Dear FreeSurfer experts,
Really sorry for send my queries again (please see below). Could you please kindly offer us some advices in dealing with semi-inflated surface?
Many thanks in advance and kind regards, Zixuan
From: Zixuan Yang Sent: Monday, 2 June 2014 6:10 PM To: 'freesurfer@nmr.mgh.harvard.edu' Cc: Jiyang Jiang Subject: Queries about semi-inflated surface for overlay
Dear Freesurfer experts,
I would like to overlay the significance map and gamma.mgh map from cortical thickness GLM on a semi-inflated surface according to one previous post in the mailing list (shown as below) by using the command (shown) under the directory of fsaverage.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-November/012445....https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2009-November/012445.html
mris_inflate -n <steps> lh.white lh.partially_inflated
My questions are:
1) Is it right to generate semi-inflated surface under fsaverage file? Or, I need to generate a semi-inflated surface for each subject (n>500) and make an average surface? How?
2) I tried different 'n', the new generated surface while n=5, 10 or 55 didn't look different at all! Is this normal? It did look very different from lh.white though.
3) Why the generated surface can only be open using tksurfer toolbox, but not a similar command like below?
tksurfer fsaverage lh inflated -overlay ./directory_path/gamma.mgh
Many thanks for your attention and looking forward to your answers.
Best regards, Zixuan
-- Zixuan YANG
Ph.D candidate Centre for Healthy Brain Ageing (CHeBA) School of Psychiatry, UNSW Medicine NPI, Euroa Centre, Barker Street, Randwick NSW 2031 AUSTRALIA T: +61 (2) 9385 0427 W: www.cheba.unsw.edu.auhttp://www.cheba.unsw.edu.au/ E: z.yang@student.unsw.edu.aumailto:s.reppermund@unsw.edu.au ______________ Mailing address: University of New South Wales Randwick Campus, Building R1f 22-32 King Street, Randwick NSW 2031 Australia
Hi Zixuan
didn't I answer this? If you run
mris_inflate -w 1 -scale 1 lh.white lh.white_inflated
it will save snapshots at every iteration and you can pick how inflated you want it.
cheers Bruce
On Wed, 4 Jun 2014, Zixuan Yang wrote:
Dear FreeSurfer experts,
Really sorry for send my queries again (please see below). Could you please kindly offer us some advices in dealing with semi-inflated surface?
Many thanks in advance and kind regards,
Zixuan
From: Zixuan Yang Sent: Monday, 2 June 2014 6:10 PM To: 'freesurfer@nmr.mgh.harvard.edu' Cc: Jiyang Jiang Subject: Queries about semi-inflated surface for overlay
Dear Freesurfer experts,
I would like to overlay the significance map and gamma.mgh map from cortical thickness GLM on a semi-inflated surface according to one previous post in the mailing list (shown as below) by using the command (shown) under the directory of fsaverage.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2009-November/012445....
mris_inflate -n <steps> lh.white lh.partially_inflated
My questions are:
1) Is it right to generate semi-inflated surface under fsaverage file? Or, I need to generate a semi-inflated surface for each subject (n>500) and make an average surface? How?
2) I tried different ‘n’, the new generated surface while n=5, 10 or 55 didn’t look different at all! Is this normal? It did look very different from lh.white though.
3) Why the generated surface can only be open using tksurfer toolbox, but not a similar command like below?
tksurfer fsaverage lh inflated -overlay ./directory_path/gamma.mgh
Many thanks for your attention and looking forward to your answers.
Best regards,
Zixuan
--
Zixuan YANG
Ph.D candidate Centre for Healthy Brain Ageing (CHeBA)
School of Psychiatry, UNSW Medicine
NPI, Euroa Centre, Barker Street, Randwick
NSW 2031 AUSTRALIA
T: +61 (2) 9385 0427
W: www.cheba.unsw.edu.au
E: z.yang@student.unsw.edu.au
______________
Mailing address:
University of New South Wales
Randwick Campus, Building R1f
22-32 King Street, Randwick NSW 2031
Australia
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Zixuan Yang