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 <gr...@nmr.mgh.harvard.edu
<mailto:gr...@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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