linux-gnu/libc.so.6(+0x6b961)[0xb761d961] /lib/i386-linux-gnu/libc.so.6(+0x6e15d)[0xb762015d] /lib/i386-linux-gnu/libc.so.6(__libc_malloc+0x63)[0xb7621f53] /lib/i386-linux-gnu/libc.so.6(+0x5c2b8)[0xb760e2b8] /lib/i386-linux-gnu/libc.so.6(fopen64+0x2c)[0xb76109cc] mri_segstats(vfprintf+0x3e9e)[0x80526d6] /lib/i386-linux-gnu/libc.so.6(__libc_start_main+0xe7)[0xb75c8e37] mri_segstats(__gxx_personality_v0+0x1c9)[0x804f791] ======= Memory map: ======== 08048000-087f2000 r-xp 00000000 00:00 0 087f2000-2e568000 rwxp 00000000 00:00 0 2f288000-2f34e000 rwxp 00000000 00:00 0 [heap] b2f00000-b2f21000 rwxp 00000000 00:00 0 b2f21000-b3000000 ---p 00000000 00:00 0 b30e5000-b74d1000 rwxp 00000000 00:00 0 b7572000-b757c000 r-xp 00000000 08:15 11666287 /lib/i386-linux-gnu/ libnss_files-2.13.so b757c000-b757d000 r-xp 00009000 08:15 11666287 /lib/i386-linux-gnu/ libnss_files-2.13.so b757d000-b757e000 rwxp 0000a000 08:15 11666287 /lib/i386-linux-gnu/ libnss_files-2.13.so b757e000-b7591000 r-xp 00000000 08:15 11666281 /lib/i386-linux-gnu/ libnsl-2.13.so b7591000-b7592000 r-xp 00012000 08:15 11666281 /lib/i386-linux-gnu/ libnsl-2.13.so b7592000-b7593000 rwxp 00013000 08:15 11666281 /lib/i386-linux-gnu/ libnsl-2.13.so b7593000-b7595000 rwxp 00000000 00:00 0 b75b0000-b75b2000 rwxp 00000000 00:00 0 b75b2000-b770c000 r-xp 00000000 08:15 11666241 /lib/i386-linux-gnu/ libc-2.13.so b770c000-b770d000 ---p 0015a000 08:15 11666241 /lib/i386-linux-gnu/ libc-2.13.so b770d000-b770f000 r-xp 0015a000 08:15 11666241 /lib/i386-linux-gnu/ libc-2.13.so b770f000-b7710000 rwxp 0015c000 08:15 11666241 /lib/i386-linux-gnu/ libc-2.13.so b7710000-b7714000 rwxp 00000000 00:00 0 b7714000-b772e000 r-xp 00000000 08:15 11666269 /lib/i386-linux-gnu/libgcc_s.so.1 b772e000-b772f000 r-xp 00019000 08:15 11666269 /lib/i386-linux-gnu/libgcc_s.so.1 b772f000-b7730000 rwxp 0001a000 08:15 11666269 /lib/i386-linux-gnu/libgcc_s.so.1 b7730000-b7754000 r-xp 00000000 08:15 11666278 /lib/i386-linux-gnu/ libm-2.13.so b7754000-b7755000 r-xp 00023000 08:15 11666278 /lib/i386-linux-gnu/ libm-2.13.so b7755000-b7756000 rwxp 00024000 08:15 11666278 /lib/i386-linux-gnu/ libm-2.13.so b7756000-b7835000 r-xp 00000000 08:15 24387549 /usr/lib/i386-linux-gnu/libstdc++.so.6.0.14 b7835000-b7839000 r-xp 000de000 08:15 24387549 /usr/lib/i386-linux-gnu/libstdc++.so.6.0.14 