That is on if the outputs of the default freesurfer
analysis pipeline. Did you run recon-all --all yet?
Peace,
Matt.
From: FSL - FMRIB's
Software Library [mailto:[log in to unmask]] On
Behalf Of Iwo Bohr
Sent: Wednesday, May 27, 2009 7:04
AM
To: [log in to unmask]
Subject: [FSL] brainmask.mgz - how
to produce for Freeesurfer ?
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?
School of Computing Science
Share your photos with Windows Live Photos – Free. Try it
Now!