Hi Christian,
Thanks, this has worked out well.
Best wishes,
Xaver
-----Ursprüngliche Nachricht-----
Von: FSL - FMRIB's Software Library [mailto:[log in to unmask]] Im Auftrag von Christian F. Beckmann
Gesendet: Mittwoch, 11. Dezember 2013 12:08
An: [log in to unmask]
Betreff: Re: [FSL] melodic group ica without standard space registration
Hi
On 11 Dec 2013, at 12:00, Xaver Fuchs <[log in to unmask]> wrote:
> Dear experts,
> I am dealing with fmri images from a resting state paradigm which have turned out to be pretty hard to register. Because of that I was doing all preprocessing steps manually via the FSL command line tools (including registration to MNI space).
>
> I want to feed the registered images into a temporal concatination ica. However, the Melodic GUI does not allow to uncheck the register to standard space box whenever group ica options are selected.
> I have tried to turn off the registration in the design.fsf and run feat to redo the analysis without registration. This did not work this easily because melodic starts searching for files it can't find. Something else needs probably to be changed in the design.fsf, but I have no idea what.
>
> Thus i have turned to the melodic command line tool running the following command
>
> /usr/local/fsl/bin/melodic -i ./filelist -o groupmelodic.ica -v --nobet --bgthreshold=10 --tr=3.3 --report --guireport=./report/report.html --bgimage=${FSLDIR}/data/standard/MNI152_T1_2mm -d 0 --mmthresh=0.5 -a concat
>
Yep, that looks right
> This is actually a modified version of the command that the GUI finally runs and it seems to work out.
>
> However, I was now wondering if I should have smoothed the images and run high-pass filtering beforehand as this is default in the Melodic GUI. I think these steps are not run from melodic itself, right? If so, however, I would want to run exactly the same fslmaths commands as it would have been done from Melodic GUI because my goal is to get the same processing as if I was actually using the GUI, only that I skipped the registration to standard space.
>
Correct, melodic command line does not do any spatial/temporal filtering. I suggest you run Feat pre-proc on all original functional data and then apply the registration to standard space before feeding thisngs into melodic as per your command line above.
hth
Christian
> I would be very thankful for help.
>
> Best wishes,
> Xaver
>
>
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