Hi Gwenaelle,
Once again, thanks for your help. This all makes sense.
Best wishes
Suzanna
On 21 Feb 2008, at 13:55, Gwenaëlle DOUAUD wrote:
> Hi Suzanna,
>
>> I was wondering if I could clarify measuring the
>> mean FA within a ROI.
>>
>> I have drawn some masks in FSLview using the MN152
>> and all_FA images
>> as guidelines. I'm interested in the mean FA within
>> those masks in
>> each individual.
>>
>> From the list, I gathered that the following should
>> do what I wanted:
>> fslmeants -i all_FA -m my_mask -o output.txt
>>
>> The output of this was a list of values,
>> corresponding to each
>> participant. I presume they're the mean scaled FA
>> for the ROI in a
>> participant.
>>
>> Does this process sound okay?
> Yes, it does. Don't forget to divide by 10000 the FA
> values. You might also prefer to look at:
> fslmeants -i all_FA_skeletonised -m
> my_mask_intersected_with_skel_mask -o
> output_on_skel.txt
> if you looking for mean FA inside white matter tracts.
>
>> Secondly, is there a way of determining the exact
>> order of
>> participants within the all_FA? Would the
>> index.html in FAi/slicedir
>> do this?
> Yes, or a ls *_hr.nii.gz. Basically, the images are
> concatenated in the alphabetical order. So, this is up
> to you to put prefices so that the concatenation makes
> sense with your design.mat file...
>
> Hope this helps,
> Gwenaelle
>
>
>
>
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