Dear FSL-Freesurfer experts,
I would like to use Freesurfer to segment functional time series images.
To do so, first I have to register example_func.nii to anatamical using routine:
reg-feat2anat
however I can't run it, since I don't have this mask file, the complain is as follows:
FeatDir is 1_Left+.feat
template volume is 1_Left+.feat/example_func.nii.gz
ERROR: cannot find brainmask for test
How can I produce this mask? I thought that following the tutorial on FLIRT will help me , but the mask produced by FLIRT:
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http://www.fmrib.ox.ac.uk/fslcourse/lectures/practicals/reg/index.html:
Standard-space masking - a useful application
Now let's use a saved FLIRT transform to mask out the ventricles, cerebellum and brain stem in example_func, using a crude standard-space mask which excludes those regions.
The registration from example_func to the standard-space template has already been done and is saved as exfunc2std.mat. We want to take this matrix and transform a standard-space mask to the functional space.
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The description above sounds like the relevant procedure, but did not change anything
Can anybody please advice me on this matter?
Iwo Bohr, PhD
School of Computing Science
Newcastle University
UK
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