Best,

-SG

Hi Seung-Goo

I would have that that your command line would work as is. Can you send us the full screen output?
cheers
Bruce
On Fri, 16 Oct 2015, Seung-Goo KIM 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