Hi Qiongmin
1. I think this is a bug in the open GL code that is outside of our
control. We will try to track it down
2. The flat maps aren't really any different than say the inflated
fsaverage surface. If you can generate group (or individual maps) in
fsaverage space you can display them on the flat maps.
3. The index of each vertex in the flattened space is stored in the patch
files so you can always look up what vertex it was on inflated, sphere,
etc...
cheers
Bruce
On Mon, 26 May 2014, Caka
wrote:
Dear Bruce, Doug and all,
Thanks for your suggestion, it helped a lot.
(1) I load the fsaverage surface (lh.inflated) in tksurfer, and then load
the fsaverage patch (lh.cortex.patch.flat). The flat map was shown for
several seconds, and then an error occurred and tksurfer was shut down. The
terminal said: ‘tksurfer.bin:tnl/t_vertex.c:407: update_input_ptrs:
Assertion ‘a[j].inputstride == vptr-> stride’ failed. Abort(core dumped)’.
Could you give me some advice?
I use a 'CentOS release 6.2' system. The freesurfer is
‘freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0’.
(2) Indeed, I want to flatten all cortical thickness surfaces of 140
subjects onto the ‘lh.cortex.patch.flat’ of fsaverage. I just don’t
understand your idea how to do this. After I load ‘lh.cortex.patch.flat’ of
fsaverage, the tksurfer only shows this flat map (now it lasted for several
seconds and crashed), so how can I ' load whatever overlay you want in the
same way you would on the inflated surface’?
Does it mean that I load the individual flat map on the individual inflated
surface? But I haven’t got the individual flat map yet.
(3) I am wondering if there are some table recording the transformation
relationships between the fsaverage surface vertices and the flat map
vertices? If so, then I think all I need to do is extracting the cortical
thickness value of every vertex in individual inflated surface, and then
putting into the corresponding vertex in the flat map.
Thank you very much!
Best regards,
Qiongmin
---------------------------------------------------------------------------
----------------------------------------------------------------------
Load the fsaverage surface in tksurfer (say lh.inflated) then load the patch
we distribute with fsaverage (I think it's called something like
lh.cortex.patch.flat) with file->load patch. Then load whatever overlay you
want in the same way you would on the inflated surface
Cheers
Bruce
On May 19, 2014, at 10:06 PM, Caka <qiongmin...@gmail.com>
wrote:
Hi Doug,
Thanks for your suggestion on tksurfer, it works.
I would like to map all the subjects into a flat map because I
am curious about the 2-D thickness patterns between different
groups. I think there will be some distinctions.
But if I flatten fsaverage, how can I map everyone?s 3D surface
onto the fsaverage?s 2D map? Is there a command?
Best,
Qiongmin
On 05/13/2014 11:19 PM, 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)?.
Try tksurfer fsaverage lh inflated -aparc -overlay
sub001-thickness-lh.mgz -fminmax .01 4
(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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I don't think so, though I think bruce was working on something.
You
could just flatten fsaverage and then map everyone to fsaverage
(as you
have already done). Why do you want to map everyone to a flat
map?
doug
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