Try -odt short to stop it from changing the data type to uchar
On Feb 21, 2012, at 12:04 AM, David Grayson <gray...@ohsu.edu> wrote: > Hi freesurfer folks, > > I am using mri_convert to reorient my custom cortical parcellation (a nifti > file generated from an annotation file), and I have run into some unexpected > blips with some seemingly errant reindexing. Here is the command I am using: > > mri_convert -rl FREESURFER/mri/orig/001.mgz -rt nearest > FREESURFER/label/ROIs_custom.nii.gz -nc reorient/ROIs_custom_reorient.nii.gz > > For the most part, this works well for most of the indices. The biggest > problem is that the highest value index (2063) is being completely relabeled > in ‘ROIs_custom_reorient.nii.gz’ with several smaller values in the 20’s > range. But this occurs to a smaller extent with many of the other regions as > well, where small parts of those regions are being relabeled with values > anywhere from 1 to 20. > > Can anyone give me some insight as to what’s up with this and what I might be > able to do to fix it? Thank you very much for any help. > > -David > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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