Re: [Freesurfer] mri_convert orientation problem
Hi Aaron, does the file.img have an accompanying file.mat? This defines what's left and right. If so, where did it come from and do you think it's right? There are no options in mri_convert to flip LR, but you can specify the direction cosines on the command-line with something like: -iid x_r x_a x_s -ijd y_r y_a y_s -ikd z_r z_a z_s where -iid refers to the direction of the columns (ie, perpendicular to the plane formed by the rows and slices), and x_r x_a x_s are the RAS components of the direction. -ijd is for the rows, and -ikd is for the slices. Having said that, you are generally MUCH (MUCH!) better off making sure that your images come off the scanner with correct geometry information and that that information is correctly propagated through your analysis stream. You can screw things up badly trying to fix the geometry somewhere along the way. The image geometry is extremely confusing and non-intuitive, and you just cannot afford to have an LR flip in this business. OK, I'm off my soap box. doug ps, you can also run mri_info file.img To get info about the geometry. It will print out a bunch of stuff, among which will be the voxel-to-ras transform, an example of which is below. voxel to ras transform: -3.1250 0. 0. 101.2500 0. -3.1250 0. 113.6170 0. 0. 5.5000 -42.2911 0. 0. 0. 1. On Wed, 10 Nov 2004, Goldman, Aaron (NIH/NIMH) wrote: Hi, I'm planning to use mri_convert to convert a large number of analyze images into COR format. To test the orientation, I first ran the command on an image with a pill marking the right side. When I did this, the resulting COR files were reversed in the left-right dimension (in tkmedit, the r coordinates got lower as I moved the cursor towards the side with the pill, and when I ran recon-all stage1, the side with the pill was created as the left-hemisphere surface). What option should I add to the mri_convert command to correct the left right orientation? Right now, I'm using: mri_convert --in_type analyze subj/mri/orig/file.img subj/mri/orig Thanks, -Aaron- Aaron L. Goldman Post-Bacc IRTA Genes, Cognition and Psychosis Program, NIMH Building 10, Room 3C108 Phone: (301) 435-0944 Email: mailto:[EMAIL PROTECTED] [EMAIL PROTECTED] -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] functional overlay
Hi all, If someone can give me help, it would be greately appreciated. in csurf GUI, I choose New Functional, and I give it a name. (1) The name is entirely new for analysis or is it the directory that contains functional scan. If I give it a name, it asks for Now, locate the single subject directory that matches this functional scan (2) Is it the structural scan direcotory or the directory that includes the actual functional scan image, or something other? Nam. ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Problems installing freesurfer on Mac OS X (Darwin)
If you launch tixwish, can you then type the following command and get
this result?
% info commands tix
tix
%
Try commenting out the line in csurf tht calls tixwish4.1.7.4 and
replacing it with the following:
exec tixwish $0 ${1+$@}
On Thu, 11 Nov 2004, Catherine Schevon wrote:
Hi,
I have been trying to get freesurfer installed on my Mac, and ran into a
problem getting csurf to run. I figured out to put the correct path to
tclsh into csurf (it's in /usr/bin, not /bin), but now I get an error
message:
$ tcsh
% source fs_setup
Setting up enviroment for FreeSurfer/FS-FAST
$ Id: FreeSurferEnv.csh,v 1.3 2003/08/05 19:19:16 kteich Exp $
FREESURFER_HOME /freesurfer
FSFAST_HOME /freesurfer/fsfast
AFNI_DIR/freesurfer/afni
FSL_DIR /freesurfer/fsl
SUBJECTS_DIR/freesurfer/subjects
WARNING: /freesurfer/afni/Darwin does not exist.
WARNING: /freesurfer/fsl/bin does not exist.
[mccec-061135:/freesurfer] cschevon% csurf
tix not found--setenv problem?
%
Also, I notice that the tixwish command doesn't seem to execute when it's
run from csurf, although it does create a window when I run it from the
command line.
Any suggestions would be most welcome!
Cathy
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Kevin Teich
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Re: [Freesurfer] functional overlay
Hi Nam, what format are your functional data in? You should be able to load them directly in tksurfer using file-load functional overlay. cheers, Bruce On Thu, 11 Nov 2004, Joongnam Yang wrote: Hi all, If someone can give me help, it would be greately appreciated. in csurf GUI, I choose New Functional, and I give it a name. (1) The name is entirely new for analysis or is it the directory that contains functional scan. If I give it a name, it asks for Now, locate the single subject directory that matches this functional scan (2) Is it the structural scan direcotory or the directory that includes the actual functional scan image, or something other? Nam. ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list [EMAIL PROTECTED] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
