Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30053 discussions

Update for mris_register
by Kevin Teich 16 Sep '04

16 Sep '04

There is an updated version of mris_register available for download. Darwin: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Darwin.tar… Linux: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/mri_watershed-20040407-Linux.tar.… Download the tarfile and expand it in your FREESURFER_HOME/bin/OS/ directory. -- Kevin Teich

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mris_reverse
by Rutvik Desai 15 Sep '04

15 Sep '04

We need to L-R flip our surface data. I found a mention of mris_reverse in the mail archive and it appears that this program can do this, but it is not in the distribution we have. Is there a way to get it? There is no need for the flipped surfaces to be aligned to the volume; we just need the surfaces to look like they are from the other side. thanks, Rutvik

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Fw: Freesurfer new release
by F.Musso 15 Sep '04

15 Sep '04

Hi to all, On the Freesurfer homepage I notice that via 'ftp' it's avaliable a new version of Freesurfer x Linux (26.08.2004). But there's nothing about it neither on the mail list nor on the homepage... It's just a 'beta' version? Cheers Francesco Musso MD Laboratory of Molecular Neuroimaging & Electrophysiology, Department of Psychiatry, Johannes Gutenberg-University, Mainz, Germany

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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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