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FSL  March 2009

FSL March 2009

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Subject:

Re: Using atlas regions as a mask

From:

Gwenaëlle DOUAUD <[log in to unmask]>

Reply-To:

FSL - FMRIB's Software Library <[log in to unmask]>

Date:

Tue, 17 Mar 2009 11:14:34 -0700

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (149 lines)

Hi Jennifer,

if you find Brian script a bit too fancy for you, I believe Michael Scheel has replied early this morning with another very straightforward and appropriate way to do exactly what you want to do...

Cheers,
Gwenaelle


--- En date de : Mar 17.3.09, Bramen, Jennifer E. <[log in to unmask]> a écrit :

> De: Bramen, Jennifer E. <[log in to unmask]>
> Objet: Re: [FSL] Using atlas regions as a mask
> À: [log in to unmask]
> Date: Mardi 17 Mars 2009, 19h01
> Yes, I already know about the mask, which contains all roi
> in it. Each ROI is identified by making it a different
> interger value and color. What I do not know is if there is
> a way to break apart this mask into several. individual ROI
> rather than one mask with ALL roi. Is there a command that
> will do this? Create seperate files for each region? Or do I
> have to trace over each one and save a new mask?
> 
> Thank you.
> 
> Best regards,
> 
> 
> Jennifer Bramen, Ph.D.
> Assistant Research Neuroscientist
> UCLA Center for Cognitive Neuroscience
> Developmental Cognitive Neuroimaging
> David Geffen School of Medicine at UCLA
> 635 Charles Young Drive South
> Los Angeles, CA 90095-7332
> Phone: (310)267-5116
> Fax:  (310)525-0865
> Email: [log in to unmask]
> Campus Mail Code 176919
> 
> ________________________________________
> From: FSL - FMRIB's Software Library
> [[log in to unmask]] On Behalf Of Nestor, Liam (Contractor)
> [[log in to unmask]]
> Sent: 17 March 2009 09:53
> To: [log in to unmask]
> Subject: Re: [FSL] Using atlas regions as a mask
> 
> 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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