Hi Carlotta,
What command did you use? Using fslmeants should be straightforward, e.g.:
fslmeants -i data4D -o roi_timeseries.txt --label=atlas3D
Cheers,
Paul
On 06/12/2018, Carlotta Fabris <[log in to unmask]> wrote:
> Hi Paul!
>
> Thank you for your answer, I tried both approaches, but what I get is not
> what I was expecting.
>
> I thought I will have had a time course for each one of the rois of the
> atlas, but in the output I am getting a lot more time courses.
>
> Why do I get this? Fslmeants should get me the average time course of one
> roi right?
>
> Thank you,
> Carlotta.
>
> Il giorno Lun 3 Dic 2018, 11:02 paul mccarthy <[log in to unmask]> ha
> scritto:
>
>> Hi Carlotta,
>>
>> Either approach should work fine.
>>
>> Cheers,
>>
>> Paul
>>
>> On 01/12/2018, Carlotta Fabris <[log in to unmask]> wrote:
>> > Thank you so much Paul!
>> >
>> > Once I have the atlas in the functional space, I can just use fslmeants
>> with
>> > the --label option without having to use fslroi to extract all the rois
>> from
>> > the atlas?
>> > What I was thinking was something like this:
>> > for roinum in 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21; do
>> > fsl5.0-fslmaths <atlas> -thr $roinum -uthr $roinum -bin
>> SubCort_ROIMask
>> > fsl5.0-fslmeants -i <fMRI data> -m SubCort_ROIMask -o
>> > SubCort_meants_roi${roinum}.txt
>> > done
>> >
>> > paste SubCort_meants_roi*.txt > SubCort_allmeants_roi.txt
>> >
>> > I hope my question is clear,
>> > Carlotta.
>> >
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