b7839000-b783a000 rwxp 000e2000 08:15 24387549 /usr/lib/i386-linux-gnu/libstdc++.so.6.0.14 b783a000-b7841000 rwxp 00000000 00:00 0 b7841000-b7856000 r-xp 00000000 08:15 11666306 /lib/i386-linux-gnu/ libpthread-2.13.so b7856000-b7857000 r-xp 00015000 08:15 11666306 /lib/i386-linux-gnu/ libpthread-2.13.so b7857000-b7858000 rwxp 00016000 08:15 11666306 /lib/i386-linux-gnu/ libpthread-2.13.so b7858000-b785a000 rwxp 00000000 00:00 0 b785a000-b785c000 r-xp 00000000 08:15 11666251 /lib/i386-linux-gnu/ libdl-2.13.so b785c000-b785d000 r-xp 00001000 08:15 11666251 /lib/i386-linux-gnu/ libdl-2.13.so b785d000-b785e000 rwxp 00002000 08:15 11666251 /lib/i386-linux-gnu/ libdl-2.13.so b785e000-b785f000 rwxp 00000000 00:00 0 b785f000-b7867000 r-xp 00000000 08:15 11666247 /lib/i386-linux-gnu/ libcrypt-2.13.so b7867000-b7868000 r-xp 00007000 08:15 11666247 /lib/i386-linux-gnu/ libcrypt-2.13.so b7868000-b7869000 rwxp 00008000 08:15 11666247 /lib/i386-linux-gnu/ libcrypt-2.13.so b7869000-b7890000 rwxp 00000000 00:00 0 b7890000-b78a3000 r-xp 00000000 08:15 11666324 /lib/i386-linux-gnu/libz.so.1.2.3.4 b78a3000-b78a4000 r-xp 00012000 08:15 11666324 /lib/i386-linux-gnu/libz.so.1.2.3.4 b78a4000-b78a5000 rwxp 00013000 08:15 11666324 /lib/i386-linux-gnu/libz.so.1.2.3.4 b78ac000-b78b5000 r-xp 00000000 08:15 11666291 /lib/i386-linux-gnu/ libnss_nis-2.13.so b78b5000-b78b6000 r-xp 00008000 08:15 11666291 /lib/i386-linux-gnu/ libnss_nis-2.13.so b78b6000-b78b7000 rwxp 00009000 08:15 11666291 /lib/i386-linux-gnu/ libnss_nis-2.13.so b78b7000-b78bd000 r-xp 00000000 08:15 11666283 /lib/i386-linux-gnu/ libnss_compat-2.13.so b78bd000-b78be000 r-xp 00005000 08:15 11666283 /lib/i386-linux-gnu/ libnss_compat-2.13.so b78be000-b78bf000 rwxp 00006000 08:15 11666283 /lib/i386-linux-gnu/ libnss_compat-2.13.so b78bf000-b78c2000 rwxp 00000000 00:00 0 b78c2000-b78de000 r-xp 00000000 08:15 11666228 /lib/i386-linux-gnu/ ld-2.13.so b78de000-b78df000 r-xp 0001b000 08:15 11666228 /lib/i386-linux-gnu/ ld-2.13.so b78df000-b78e0000 rwxp 0001c000 08:15 11666228 /lib/i386-linux-gnu/ ld-2.13.so b78e0000-b78e1000 r-xp 00000000 00:00 0 [vdso] bf87f000-bf8a1000 rwxp 00000000 00:00 0 [stack] Writing to rhFwhm12Sig13/rh-Diff-M-F-Intercept-volume/mc-z.abs.13.jls.y.ocn.dat Abort Thank you for your help! Jeff Sadino

