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