Hi Carlotta,
No - the -Tmean option to fslmaths calculates the mean across time.
Just pass the 4D image to fslmeants.
Cheers,
Paul
On 06/12/2018, Carlotta Fabris <[log in to unmask]> wrote:
> I used this command and I got a time course for each Roi if my atlas for
> each of the volumes of the fMRI data I gave as input.
>
> I was a bit confused, because I wanted to obtain a mean time course for
> each roi. Because of this, I first did a -Tmean of the fMRI data and then
> executed the fslmeants command.
>
> Is this approach correct?
>
> Thank you,
> Carlotta.
>
> Il giorno Gio 6 Dic 2018, 12:33 paul mccarthy <[log in to unmask]> ha
> scritto:
>
>> 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.
>> >> >
>> >> >
>> ########################################################################
>> >> >
>> >> > To unsubscribe from the FSL list, click the following link:
>> >> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>> >> >
>> >>
>> >> ########################################################################
>> >>
>> >> To unsubscribe from the FSL list, click the following link:
>> >> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>> >>
>> >
>> > ########################################################################
>> >
>> > To unsubscribe from the FSL list, click the following link:
>> > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>> >
>>
>> ########################################################################
>>
>> To unsubscribe from the FSL list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>>
>
> ########################################################################
>
> To unsubscribe from the FSL list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
>
########################################################################
To unsubscribe from the FSL list, click the following link:
https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=FSL&A=1
|