Why are you going thru those afni cmds? If the original data are in dicom, then they should have the correct geometry info, and mri_convert should orient them correctly. As for the resolution, try running recon-all (or mri_convert) with the -cm option.
doug
Faden, Eric (NIH/NIMH) [F] wrote:
I have scans that are at .8 and .5 resolution as dicoms. Currently I am using to3d to rotate the images to the proper orientation. After that I have tried using 3drefit -xdel 1.0 -ydel 1.0 -zdel 1.0 to "resize" the image so that mri_convert doesn't resample the image, but this is also messing up the statistics for obvious reasons. Is it reasonable to just multiply the statistics by .512 (.8 ^ 3) and .125 (.5 ^ 3)? or how else can I prevent freesurfer from resampling my images to 1.0 resolution?
-Eric
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