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 172 -ojc 220 -okc 156 -odt uchar nu nu_talairach_new3.img
It ran very nicely, but the anterior and posterior (frontal and occipital) regions are cut off, like they were cropped off. I suspect it is because data is being conformed to 256^3 in all directions and is just cropping to fit into my specified dimensions, but that is not what i would like to do. How would I be able scale it to fit into my specified dimension? I have tried -sc, but no matter how much smaller i seem to scale it, it's not enough to compensate for the crop.
thanks for any help! Tracy Wang
Tracy Wang Research Assistant Cognitive Neuroscience Laboratory
Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang@artsci.wustl.edu
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:
mri_convert -at transforms/talairach.xfm --devolvexfm 000718_vc4734 -cs 1 -oc -0.0950 -16.51 9.75 -ic 0 0 0 -oic 172 -ojc 220 -okc 156 -odt uchar nu nu_talairach_new3.img
It ran very nicely, but the anterior and posterior (frontal and occipital) regions are cut off, like they were cropped off. I suspect it is because data is being conformed to 256^3 in all directions and is just cropping to fit into my specified dimensions, but that is not what i would like to do. How would I be able scale it to fit into my specified dimension? I have tried -sc, but no matter how much smaller i seem to scale it, it's not enough to compensate for the crop.
thanks for any help! Tracy Wang
Tracy Wang Research Assistant Cognitive Neuroscience Laboratory
Washington University Department of Psychology, Campus Box 1125 One Brookings Drive St. Louis MO 63130-4899 314-935-5019 twang@artsci.wustl.edu
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