Hi, I have these analyze files with wrong orientation I can change their orientation using fslswapdim but when I convert them to mgz files using mri_convert, the orientation is wrong again. i tried the following reading from 001.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, 0, -1) j_ras = (1, 0, 0) k_ras = (0, -1, 0) reordering axes... MRIreorder: incorrect dst width error reordering axes
so not sure what i should do, can you please help me on this?
Hi Nurunisa,
is analyze all you have? How do you know left from right? MRIreorder probably wants an isotropic volume with the same image dimensions in the different directions. You can try "conforming" it first and see if the reordering works then. I would be *very* careful about left/right swaps though.
cheers, Bruce
On Wed, 24 Oct 2007, Nurunisa Neyzi wrote:
Hi, I have these analyze files with wrong orientation I can change their orientation using fslswapdim but when I convert them to mgz files using mri_convert, the orientation is wrong again. i tried the following reading from 001.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, 0, -1) j_ras = (1, 0, 0) k_ras = (0, -1, 0) reordering axes... MRIreorder: incorrect dst width error reordering axes
so not sure what i should do, can you please help me on this?
You can try using the --in_orientation in mri_convert (see help). You can try various strings until it looks right in tkmedit. Though, as Bruce points out, you still won't know whether you got left and right correct.
doug
On Wed, 24 Oct 2007, Nurunisa Neyzi wrote:
Hi, I have these analyze files with wrong orientation I can change their orientation using fslswapdim but when I convert them to mgz files using mri_convert, the orientation is wrong again. i tried the following reading from 001.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (0, 0, -1) j_ras = (1, 0, 0) k_ras = (0, -1, 0) reordering axes... MRIreorder: incorrect dst width error reordering axes
so not sure what i should do, can you please help me on this?
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Doug Greve -
Nurunisa Neyzi