Dear FSL experts,
I am trying to use MELODIC by using scripts.
I have performed all the preprocessing (bet, motion correction, smoothing, temporal filter, detrending) and finally registration using the following commands:
flirt -ref highres -in rest -out rest2highres -omat rest2highres.mat -cost corratio -dof 6 -interp trilinear
convert_xfm -inverse -omat highres2rest.mat rest2highres.mat
flirt -ref standard -in highres -out highres2standard -omat highres2standard.mat -cost corratio -searchcost corratio -dof 12 -interp trilinear
convert_xfm -inverse -omat standard2highres.mat highres2standard.mat
convert_xfm -omat rest2standard.mat -concat highres2standard.mat rest2highres.mat
flirt -ref standard -in preprocessed_rest -out rest2standard -applyxfm -init rest2standard.mat -interp trilinear
then I run melodic with this command
melodic -i subject_melodic.txt -o groupmelodic.ica -v --nobet --bgthreshold=3 --tr=2.035 --report --guireport=../../report.html --mmthresh=0.5 --Ostats -a concat
Everything seemed right, but at the end I realised that the files thresh_zstatX.nii.gz and the mask.nii.gz generated by melodic are bigger than the MNI standard. What is my mistake? Do I need to specify a mask when running melodic? Or is it wrong my registration procedure? Do I need to mask after interpolation?
Thank you! and Happy New Year
Angela
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