Freesurfer

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30131 discussions

Re: [Freesurfer] ERROR: cannot find ... /surf/rh.volume
by rafael＠huberworld.ch 27 Aug '07

27 Aug '07

Hy Nick, First of all thank you for your quick answer. I understand what you wrote there is to do, but I don't know if there is a function already included to do the step you described. In which way would you multiply the area and thickness measures? Best Regards Rafael Rafael, Creation of the surf/?h.volume surface file by recon-all is a function that did not make it into recon-all into for v4.0, so it is not available yet (but selection of it was mentioned in mris_preproc, as you discovered). ?h.volume will be ?h.area times ?h.thickness at each vertices. Nick On Fri, 2007-08-24 at 11:10 +0200, rafael(a)huberworld.ch wrote: Dear Freesurfer Users Always when i try to do the mri_preproc command with the option "meas volume" i get a error message. (ERROR: cannot find ... /surf/rh.volume). I only get this error message with "volume". All other measures like area, thickness and so on work correctly. Does somebody has a clue how i can solve this problem? _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Excluded gray matter - pial surface
by Inês Souta 27 Aug '07

27 Aug '07

Hi there, I need to edit the pial surface. It isn't getting out far enough all over the cortex. I'm sure it is not a skull stripping problem. Do I need to add control points everywhere in order to correct this? Isn't there another way? Thanks Ines

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cerebellum WM.
by Jamie Hanson 24 Aug '07

24 Aug '07

Hi Fellow Freesurfers- I am new to the world of FS and just had a quick question re: cerebellar white matter. After some skull-stripping issues (and adjusting the watershed algorithm numerous times), I just edited a bad skull-strip with manual aux vol value cloning. I ran autorecon2 again (and again because of some need for control points). But while double-checking / looking at my wm.mgz, I found massive holes in cerebellar white matter. Pics here: http://brainimaging.waisman.wisc.edu/~hanson/freesurf/ 001.tiff - my brainmask.mgz with some surfaces (just to show nothing wrong with those steps) 002.tiff - brainmask.mgz + aseg.mgz + surfaces 003.tiff- brainmask.mgz + surfaces (at brain-cerebellar "junction") 004.tiff- my wm.mgz + surfaces of the cerebellum in question. My surfaces "seem" to be fine. But I have a few more subjects who show the same patterns in their wm.mgz . Any thoughts? jamie.

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FS version for old data
by Gallo, Antonio (NIH/NINDS) [F] 24 Aug '07

24 Aug '07

Hi All, We have subjects data processed by another person in the lab sometime ago and we were wondering how can we exactly know which version of FS was used at that time for those data. Thanks in advance, Antonio Antonio Gallo, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 - USA ph #: 001-301-402.6391 fax #: 001-301-402.0373 ***********************

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Re: [Analysis-bugs] Freesurfer v4.0.0 problem??
by Nick Schmansky 24 Aug '07

24 Aug '07

Jonathan, For this error you are encountering with the Linux Centos4 release only: gauss_4dfp: error while loading shared libraries: libg2c.so.0: cannot open shared object file you will either need to install the Fortran compatibility libraries, which can be obtained here: http://rpmfind.net/linux/rpm2html/search.php?query=libg2c or you can download some updated binaries which are built against the static libg2c, from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/nicks/stable/cento… copy the file talairach_avi.tar.gz to your FREESURFER_HOME/bin, then type: cd $FREESURFER_HOME/bin tar zxvf talairach_avi.tar.gz chmod a+x * The other Freesurfer releases were built against the static libg2c, but the Centos4 release was inadvertently built against the dynamic lib, which is not available on some platforms (but is on Centos4). This will be fixed by the next release. Nick On Fri, 2007-08-24 at 14:19 -0400, McDaniel, Jonathan (NIH/NIMH) [F] wrote: > Hello, I have recently downloaded and installed Freesurfer v.4.0.0 for Centos onto my Linux machine running Fedora 6. I keep getting the same error message during autorecon1. It is not clear to me if I have set up the package wrong or if possibly there is a problem with this new version of Freesurfer. Any assistance you can provide would be much appreciated. I am attaching the error log file that I receive. > > Thank you, > > Jonathan > > _______________________________________________ > Analysis-bugs mailing list > Analysis-bugs(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/analysis-bugs

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ERROR: cannot find ... /surf/rh.volume
by rafael＠huberworld.ch 24 Aug '07

24 Aug '07

Dear Freesurfer Users Always when i try to do the mri_preproc command with the option "meas volume" i get a error message. (ERROR: cannot find ... /surf/rh.volume). I only get this error message with "volume". All other measures like area, thickness and so on work correctly. Does somebody has a clue how i can solve this problem?

