On Mon, Feb 9, 2009 at 10:22 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

It will probably be the case that it just gives the entire volume (the "masking" routine just looks for 0-valued voxels). I don't think it actually uses the mask for anything, though.

glmfit is run because that's what the tensor analysis is.

Siddharth Srivastava wrote:

Hi everyone,
I have recently started using the dt_recon processing pipeline
in freesurfer. I just ran a dataset through it, and had a few questions about
the methodology
1) How does the script calculate the mask from the DW data set. Is there any way
to influence the mask calculation routine? I am familiar with bet/bet2 and i have
an set of parameters tuned to my dataset. within dt_recon, i get the entire volume
as a mask, while fsl generated a nice inclusive mask. Is there any way i can use
the bet generated mask with dt_recon?
2) why is a glm fit done at the end of the processing stage?

best regards,
sid.
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