Hi Qiongmin
1) The command you ran resamples the thickness from being a scalar field
over the subject surface to being a scalar field over the fsaverage
surface. If you load fsaverage (say inflated) in tksurfer or freeview you
should then be able to load the overlay onto it.
2) We provide pre-flattened patches named ?h.cortex.patch.flat for
fsaverage so if you have mapped the data there, there is no need to
cut and flatten again
cheers
Bruce
On Wed, 14 May 2014, Caka wrote:
Dear Doug and all,
I have already done two things:
(1) 'recon-all’ to the segmentation for 140 subjects;
(2) surface registration to fsaverage template for 1 subject using:
mri_surf2surf --hemi lh --srcsubject sub001 --srcsurfval thickness --src_type
curv --trgsubject fsaverage --trgsurfval ./sub001-thickness-lh.mgz
Now I have got the 'sub001-thickness-lh.mgz' file.
I have two questions:
(1) Is this 'sub001-thickness-lh.mgz’ a surface file or a volume file? How can
I read it?
I used ‘freeview sub001-thickness-lh.mgz’ to read it, but a dark scene was
shown, nothing can be found.
I also used ‘mris_convert -c $SUBJECTS_DIR/sub001/sub001-thickness-lh.mgz
$SUBJECTS_DIR/sub001/surf/lh.orig lh.thickness.asc’, an error occurred like
‘ERROR: number of vertices in
/disk250/data_analysis/sub001/sub001-thickness-lh.mgz does not match surface
(163842, 132230)’.
(2) After the registration, I want to flatten the surface of curvature or
thickness into a full plane. The wiki says we should first specify 5 vertices
and cut the whole area without the midline region, then ‘kris_flatten’ can be
used. Indeed, this procedure requires quite a lot manually operation. I am
wondering if there are some automatically commands that can do this flatten
projects for 140 subject?
Any reply would be really appreciated!
Qiongmin
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