---------- Forwarded message ---------- From: Bruce Fischl fischl@nmr.mgh.harvard.edu Date: 06/08/2007 14:23 Subject: Re: [Freesurfer] Fake thickness map 2 To: Inês Souta ines.souta@gmail.com

they don't matter. For a real volume they would be the ras2vox transform and the mr parameters. For your purposes they can be any 4x4 and you can leave the mri_parms one out (it will detect and fill it in with zeros).

Send these to the list so other people can answer!

Bruce On Mon, 6 Aug 2007, Inês Souta wrote:

Hi again,

I still don't understand what all the input objects of save_mgh function stand for. 'vol' is the vector of thickness values, 'fname' is the name of the output .mgh file, and what about M and <mr_parms>? What do they stand for and how should I define them?

Thanks again,

Ines

2007/7/31, Bruce Fischl fischl@nmr.mgh.harvard.edu:

...

Hi Ines,

use the mgh route. The "vol" is actually the vector of thickness values, with one entry per vertex on the surface.

cheers, Bruce On Tue, 31 Jul 2007, Inês Souta wrote:

...

Hello,

I was trying to create a cortical thickness map with constant values in order to perform some tests. At first I tried using mris_convert. I converted my thickness file into ascii:

mris_convert lh.thickness lh.thickess.asc

then I used matlab to change all the values in the last column to 2,0. I tried to convert the ascii file back to surface file by doing

mris_convert lh.thicness.asc lh.thickness

but I got "Segmentation fault". How can I convert may ascii file into a surface one?

After failling to acomplish this, I tried using the save_mgh and

load_mgh

...

file, nevertheless I'm not quite sure which input values are needed.

Where

...

can I put my fake values in the save_mgh file? And what is "vol"?

Thanks,

Ines