And macaque_25_model-MNI.nii is the non-binary image? And macaque_stripped_mask.nii.gz is the binary mask? If so, the command looks right to me.
doug

On 12/30/13 12:08 PM, Caspar M. Schwiedrzik wrote:

Hi Doug,
this is the command line input:
mri_mask macaque_25_model-MNI.nii macaque_stripped_mask.nii.gz macaque_stripped_final2.nii
this is the terminal output:
DoAbs = 0
Found 14652800 voxels in mask
Writing masked volume to macaque_stripped_final2.nii...done.

The same thing happens when I use nii.gz or mgz files.

Caspar

2013/12/30 Douglas Greve <greve@nmr.mgh.harvard.edu>

what is your command line and terminal output?

On 12/30/13 10:22 AM, Caspar M. Schwiedrzik wrote:

Hi Freesurfer Experts,

I am trying to apply a mask that I made with FSL's bet to a NIFTI file that I got from someone else.

The mask looks fine, the NIFTI file is in float format, does not contain NaNs or negative values, but the overall values are all pretty low (in the 40ies). When I try to apply the mask to the NIFTI file using mri_mask, the output I get is essentially a copy of the mask (only zeros and ones). The same happens if I use fslmaths.

Any advice would be very much appreciated.

Thanks, Caspar

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