Bastion,
Hi, I'm a bit late in this reply. You can use 'mris_info lh.white.gii'
to display the matrices in that file. The one labeled 'FS_VOLGEOM_RAS'
is the one that will register the surface with the orig.mgz volume file.
Note that it will always be three numbers (c_r, c_a, c_s) which just
shi
Problem solved!
took some effort trying everything out, but finally found a simple
solution by transforming everything into MNI
Here's how to convert from surface RAS to mni305
mni305ras = X*S*inv(K)*ras
X = talairach.xfm
S = scanner vox2ras (mri_info --vox2ras orig.mgz)
K = tkreg vox2ras (mri_i
Hi Nick,
again thank you your help! That works nicely.
Where to I find the transformation matrix to register my structural
volume data to the gii. surface file?
I found two matrices in the lh.white.gii (), but not sure
if it fits.
I have to use the volume scan and gii suface in matlab for
local
Bastian,
Are you using freeview to display the surface? If so, you will need to
get the newest freeview.bin, which is here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/freeview/linux_centos6_x86_64/
this has been updated to read the new volume geometry info now included
in the lh.white
Hi,
Ok, thank you!
One additional follow up:
Once I converted the lh.white (freesurfer) to the lh.white.gii
(gifti), the converted surface (.gii) does not fit on the structural
scan from freesurfer anymore (neither brain.mgz or orig.mgz or
nu.omz).
How can I register my freesurfer structural da
Hi Bastian
do you mean a surface that is only a piece of th original surface? You can
use label2patch for that, but I'm not sure if we can convert patches to
gifti. You should ask the FSL crew about label2surf though - we can't help
with that.
cheers
Bruce
On Thu,
29 May 2014, Bastian Cheng
Hi Nick,
That works PERFECTLY! Thank you so much, it has been a big help!
I hope I may ask you another question:
I am actually trying to convert each freesurfer-label (from
aparc.annot) into separate surfaces (not gifti-labels)
So ideally I would convert lh.precentral.label > lh.precentral.gii.
Bastian,
Hi, I've posted a new mris_convert which should solve the problem for
you. It's built for Centos 6, so if you need it for another platform,
let me know. It's here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/linux-centos6_x86_64/
Nick
On Wed, 2014-05-28 at 11:42 +0200
Dear Freesurfer-Experts,
I would like to create gifti-surfaces to use in matlab.
That's what I am doing so far (latest FS-Version):
mris_convert lh.white lh.white.gii
I then try to open it using the "gifti" command (g=gifti('file.gii'))
(http://www.artefact.tk/software/matlab/gifti/)
however,
