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
Laboratory for Molecular Neuroimaging
Semel Institute for Neuroscience and Human Behavior
760 Westwood Plaza
Los Angeles 90024
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
>> 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.
>> 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] http://www.fmrib.ox.ac.uk/~steve
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