I see. For thickness you will need both white and pial, and you can use mris_thickness to compute it. The easiest thing to do would be to run recon-all on a subject then replace the surfaces with your own when it has completed (and recompute the thickness) On Wed, 20 Mar 2013, Valtina Pouegue wrote:
Hi bruce, I want cortical thickness, total surface area, instrinsec curvature index and folfing index.
VP
Date: Wed, 20 Mar 2013 13:09:54 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Brainsuite --> FreeSurfer
it depends on what measures you want Bruce On Wed, 20 Mar 2013, Valtina Pouegue wrote:
Hi Bruces, It's because i'm doing a comparison between brainsuite and freesrufer. So
, I would like to export results of
segmentation with Brainsuite and make measurements with FreeSurfer. In Fac
t, with freesurfer I can have more parameters
than with freesurfer. Does it exist another way for get measurements with surfaces ( not generat
ed by Freesurfer)?
Thx .
VP Date: Wed, 20 Mar 2013 08:38:26 -0400 From: fischl@nmr.mgh.harvard.edu To: pvaltti@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Brainsuite --> FreeSurfer
Hi Valtina
you can try opening it with freeview if all you want is visualization. If you are trying to produce anatomical stats you will need a lot more than just the pial surface, as mris_anatomical_stats computes many things from an array of inputs (such as the wm.mgz, the aseg.mgz, etc....). Why not just run recon-all and generate them? Bruce
On Tue, 19 Mar 2013, Valtina Pouegue wrote:
I could see the created surface in MAtlab ( 'read_surf,) but I could't
open the file in Freesurfer with tksurfer....
VP
__
From: pvaltti@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Brainsuite --> FreeSurfer Date: Tue, 19 Mar 2013 22:34:39 -0400
Hi,
I've done a segmentation with Brainsuite ( and FreeSurfer) and I would l
ike to get measurements with FreeSurfer. SO, I
convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to
be usable with Freesurfer. Then, I tried to get
measurements with the command .'mris_anatomical_stats' . with the file
created previously in Matlab (I called it
'rh.pial'). But I got this error like the system is not able to read wm
.mgz.
That's why I thought I could juste replace th 'rh.pial' of the segmentat
ion with Freesurfey by the 'rh.pial' created wi
th
Matalb and then run mris_anatomical_Stats. IS this a good approximation.
Could you recommand another way.
VP
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