Freesurfer September 2004

freesurfer@nmr.mgh.harvard.edu

19 participants
20 discussions

edits not effective
by Kevin DeSimone 09 Sep '04

09 Sep '04

i have a subject (who is not out of the ordinary) where the cerebellum is sticking to one hemisphere. i make the usual edits on the segmentation, and indicate the coordinates for the cutting planes to rid myself o the cerebellum. i then save everything and re-run the create surface program. nothing happens! literally nothing happens, my edits still appear in the wm volume, but looking at the filled volume, it looks like nothing is even affected. in addition, the surfaces don't seem to have been altered. what's going on?

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edits not effective
by Kevin DeSimone 09 Sep '04

09 Sep '04

not certain what talairach.xfm does to the brain. will it just rotate, translate of my brain to match the location of the average brain--or will it change shape to match the average? we'd like to keep the shape of our brain, and not warp it to a standard space. i.e., will xfm warp the brain?

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edits not effective
by Kevin DeSimone 09 Sep '04

09 Sep '04

evelina et al -- The subject's brain has not been transformed to talairach space. The logs say talairach.xfm not found (ignored). I input "volume indices" for the cutting planes. Am I doing anything wrong?

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still getting up and running...
by Daniel Schwartz 09 Sep '04

09 Sep '04

I've tried to install tiff-v3.6.1.tar.gz (from libtiff.org) and jpegsrc.v6b.tar.gz (from freshmeat.net/projects/libjpeg) Unfortunately, I don't have enough solid UNIX (or programming) background to get them to install correctly on my machine (G5 OSX Panther). Is there anyone who would be willing to take a second to write some general (or specific) instructions on how to get Freesurfer, Fink, libtiff, and libjpeg to work together and be friends? Is there a fink package that includes the libs I need? In what order do I need to install and configure the Fab Four? I'm willing to junk it all, reload my OS, and start over. Thankou so much for everyone's help, and quick replies... I'd be lost without you. -Daniel Daniel Schwartz, CIC Functional Brain Imaging Lab Oregon Health & Sciences University 3181 SW Sam Jackson Pk. Rd. Portland, OR 97239 (503) 494-6494

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flattening produces invisible flatmap and viewcuts surfaces
by Kevin DeSimone 08 Sep '04

08 Sep '04

hi -- i've been running into a problem w/ one of my surface reconstructions... i've run the subject through all the processing steps leading up the cutting and flattening. when i make my cuts, i save the new surface as ?h.full.3d i then run the flatten surface program via the csurf GUI. the process, though, takes only ~10mins, finishing w/o any error messages that i can detect. problem is, when trying to view my flattened surface the tksurfer window is empty. additionally, i can no longer see my inflated surface + cuts (viewcuts surface). i think i've run into a similar problem b/f (except for the brief processing time) and solved it by using the zoom in the tksurfer window. that doesn't seem to be the case now, though. anyone know what's going on? i've included a .txt of the log as recorded in the csurf GUI.

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getting up and running...
by Daniel Schwartz 08 Sep '04

08 Sep '04

Hello all. I'm having a problem using mri_normalize... when I run the program, it says that it can't find libtiff.3.dylib in root folder /sw. I found "fink" on the web which, when decompiled, creates /sw and a ton of libraries, but still no libtiff.3.dylib. I assume that this is part of an image processing toolbox somewhere (tiff?), but I can't find it for the life of me. Anybody got any ideas? Have I somehow completely skipped an integral part of the installation process? Thankyou -Daniel Daniel Schwartz, CIC Functional Brain Imaging Lab Oregon Health & Sciences University 3181 SW Sam Jackson Pk. Rd. Portland, OR 97239 (503) 494-6494

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tkmedit bug
by Ketwaroo, Gyanprakash Avinash 07 Sep '04

07 Sep '04

Hi, I have encountered a problem with tkmedit. I loaded in a .bfloat volume and then attempted to load in a main surface. However, every time I do so, tkmedit crashes with a segmentation fault. Below are the contents of the .xdebug_tkmedit file. tkmedit started: Fri Sep 3 13:50:55 2004 tkmedit -f _000.bfloat $Id: tkmedit.c,v 1.220 2004/08/12 21:29:40 kteich Exp $ $Name: $ Set user home dir to /autofs/homes/009/avinash/Vol2Vol Set subject home dir to _000.bfloat Using interface file /space/lyon/1/fsdev/freesurfer_dev/lib/tcl/tkmedit.tcl Tcl: Successfully parsed tkmedit.tcl Tcl: Successfully parsed tkm_functional.tcl Segfault Creating surface xDebug stack (length: 3) 02: LoadSurface( iType=0, isName=/homes/9/avinash/projdist/falhneg1.w ) 02: Creating surface 01: main() 01: Entering main loop 00: 00:

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holes in the surface
by Goldman, Aaron (NIH/NIMH) 03 Sep '04

03 Sep '04

Hi, I'm trying to do surface-based cross-subject analysis on a quite large group of participants, but I've been having unexpected problems with holes remaining on the finished surface. They aren't detected with euler's number, but they create problem areas when I try to convert the surfaces to a standard mesh using another program (SUMA), and produce visible distortions on the sphere.reg. When I go back to freesurfer, I can find the holes by opening the sphere and zooming in on the problem area, and as far as I can tell it usually turns out to be a single voxel causing the problem, rather than a large area that should have been manually edited. Is there any automated way to correct these defects with freesurfer, since trying to manually fix them would be extremely inefficient? Thanks. -Aaron- PS - I have some jpeg examples I can send if it would be helpful, but didn't attach them because of the list's limitation on email size. Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: <mailto:aarong@mail.nih.gov> aarong(a)mail.nih.gov

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Running freesurfer remotely
by Nate Delage 02 Sep '04

02 Sep '04

Hi, After getting freesurfer to run smoothly on my Debian Linux computer, I have been trying unsuccessfully to run freesurfer remotely. Some solutions work, although *very* slowly (just the 3D rendering portion is slow). For example freesufer will run, and render OK on another Linux client, or the Starnet X-Win32 MS Windows based X server, but so slowly it is unusable. I can run glxgears remotely with reasonable speed (at least on the Linux client) so GLX seems to be working, but running freesurfer remotely is too slow to be considered useful. I have tried a number of things, such as checking my GLX extensions and using the tksurfer.static binary and trying a GLX enabled VNC server. None of these have improved the speed at all. I'd like to hear the groups experiences with running freesufer remotely. Does anyone do this on a regular basis? What method to you use? Are you satisfied with the performance? Does anyone have a tricks needed to accomplish this? Or is freesufer really meant to be run locally? Please share any experience you've had. Thanks! -Nate Delage Vous manquez despace pour stocker vos mails ? Yahoo! Mail vous offre GRATUITEMENT 100 Mo ! Créez votre Yahoo! Mail sur http://fr.benefits.yahoo.com/ Le nouveau Yahoo! Messenger est arrivé ! Découvrez toutes les nouveautés pour dialoguer instantanément avec vos amis. A télécharger gratuitement sur http://fr.messenger.yahoo.com

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*h.thickness and labels mismatch
by Irina Sigalovsky 02 Sep '04

02 Sep '04

Hi, I created some anatomical labels in tksurfer (on individual brain) and now I am trying to get statistics from *h.thickness files (e.g., mean) from the same individual for a particular label using matlab. Somehow, the number of points in *h.thickness file (always on the right side, for some reason) is smaller than max index in the label (sometimes by as much as ~2000). I use read_curv to read in thickness file and read_label to read in the label. Thanks. Irina

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Freesurfer September 2004