Iwo, this should be produced automatically by FreeSurfer. If you do not
have it, then something probably went wrong with your recon.
doug
Iwo Bohr wrote:
> 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:
>
> ------------------
> 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.
> ---------------------
>
> 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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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