2 1

longitudinal processing for lgi comparison
by Sabin Khadka 11 Apr '12

11 Apr '12

Hi all, Is there a longitudinal processing stream to compare local gyrification index (lgi) across two time points. -Sabin

2 1

Clarification on centos version/updates/patches
by Irwin, William 11 Apr '12

11 Apr '12

Hi- It would appear the stable release for centos6 is ready for primetime 'stable5.1-bin.tgz'; Is this correct? There is an updated version of 'mri_info' based on file size (ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86…) mri_info in 'stable5.1-bin.tgz': 9787048 04-Oct-2011 13:45 mri_info outside of 'stable5.1-bin.tgz': 9866032 04-Oct-2011 11:32 Which version is the most current? Can the contents of 'stable5.1-bin.tgz' be extracted into /freesurfer/bin to overwrite the extant files? Additionally, there is a versioning discrepancy between 'trac-all' located in (http://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/) '$Id: trac-all,v 1.35 2011/09/02 19:19:22 ayendiki Exp $'a and the version packaged with the cenos6_x86_65 'stable5.1-bin.tgz' '$Id: trac-all,v 1.22.2.9 2011/09/02 19:21:03 ayendiki Exp $' I did not comprehensively look for any other discrepancies-these just happened to stand out based on the work I was doing today. Thanks much, Wil

3 3

consult
by 传玺 11 Apr '12

11 Apr '12

Dear FS expert： Today I put two contrast in the file {subjects},and run the command line "recon-all -s mgz -all", several minutes later,the terminal tells error,it says: [brain@localhost ~]$ recon-all -s mgz -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects Actual FREESURFER_HOME /usr/local/freesurfer Linux localhost.localdomain 2.6.25-14.fc9.i686 #1 SMP Thu May 1 06:28:41 EDT 2008 i686 i686 i386 GNU/Linux #-------------------------------------------- #@# MotionCor Wed Apr 11 17:49:05 HKT 2012 Found 3 runs /usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz /usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz /usr/local/freesurfer/subjects/mgz/mri/orig/004.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /usr/local/freesurfer/subjects/mgz mri_robust_template --mov /usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz /usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz /usr/local/freesurfer/subjects/mgz/mri/orig/004.mgz --average 1 --template /usr/local/freesurfer/subjects/mgz/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /usr/local/freesurfer/subjects/mgz/mri/orig/002-iscale.txt /usr/local/freesurfer/subjects/mgz/mri/orig/003-iscale.txt /usr/local/freesurfer/subjects/mgz/mri/orig/004-iscale.txt --subsample 200 --lta /usr/local/freesurfer/subjects/mgz/mri/orig/002.lta /usr/local/freesurfer/subjects/mgz/mri/orig/003.lta /usr/local/freesurfer/subjects/mgz/mri/orig/004.lta $Id: mri_robust_template.cpp,v 1.37 2011/03/02 00:04:24 nicks Exp $ --mov: Using /usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/mgz/mri/orig/004.mgz as movable/source volume. Total: 3 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/freesurfer/subjects/mgz/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz'... reading source '/usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz'... reading source '/usr/local/freesurfer/subjects/mgz/mri/orig/004.mgz'... MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /usr/local/freesurfer/subjects/mgz/mri/orig/003.mgz ) to TP 1 ( /usr/local/freesurfer/subjects/mgz/mri/orig/002.mgz ) Registration::setSourceAndTarget ... Mov: (0.4688, 0.4688, 1.19996)mm and dim (512, 512, 156) Dst: (0.4688, 0.4688, 1.20005)mm and dim (512, 512, 156) Asserting both images: 0.4688mm isotropic and (512, 512, 400) voxels Original : (0.4688, 0.4688, 1.19996) mm size and (512, 512, 156) voxels. Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 400) voxels. Reslicing using trilinear interpolation Original : (0.4688, 0.4688, 1.20005) mm size and (512, 512, 156) voxels. Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 400) voxels. Reslicing using trilinear interpolation Registration::findSaturation - Gaussian Pyramid MRIalloc(512, 512, 400): could not allocate 1048576 bytes for 367th slice Cannot allocate memory Linux localhost.localdomain 2.6.25-14.fc9.i686 #1 SMP Thu May 1 06:28:41 EDT 2008 i686 i686 i386 GNU/Linux recon-all -s mgz exited with ERRORS at Wed Apr 11 17:51:20 HKT 2012 For more details, see the log file /usr/local/freesurfer/subjects/mgz/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting BUT,when I process a single contrast,the software runs well! could you tell me what is wrong in the process? Thank you very much.

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Freesurfer April 2012