Hi Maarten,
Thanks for your comments!
The purpose of the full brain mask is to restrict the fsl_glm and
randomise calculations to voxels containing brain. The seed mask in
this case is a binary image called "roi".
Best,
Anders
2016-01-17 21:25 GMT+01:00 Maarten Mennes <[log in to unmask]>:
> hello,
>
> apart from the fact that you are creating a mask of the full brain in step
> 1) instead of using a certain seed location (or did I miss something?), I'd
> say the rest of your steps look fine.
>
> cheers,
> Maarten
>
> On Sun, Jan 17, 2016 at 6:09 PM, Anders Hougaard <[log in to unmask]>
> wrote:
>>
>> Dear all,
>>
>> I have preprocessed my resting state data using FEAT without highpass
>> filtering, then denoised them using ICA-AROMA as described in the
>> manual.
>> I have then created CSF and WM segmentations using fast, eroded the
>> segmentations, and extracted the CSF and WM timeseries to regress out
>> the CSF and WM signals using fsl_glm (with demeaning) to output the
>> residuals. Finally, I have readded the means of the residuals,
>> highpass filtered the data and registered the images to standard space
>> (using applywarp and the warp field generated by FEAT).
>>
>> Now I need to do a seed-based analysis (I know this is not generally
>> recommended, but please bear with me).
>> Would it be sufficient to do the following:
>>
>> 1) Create a common mask
>> for i in (subjects)
>> do
>> fslmaths func_$i -Tstd -bin mask_$i
>> done
>> fslmerge -t maskALL mask_*
>> fslmaths maskALL -Tmin mask
>>
>> 2) Extract time series and calculate correlation maps
>> for i in (subjects)
>> do
>> fslmeants -i func_$i -o roi_$i -m roi
>> fsl_glm -i func_$i -d roi_$i -o map_$i -demean -m mask
>> done
>>
>> 3) Merge maps and run randomise
>> fslmerge -t mapALL map_*
>> randomise -i mapALL -o output -d design.mat -t design.con -e
>> design.grp -m mask -T 5000
>>
>> I would appreciate any comments. Thank you very much.
>> All the best,
>>
>> Anders
>
>
>
>
> --
> Maarten Mennes, Ph.D.
> Senior Researcher
> Donders Institute for Brain, Cognition and Behaviour
> Radboud University Nijmegen
> Nijmegen
> The Netherlands
>
> Google Scholar Author Link
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