Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30055 discussions

Cluster version of FreeSurfer
by Satrajit Ghosh 21 Feb '05

21 Feb '05

Is there a cluster/parallel version of freesurfer available? Thanks, Satra -- Satrajit S. Ghosh Postdoctoral Associate Speech Communication Group Research Laboratory of Electronics, MIT

2 1

new tkmedit and tksurfer
by Wan Park 17 Feb '05

17 Feb '05

I am supposed to have libtiff, glut, tclkt, tix and blt installed, but I still receive this message: for volume: Command Finished /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit 22970 T1 -csurf dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit can't open library: /sw/lib/libtix8.1.8.4.dylib (No such file or directory, errno = 2) Command Finished for surface: Command Finished /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit 22970 T1 -csurf dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit can't open library: /sw/lib/libtix8.1.8.4.dylib (No such file or directory, errno = 2) Command Finished Curiously, I did not have this problems before the new binaries. Do you think that may be a line or it is more about env? thanks! wan

2 1

surface atlas
by Nguyen, Thang Q 16 Feb '05

16 Feb '05

Hello all, I have a question: What atlas freesurfer uses when it parcellates the final surface? If I were using a different atlas for my functional volumes, can I warp the data to the proper atlas? Thank you, Thang Nguyen

2 1

Re: [Freesurfer] new binaries for tkmedit and tksurfer
by Wan Park 16 Feb '05

16 Feb '05

hi kevin, i reinstalled fink and installed the blt package. then i copied the new binaries. now i cannot open the tkedit nor the tksurfer. these are the messages i receive: when i press volume: Command Finished /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit 22970 T1 -csurf dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tkmedit can't open library: /sw/lib/libtix8.1.8.4.dylib (No such file or directory, errno = 2) Command Finished when i press surface: Command Finished env tksurferinterface=csurf patchname= /usr/local/freesurfer_package/freesurfer/bin/Darwin/tksurfer -22970 rh white -tcl /tmp/TmpTclSurf.20719 dyld: /usr/local/freesurfer_package/freesurfer/bin/Darwin/tksurfer can't open library: /sw/lib/libtix8.1.8.4.dylib (No such file or directory, errno = 2) Command Finished any suggestion? thanks a lot, wan On Feb 14, 2005, at 2:15 PM, Kevin Teich wrote: > > Do you have BLT installed via Fink or FinkCommander? > > > On Sun, 13 Feb 2005, Wan Park wrote: > >> hi teich, >> >> i went to this place: >> >> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ >> tkmedit_tksurfer-20050211-Darwin.tar.gz >> >> and I Unziped it in a temp directory, then move bin/tkmedit and >> bin/tksurfer into your freesurfer/bin/Darwin directory, and the >> lib/tcl/* files into freesurfer/lib/tcl. >> >> now when i put: >> >> $tksurfer >> >> i receive this new message: >> >> dyld: tksurfer can't open library: /sw/lib/libBLT.2.dylib (No such >> file or directory, errno = 2) >> Trace/BPT trap >> [ogden:freesurfer_package/freesurfer/subjects] wpark% >> >> how can i solve this problem? >> >> thanks >> >> wan > > -- > Kevin Teich >

2 1

Preparing cortical surface for EEG source localization
by Alex Wade 14 Feb '05

14 Feb '05

I have recently started to use FS to generate cortical surfaces for boundary element modelling in EEG source localization. In particular I would like to use the pial surface generated by FS. I have three problems: 1: I can only get FS to generate individual hemispheres. For the BEM, I need a single, connected, mesh for the entire brain. Is there a way to get this (perhaps by fooling FS into not disconnecting the hemispheres early in the segmentation process)? 2: The white/gray boundary mesh is topologically correct (no bridges / handles / holes etc..). Is the pial surface mesh also correct? 3: Is there a way to generate the volume inside the pial surface? That is - can I flood fill the pial surface in some way to extract the voxels that lie inside it as 3d volume? Many thanks Alex A.R. Wade Ph.D. Associate Scientist The Smith-Kettlewell Eye Research Institute 2318 Fillmore Street San Francisco, CA 94115 tel. 415 345 2083 fax. 309 416 6533

4 3

new binaries for tkmedit and tksurfer
by Wan Park 14 Feb '05

14 Feb '05

hi teich, i went to this place: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/ tkmedit_tksurfer-20050211-Darwin.tar.gz and I Unziped it in a temp directory, then move bin/tkmedit and bin/tksurfer into your freesurfer/bin/Darwin directory, and the lib/tcl/* files into freesurfer/lib/tcl. now when i put: $tksurfer i receive this new message: dyld: tksurfer can't open library: /sw/lib/libBLT.2.dylib (No such file or directory, errno = 2) Trace/BPT trap [ogden:freesurfer_package/freesurfer/subjects] wpark% how can i solve this problem? thanks wan

2 1

Freesurfer MAC OSX Installlation
by willcott＠pop.ruf.rice.edu 11 Feb '05

11 Feb '05

I have downloaded and installed freesurfer-20040218-Darwin.tar.gz with no seeming problems. I modified my .tcshrc file, checked directories and think all is in order. I operate in X11 windows. I still can not find csurf or any work-around. Does anyone have any ideas about my problem? -- M. Robert Willcott 1807 Orchard Country Lane Houston, TX 77062 713.302.5148

4 3

MNI align
by Wan Park 11 Feb '05

11 Feb '05

I think I need to do the MNI align. Could someone teach me how to do this? Thanks, Wan

1 0

about tkmedit
by Wan Park 10 Feb '05

10 Feb '05

after processing the volume, when i try to see the images (orig, T1, brain, wm) with the tkmedit tools, i press coronal view but i see horizontal and when i press horizontal i see the coronal view. when i press sagittal, i see the brain "looking" (face) down. interestingly, after doing the talairach, the coordinates seems to keep the coronal, horizontal and sagittal order as i was in correct order (i discovered this when i try to go to a point where it is supposed to be amygdala and it seemed over the place, but if you "draw o mark" that point in the coronal view on my monitor and change to coronal to sagittal view seems to be correct). any solution? thanks a lot, wan ps: any news with the new binaries for OSX endian issue for the visualization of the parcellation? thanks!

1 0

mri_convert
by Joongnam Yang 07 Feb '05

07 Feb '05

Hi I tried to convert *.img functional data into *.mnc file, using "mri_convert" and when I checked the *.mnc file for functional using "mincinfo", it gave me some "unknowns" for the time dimension. image: signed__ short 0 to 1131 image dimensions: xspace yspace zspace time dimension name length step start -------------- ------ ---- ----- xspace 64 3.8 -121.6 yspace 64 3.8 -121.6 zspace 23 5 -57.5 time 240 unknown unknown Does anyone know a way to specify the time dimension during the conversion using "mri_convert"? Thanks. Nam.

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Freesurfer