I agree that the Harvard/Oxford subcortical atlas is a good resource
for this purpose. For those more oriented toward a scripting-based
solution, one could easily obtain L/R caudate and VS masks using:
3dcalc -a $FSLDIR/data/atlases/HarvardOxford/HarvardOxford-sub-maxprob-thr25-1mm.nii.gz
-prefix caudateVSMasks -expr 'a*amongst(a,11,26,50,58)'
(Not exactly sure how to do that in FSL, but 3dcalc from AFNI makes it
straightforward)
For reference:
11=L caudate
50=R caudate
26=L accumbens
58 = R accumbens
Depending on your setup, you may need to compute two binary masks, one
for L&R caudate, one for L&R VS. That would just be a matter of:
3dcalc -a $FSLDIR/data/atlases/HarvardOxford/HarvardOxford-sub-maxprob-thr25-1mm.nii.gz
-prefix caudateMasks -expr 'a*amongst(a,11,50)'
fslmaths caudateMasks -bin caudateMasksBinary -odt char
And similarly for VS.
Hope that helps,
Michael
On Tue, Jan 24, 2012 at 7:51 PM, Cunningham, Dustin
<[log in to unmask]> wrote:
> You should be able to load the L/R caudate masks from the Harvard/Oxford subcortical atlas in fslview and save them as nifti files.
>
> Hope this helps.
>
> -Dustin
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of David S Chester [[log in to unmask]]
> Sent: Tuesday, January 24, 2012 6:29 PM
> To: [log in to unmask]
> Subject: [FSL] Caudate ROI mask
>
> Hello,
>
> I am looking for .hdr or .nii mask files for the left and right caudate. Would anyone happen to have any reliable files they could send my way so I can enter it in the pre-threshold masking of FEAT?
>
> I am also looking for a mask of the ventral striatum if anyone has one. I have a mask of the entire striatum, but I just need the ventral portion for this analysis.
>
> Thanks,
> Dave
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