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design matrix Q ?
by Kirk, Gregory 22 Aug '07

22 Aug '07

Hi refering to http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/DesignMatrix Design Matrices with DOSS and DODS I want to make an analysis of same offset different slope between classes with a continuous age variable If I was doing this with the example( 3 variables ) starting with for dods 1 0 10 0 100 0 1000 0 1 0 15 0 150 0 1500 0 0 1 0 20 0 200 0 2000 0 1 0 25 0 250 0 2500 I would change to for same offset different slope 1 10 0 100 0 1000 0 1 15 0 150 0 1500 0 1 0 20 0 200 0 2000 1 0 25 0 250 0 2500 for my example with 2 classes and one variable, age I would have.. for same offset different slope a contrast vector [ 0 1 -1] in file sodsage.mat --direct comparison between thickness and age between class and do glm_fit with my design in file Xgsods.dat matrix of the form, 4 subj for brevity 1 n1 0 1 n2 0 1 0 n3 1 0 n4 mri_glmfit --y lh.sickle.thickness.10.mgh --glmdir lh.sickle_sodsage.glmdir --surf SICKLECELLAVE lh --C sodsage.mat --X Xgsods.dat did I get it correct ? thanks Greg.

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Re: [Freesurfer] tksurfer: "window type not found"
by Stefan Vollmar 22 Aug '07

22 Aug '07

Dear Bruce, dear Kevin, we have upgraded to Freesurfer 4.0.0. Now "doublebufferflag" does make a difference: if we set it to "1" and execute tksurfer bert lh pial we see a tiny sliver of the brain on the right hand side when running Freesurfer remotely on a Linux x86 system (Fedora Core 7, SunFire X2200). This seems to be independent of the X-Server we use (the same effect was observed using MacOSX, Linux32 and Solaris10). Without setting "doublebufferflag" tksurfer's window is not updated. Is there something else we could try? Many thanks in advance, Stefan Am 20.08.2007 um 15:17 schrieb Bruce Fischl: > sorry, I'll maybe Kevin can help > > Bruce > On Mon, 20 Aug 2007, Stefan Vollmar wrote: > >> Dear Bruce, >> >> Am 20.08.2007 um 03:33 schrieb Bruce Fischl: >> >>> try this: >>> setenv doublebufferflag 1 >>> tksurfer ... >> >> On the SunFire T2000 server (Solaris 10) I get: >> >> [...] >> Loading /daten/share/opt/freesurfer/freesurfer/surface_labels.txt >> surfer: ### redraw failed: no gl window open >> surfer: single buffered window >> Window type not found! >> surfer: failed, trying double buffered window... >> [...] >> >> resulting in a blank graphic's window. >> >> We tried >> doublebufferflat=0 >> and >> doublebufferflat=1 >> but did not see any difference - and this is odd. >> >> Using "env" after the tksurfer call we made sure that indeed this >> variable was correctly set. I assume, there should be a difference? >> >> Many thanks in advance, >> Stefan >> -- Dr. Stefan Vollmar, Dipl.-Phys. Max-Planck-Institut für neurologische Forschung Gleuelerstr. 50, 50931 Köln, Germany Tel.: +49-221-4726-213 FAX +49-221-4726-298 Tel.: +49-221-478-5713 Mobile: 0173-5340707 Email: vollmar(a)nf.mpg.de http://www.nf.mpg.de

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mri_watershed problem
by Cameron Ellis 21 Aug '07

21 Aug '07

Hi everyone, I am trying to output bem surfaces using mri_watershed and I receive badly distorted surfaces. During the autorecon process there did not appear to be any errors generated, and the final surfaces look good, it is just in producing the bem surfaces independent from autorecon that errors arise. I am trying to get any information as to why these surfaces would come out distorted and potential correction strategies. Any advice is much appreciated! Cameron

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talairach
by Akram Bakkour 21 Aug '07

21 Aug '07

Hi, Is the talairach read differently in std and in dev? When I check the talairach on a single subject using tkmedit $s brain.mgz -main-transform talairach.xfm it looks different if I'm in dev vs std. so for example: setenv $SUBJECTS_DIR /space/banzai/3/users/efenster/OFRR_processing source /usr/local/freesurfer/nmr-std-env tkmedit OFRR78 brain.mgz -main-transform talairach.xfm it looks right vs source /usr/local/freesurfer/nmr-dev-env tkmedit OFRR78 brain.mgz -main-transform talairach.xfm which looks different. Is the dev today what is going to become std (stable4) tomorrow? Thanks! Akram. -- Akram Bakkour Gerontology Research Unit 149 13th Street, Suite 2691 Charlestown, MA 02129 tel: 617-726-5571 fax: 617-726-5760 web: http://www.dickersonlab.org

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