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 0.0000 0.0000 101.2500 0.0000 -3.1250 0.0000 113.6170 0.0000 0.0000 5.5000 -42.2911 0.0000 0.0000 0.0000 1.0000
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:aarong@mail.nih.gov aarong@mail.nih.gov