That should not be a problem. Certainly it should not cause everything to go to 1s and 0s. What version of FS are you using? And you say the same thing happens with FSL? Try using mri_convert to convert the nonbinary image to another nifti file and see if you get 1s and 0s. If not, then try that file as input. You can also try fscalc, something like

fscalc input.nii mul mask.nii -o output.nii

should accomplish the same thing

doug

On 12/30/13 1:12 PM, Caspar M. Schwiedrzik wrote:

Hi Doug,
that's correct.

I think the problem is perhaps that the original NIFTI file has a very narrow range of values, between 43.7308 and 43.8476, to cover the whole range of tissues in the image.
It is an average over several subjects, and before skull stripping, there are hardly any zeros in the image.
Is there a way to rescale the file?

Thanks, Caspar

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

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

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.