Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30127 discussions

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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cortical thickness stats.
by L.Scheef＠uni-bonn.de 30 Aug '04

30 Aug '04

Dear list members! I would like to analye cortical thickness data and wonder which is the best way to proceed... So far I have processed the data using recon all (including manual top fixing). This includes the registration using the average7 subj. on the sphere. 1) Is it a valid approach to use the coreg. on the average7 or should I take a similar approach as used by VBM building a study specific template and do the coreg step on this template once again. 2) For doing the cortical thickness group analysis (using mris_glm) it seems to be the best to use a specific group average. Is there any "ready to use script" which I could use to build the average_study data and all the stuff needed by mris_glm? 3) Which files should be calculated to use them later for the stat. analysis and overlay? Many thanks for your help! Best wishes, Philppe and Lukas Lukas Scheef, MD, MSc MR-Tomography Department of Radiology University of Bonn Sigmund-Freud-Straße 25 D-53105 Bonn Fax: +49-228-287-5598 Phone:+49-228-287-4496 E-mail: L.Scheef(a)uni-bonn.de

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bert's data
by Daniel Schwartz 27 Aug '04

27 Aug '04

I'm just starting to learn FreeSurfer, and am trying to go through bert's data step by step. When I click "Read Header" in the Setup Structural Scan Parameters, after selecting "COR-.info", it returns "-unset-" in the file type field. When I try this with another data set (mine) it does the same thing. Are the formats the problem? Is this something that I've done wrong? Thankyou for ANY help you can give me... -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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skull striping issue
by camilo 27 Aug '04

27 Aug '04

Hi everyone, I am having problems with the skull striping. I see that there is some skull left on the brain images, and also on the wmfilled images. I tryed, to lower the prefloding height in the RMSkull menu on the expert preferences. It did not work. Then I select the option "Don't use watershed analyze", but agian it did not work. Is there anythig else I can do? Thanks, Camilo

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Freesurfer