Hi Liam,

I downloaded the FSL-ROI toolbox and was able to get the regions you 
mentioned roi004.  You said that this represented the Left DLPFC, but the 
HarvardOxford-combo-labels.txt file states that this is the Left Middle Frontal 
Gyrus.  Is the Left DLPFC in fact the Left Middle Frontal Gyrus?  I know they 
are in a similar area in the brain, but I need to know if this includes the entire 
Left DLPFC.  I am trying to compute the total number of activated volxels in 
this area.


On Thu, 6 Aug 2009 13:02:23 -0700, Nestor, Liam (Contractor) 
<[log in to unmask]> wrote:

>On your system, navigate to where the "HarvardOxford-combo-maxprob-
thr25-2mm" is.
>When you get there, type "fslview" at the command line.
>You need to select "openstandard" and then select "avg152T1_brain.nii.gz".
>Then select "Tools", "Toolbars", "Atlas tools".
>When you have these open, you can start overlaying (by selecting "Add") 
the different roi.nii.gz files, to see which ones represent the regions you would 
like to look at.
>For example, I know that roi004 = left DLPFC and roi052 = right DLPFC. I 
don't know the numbers for the other regions you are looking for. Therefore, 
you will just have to play around and take note of which roi number represents 
which region.
>Hope this helps,
>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 
Eric Zalusky [[log in to unmask]]
>Sent: Thursday, August 06, 2009 12:22 PM
>To: [log in to unmask]
>Subject: Re: [FSL] Mask for region of interest activation analysis
>Steve, thanks for the reply.  I am completely new to fsl and fMRI processing.
>I greatly appreciate your advice.
>I have looked through the atlases in FSLView, but I'm unable to find these
>regions.  Specifically I need to find:
>1. Left Dorsolateral Prefrontal Cortex (LDLPFC)
>2. Left Ventrolateral Prefrontal Cortex (LVLPFC)
>3. Left Posterior Parietal Cortex (LPPC)
>Are these named differently in the atlases?  If so, how would I find the
>On Wed, 5 Aug 2009 06:56:18 +0100, Steve Smith <[log in to unmask]>
>>Hi - many of these regions are covered in one or more of the atlases -
>>have a look at these inside FSLView.
>>On 3 Aug 2009, at 01:07, Eric Zalusky wrote:
>>> I am trying to run a regional brain activation analysis in FSL. In
>>> order to
>>> calculate the number of activated voxels in these regions, I know
>>> that I
>>> need to have a mask for each specific ROI.  The problem is that I am
>>> unable
>>> to find these specific masks:
>>> 1. Left Dorsolateral Prefrontal Cortex (LDLPFC)
>>> 2. Left Ventrolateral Prefrontal Cortex (LVLPFC)
>>> 3. Left SMA involved in the right SMA (Supplementary Motor Area)
>>> 4. Left Posterior Parietal Cortex (LPPC)
>>> 5. Left Thalamus
>>> 6. Left Cerebellum
>>> 7. Right Dorsolateral Prefrontal Cortex (RDLPFC)
>>> 8. Right Ventrolateral Prefrontal Cortex (RVLPFC)
>>> 9. Right Posterior Parietal Cortex (RPPC)
>>> 10. Right Thalamus
>>> 11. Right Premotor Area
>>> If you know where I can find these masks, please let me know.
>>> Otherwise, if
>>> you know how to create these masks, please let me know.
>>> Thanks,
>>> Eric Zalusky
>>Stephen M. Smith, Professor of Biomedical Engineering
>>Associate Director,  Oxford University FMRIB Centre
>>FMRIB, JR Hospital, Headington, Oxford  OX3 9DU, UK
>>+44 (0) 1865 222726  (fax 222717)
>>[log in to unmask]
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