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FSL  March 2009

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Subject:

Re: Using atlas regions as a mask

From:

"Bramen, Jennifer E." <[log in to unmask]>

Reply-To:

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

Date:

Tue, 17 Mar 2009 11:21:45 -0700

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (138 lines)

Ah! Ok, I do not know the location of that folder. I have only found 2 masks for each atlas, one on the 1mm standard brain and the other on the 2mm. Each mask contains all ROI, not the individual masks. If you can give me the path to the individuals, starting with $FSLDIR, I would be gratefule. Thank you.


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 11:10
To: [log in to unmask]
Subject: Re: [FSL] Using atlas regions as a mask

I am not sure I understand Jennifer.

If you have the left anterior cingulate roi mask, for example, why would you want to split that up into a smaller roi mask?

I think you are talking about a different mask, which encompasses many structures. The roi masks I am referring to are individual ones for every single region in each hemisphere (i.e. there 111 of them in total).

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 Bramen, Jennifer E. [[log in to unmask]]
Sent: Tuesday, March 17, 2009 11:01 AM
To: [log in to unmask]
Subject: Re: [FSL] Using atlas regions as a mask

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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IMPORTANT WARNING:  This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential.  You, the recipient, are obligated to maintain it in a safe, secure and confidential manner.  Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

IMPORTANT WARNING:  This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential.  You, the recipient, are obligated to maintain it in a safe, secure and confidential manner.  Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

IMPORTANT WARNING:  This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential.  You, the recipient, are obligated to maintain it in a safe, secure and confidential manner.  Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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