Hi,
Here's how you do it in FSL:
fslmaths $FSLDIR/data/atlases/HarvardOxford/HarvardOxford-sub-maxprob-thr25-1mm.nii.gz -thr 11 -uthr 11 LCaudateMask
and just use different names and numbers as appropriate.
If you want to get a combined mask then just add up the results from these individual calls and binarise like this:
fslmaths LCaudateMask -add RCaudateMask -add LAccMask -add RAccMask -bin AccCaudateMask
All the best,
Mark
On 25 Jan 2012, at 13:43, Michael Hallquist wrote:
> 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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