Re: [Freesurfer] mri_convert with --like and -rt options

-- Seung-Goo KIM > On 2015-10-16, at 10:01, Seung-Goo KIM solleo@gmail.com wrote: > > Dear all, > > I wish to know whether mri_convert provide a nifty way to reslice and crop a NIFTI image with labels (positive integers) with “—like” and “-rt” options. It seems like “—like” option overrides “-rt” option, thus the result from such a command: > >> mri_convert -rt nearest —like ${referenceImage} ${inputImage} ${outputImage} > > > is resampled with trilinear interpolation. I don’t know if I did something wrong (maybe file format?) or this is a bug in mri_convert. > > Of course, one can write a script that creates binary images for each label values, transforms it (using "mri_convert —like"), threshold it (like value>0.1), and finally finds the label with the highest value (probability) for each voxel in the reference space. But I believe there should be a simpler and faster way to do this with mri_convert or any other program in freesurfer :) > > FIY, the version of freesurfer package I use is "Linux-centos6_x86_64-stable-pub-v5.3.0”. > > Best regards, > -- > Seung-Goo KIM >