Hi Doug,
thanks for your input. I turns out that there is some problem when
converting minc to NIFTI with float. I got a hold of the original minc file
and converted it to NIFTI with minc2nii using integer, and now the values
are in a reasonable range and the skull stripping works.
Thanks!
Caspar
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 t
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 th
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_m
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
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
conta
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
