On Tue, Mar 17, 2009 at 9:53 AM, Nestor, Liam (Contractor) <[log in to unmask]> wrote:

If you go to:

fmri/atlases/HarvardOxford/HarvardOxford-combo-maxprob-thr25-2mm

You will be able to see predefined rois masks which have already been set up in FSL. There are not actually labelled, so you will have to overlay them in FSL view to establish which roi masks correspond to which region of the brain.

I am assuming that you want to use these for functional data, in which case case you input these rois (one at a time) when you perform your higher level FEAT analyses. Here you are confining the thresholding to a particular region (e.g., left ACC). FEAT will ignore all voxel outside the roi mask. In post-stats, you input the roi mask where is says "pre-threshold masking".

Perhaps there are other methods you can use, but perhaps give this one a go.

Liam.

*******************************************
Liam Nestor, Ph.D
Office C8-523
Laboratory for Molecular Neuroimaging
Semel Institute for Neuroscience and Human Behavior
760 Westwood Plaza
Los Angeles 90024
Tel: 310-206-0655
E-mail: [log in to unmask]
*******************************************
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Teena Moody [[log in to unmask]]
Sent: Tuesday, March 17, 2009 9:40 AM
To: [log in to unmask]
Subject: Re: [FSL] Using atlas regions as a mask

Jen,
Ashley, Jesse and I have some ROIs already made for several regions
from the MNI 25 and 50% atlases. We probably have slightly different
methods, I will try to send you notes that Ashley sent me. I forward
an old email if i can find it.
Teena
On Mar 16, 2009, at 2:07 PM, Jennifer Bramen wrote:

> Dear FSL List
>
> I would like to use individual regions of interest from one of the
> free atlases. However, the
> atlases are composed of multiple regions and I do not know how to
> create a separate mask
> for an individual region. Is there a command I can use?
>
> Thanks
>
> jen

Teena Moody
[log in to unmask]

> Semel Institute at UCLA
> 760 Westwood Blvd. Suite B8-169
> Los Angeles, CA 90095
> (310) 794-9360 lab
> (310)503-5630 cell
> [log in to unmask]

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