That sounds very good!
Yep, sure the atlases have the B4 and co, I was just always sceptical
about my drawing skills))
the other programs do not do smth else than taking data from
Talairach Daemon database and draw the similar regions.
thanks a lot!
Sergiu
am Samstag, 23. Februar 2008 um 18:59 schrieben Sie:
> Hi Sergi,
> I'm not familiar with the location of Brod 4 or the other programmes
> you refer to. Does one of the atlases in FSLview have Brod 4 on?
> You can get the atlas to show regions by clicking one of the
> buttons...can't remember which off the top of my head.
> I did do...possibly...something similar yesterday, I was interested
> in the planum temporale. I opened the FSL cortical atlas and clicked
> on the PT, which showed up over my all_FA image. Then I seemed to be
> able to save that region as a mask in FSL view, then did the stuff I
> mentioned in my first email.
> Might something like this work for you? I'm afraid this is the limit
> of my knowledge with FSL!
> Good luck!
> Suzanna
> On 23 Feb 2008, at 17:52, S. Groppa wrote:
>> 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
>> mailto:[log in to unmask]
--
Mit freundlichen Grüßen
S. Groppa
mailto:[log in to unmask]
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