[Freesurfer] Tksurfer

Hi, I'm trying to launch tksurfer with the command tksurfer average7 rh inflated and I'm getting the error message below. I get this message on machines ventzl and nebech. The tksurfer window pops up, but the toolbar is blank. Does anyone know what might be wrong? Thanks! Katy Tix_Init fail

[Freesurfer] center values

Hi all, I'm trying to find the anatomical center value of the image volume in the mni average_305 space. Any ideas? -Tracy Wang Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130

[Freesurfer] mris_euler_number

Hi, I am running the command recon-all -subjid SM2C4_autoreconall -autorecon2 on troy, with subjects directory being /space/troy/1/users/FREESURFER. I just got this error message, which I have never gotten before: - Euler Number rh Fri Sep 9 02:03

Re: [Freesurfer] mris_euler_number

Margaret, I think you may just need to open a new terminal and re-'source' your freesurfer environment. I've confirmed that mris_euler_number exists on machine 'troy'. You have a Fedora Core 2 Linux machine, and last night a switch was made to run the Red Hat 9 build on FC2 machines, which sho

[Freesurfer] mri_normalize

I am still having problems with mri_normalize. I have downloaded the latest snapshot- but I still get an error: [EMAIL PROTECTED] mri]$ mri_normalize orig.mgz T1.mgz reading from orig.mgz... normalizing image... talairach transform 1.103 0.048 -0.007 -4.504; -0.051 1.166 0.004 -13.012;

Re: [Freesurfer] segmentation fault during make_average_surface Hello Nick, Thanks for your reply, here are the info: mris_make_average_surface -all-info ProgramName: mris_make_average_surface Progra

Hello Nick, Thanks for your reply, here are the info: mris_make_average_surface -all-info ProgramName: mris_make_average_surface ProgramArguments -all-info ProgramVersion $Name: $ TimeStamp: 05/09/09-07:09:31-GMT CVS: $Id: mris_make_average_surface.c,v 1.9 2004/01/29 14:59:12 tosa Exp $ Use

Re: [Freesurfer] center values

mri_info should tell you. Bruce On Fri, 9 Sep 2005, Tracy Wang wrote: Hi all, I'm trying to find the anatomical center value of the image volume in the mni average_305 space. Any ideas? -Tracy Wang Tracy Wang Research Assistant Cognitive Neuroscience Laboratory Washington University Dep

Re: [Freesurfer] mri_normalize

Hi Sasha, can you do: mri_info orig.mgz and send us the results? thanks, Bruce On Fri, 9 Sep 2005, Sasha Wolosin wrote: I am still having problems with mri_normalize. I have downloaded the latest snapshot- but I still get an error: [EMAIL PROTECTED] mri]$ mri_normalize orig.mgz T1.mgz rea

Fwd: Re: [Freesurfer] mri_normalize

Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 --- Begin Message --- OK, this time it worked: [EMAIL PROTECTED] /freesurfer]# cd $SUBJECTS_DIR/2332/mri [EMAIL PROTECTED] mri]# ls aseg filled

Re: [Freesurfer] mri_normalize

I haven't conformed it, so I'll try that- thanks. -Sasha >>> Bruce Fischl <[EMAIL PROTECTED]> 9/9/2005 3:42 PM >>> Hi Sasha, the problem is that the orig.mgz volume hasn't been "conformed". Did you generate it with recon-all? It should be 1mm isotropic, 256mm^3 and UCHAR instead of SHORT. You c

[Freesurfer] resampling talairach

Hi all, I'm trying to resample an image into a talairach transformed volume from the 256^3 dimensions into 172 x 220 x 156. I've been using mri_convert in the following command line: mri_convert -at transforms/talairach.xfm --devolvexfm 000718_vc4734 -cs 1 -oc -0.0950 -16.51 9.75 -ic 0 0 0 -oic 1

Re: [Freesurfer] resampling talairach

If you have a template volume with the geometry you want, you can try: --like templatevol Tracy Wang wrote: Hi all, I'm trying to resample an image into a talairach transformed volume from the 256^3 dimensions into 172 x 220 x 156. I've been using mri_convert in the following command line

[Freesurfer] Skull stripping

Hi all, Couple of questions re: failures of skull stripping" - If you edit the brain volume after autorecon1, do you need to re-run autorecon1 again, or van you just continue on to autorecon2? - Is it a major problem if the strip removes the cerebellum, since it's excluded by the cuttting planes

Re: [Freesurfer] Skull stripping

Hi Alex, if the strip removes the cerebellum, then the aseg stuff will fail (if you're using it). If you aren't it doesn't really matter. cheers, Bruce On Sat, 10 Sep 2005, Fornito, Alexander wrote: Hi all, Couple of questions re: failures of skull stripping" - If you edit the brain volume

RE: [Freesurfer] Skull stripping

Hi Alex, Since autorecon2 uses the brain volume as the first input, there is no need to re-run anything after editing the brain volume following autorecon1. Jenni -Original Message- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Fornito, Alexander Sent: Friday, September

RE: [Freesurfer] Skull stripping

Does it affect the aseg with respect to the GCA registration? Is so, how perfect does the strip need to be to avoid biasing the aeg results, eg., are small portions of the meninges or skull around the top of the cortex going to affect the results much? I now they can affect the pial surface, bu