Hello FSL Users,

After doing a complete TBSS/FA analysis, I get the exact inverse linear relationship with a cognitive variable than what I expected. Is there anyway that an incorrect bvals or bvecs file could be to blame for this?

Thank you in advance for any suggestions.

Marc

On Fri, May 8, 2009 at 9:58 AM, Marc Dubin <[log in to unmask]> wrote:

Dear All,

I have a TBSS & linear regression question.

I have run a simple linear regression with one independent (cognitive test score) and one dependent variable (fractional anisotropy) that I set up in GLM_gui.

EV1 = constant
EV2 = cognitive test score   (which is demeaned by GLM_gui)

contrast of interest (contrast 2) is (0, -1)

The problem is I get almost the same exact region of significance as I get in a different, more direct, manual FA analysis. However, with the manual approach, the correlation is positive, not negative. Does anyone have ideas about what might be giving rise to this sign error?

Thanks in advance!

Best,
Marc

On Wed, Jan 21, 2009 at 8:44 AM, Steve Smith <[log in to unmask]> wrote:

Ah, good point.  I was thinking more of the options where other programs were run _before_ bet2 as opposed to _after_.

It _might_ be good enough to run bet2 with the mesh output option turned on, using as input the brain-extracted output from the first run of bet with the -S option.   ??

Cheers.



On 20 Jan 2009, at 18:11, Marc Lalancette wrote:

Thanks for your prompt reply.

I suspect that for you the easiest thing
would be to amend the -S option so that it gave the surface outputs
you need, and then run the betsurf second-stage stuff separately
afterwards."

I looked at the script, but I don't know how to do that.  The -S option
first runs bet2, then applies corrections to the masks with fslmaths calls.
If I add the option to output the surface meshes in the bet2 call, I would
get the same mesh as without the -S option.

Is there a tool I can use to convert a mask to a mesh directly?  Or is that
code only in bet2?

Cheers,
Marc Lalancette

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Stephen M. Smith, Professor of Biomedical Engineering
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Marc Dubin, MD PhD
Clinical Research Fellow
Brain Imaging Laboratory
NYSPI & Columbia University

Office: 212-543-6702
Mobile: 646-831-8886

--
Marc Dubin, MD PhD
Clinical Research Fellow
Brain Imaging Laboratory
NYSPI & Columbia University

Office: 212-543-6702
Mobile: 646-831-8886