Hi Suzanna!
Thanks a lot for your answer.
I am just not so sure how I can exact draw the borders of the Brod 4a and
4b for example. I was more thinking of generating a mask through WFU
Atlas or MRICro and then realign it in a way that is not yet clear to me
how and then it would be possible(as you describe) to:
"fslmaths myregion_mask -mas mean_FA_skeleton_mask myfinal_mask"
I've searched the archive and unfortunately haven't found an answer).
thanks a lot! best wishes for a nice weekend!
Sergiu
am Samstag, 23. Februar 2008 um 18:21 schrieben Sie:
> HI Sergiu,
> Actually, I asked a similar question this week. If you look back in
> the achieves for this week, it should have the answer.
> What I was advised was to draw your mask in fslview. Then run this
> command line, which generates just the skeleton within your region of
> interest (if you're only interested in the white matter tracts within
> your region):
> fslmaths myregion_mask -mas mean_FA_skeleton_mask myfinal_mask
> Then run randomise as usual with your myfinal_mask, and it should
> generate the statistical maps for the white matter tracts within your
> region of interest.
> If you are not interested in the white matter tracts, but the FA
> within all tissue types within your region (i.e. the mean FA within
> Brod 4), then running the following command line outputs the mean
> scaled FA for each subject (you need to divide by 10000 to get the
> actual FA).
> fslmeants -i all_FA -m myregion_mask -o output_filename.txt
> I think this should help you.
> Suzanna
> On 23 Feb 2008, at 17:00, S. Groppa wrote:
>> Dear list,
>>
>> I can not find a good way to generate masks for skeletonised data.
>>
>> So my direct question is how to generate a mask of for i.e Brod 4 that
>> can be included in randomise for all_FA_skeletonised.
>>
>> thanks a lot and sorry for this trivial question.
>>
>> best wishes
>>
>> Sergiu
--
Mit freundlichen Grüßen
S. Groppa
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