Dhruman,

The -seg-wlo flag should work. Possibly you have an old version of recon-all. Which version of recon-all are you using? To find out, type:

recon-all --version

Nick

On Wed, 2006-02-01 at 11:45 -0500, Bruce Fischl wrote:

Hi Dhruman,

there is no default threshold - it's determined automatically. Nick: can you point out the flags for setting the segmentation threshold (this will disable the automatic estimation).

cheers, Bruce

On Wed, 1 Feb 2006, Goradia, Dhruman D wrote:

...

Hi,

I am interested in changing the white matter low limit for the segmentation step. For this I typed the following in the command prompt:

recon-all -subjid <subjectname> -autorecon2 -seg-wlo <low limit value>

this gave me an error stating that it could not recognize -seg-wlo flag. I was wondering if there is a mistake in writing the command?

I would also like to know if there is any default lower limit for gray matter threshold used my mri_segment? If so what is it and can it be changed?

Thank you.

Dhruman

Dhruman D. Goradia

Research Specialist

Western Psychiatric Institute and Clinic

3811 O'Hara St Suit 431

Pittsburgh PA 15213.

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