I am using the command mri_convert -at transforms/talairach.xfm brain.mgz brain_in_tal.nii.gz
to convert a native-space skull-stripped T1 image to talairach space. I used recon-all to generate the transform matrix, and the segmentation and everything look good. But the T1_in_talairach image is not good - the brains are ending up different sizes, and frequently have the posterior chopped off. Please what am I doing wrong? Should I be applying the inverse of the transform?
Helen Beaumont PhD University of Manchester
Try adding -oc 0 0 0 to the mri_convert command line
On 2/2/18 7:27 AM, Helen Beaumont wrote:
I am using the command mri_convert -at transforms/talairach.xfm brain.mgz brain_in_tal.nii.gz
to convert a native-space skull-stripped T1 image to talairach space. I used recon-all to generate the transform matrix, and the segmentation and everything look good. But the T1_in_talairach image is not good - the brains are ending up different sizes, and frequently have the posterior chopped off. Please what am I doing wrong? Should I be applying the inverse of the transform?
Helen Beaumont PhD University of Manchester _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Helen Beaumont