The fslcpgeom command does not do any registration or alignment - that
is done by flirt or fnirt. All it does is copy the geometry
qform and pixdims) from one image to another. However, if the two
have a different number of voxels then the destination image is
sounds like this might be the case for you. If you simply want to
an image to a different size then you should use flirt with the -
Note that in order to check if the image is zero or not, use fslstats
with the -R
option as this will display the range of intensities that are present.
All the best,
On 5 Jan 2009, at 20:13, Hanie Elfenbein wrote:
> I used the fslcpgeom command to align my brain mask to the raw data,
> both in
> NIFTI format.
> After the command finished running, I attempted to open the brain
> mask in
> FSL View to check the data.
> Although FSL is registering the presence of non-zero voxels, the
> screen is
> blank behind the cross-hairs. I tried changing the min and max for the
> viewer as well as using different options for the look up table.
> Why might this have happened and what can I do to fix it?
> Thank you for your help