Dear FSLers
I have been trying to use Melodic on SPM pre-processed data (realigned/co-registered/normalised/smoothed) and I find myself going round in circles a bit.
Firstly it is not clear to me if I need to re-register my images - they are all in standard space following SPM normalisation, so I assumed not.
I tried to run MELODIC from the command line:
melodic -i .filelist -o groupmelodic.ica -v --nobet --bgthreshold=3 --tr=3 --report --guireport=../../report.html --bgimage=bg_image -d 30 --mmthresh=0.99 --Ostats -a concat
However, FSL cannot seem to open my images. Do you know why this may be? They are smoothed ANALYZE images converted into an 4D.nii format - the path is definitely correct and there doesn't seem to be a problem when I add them in via the GUI (I am loathe to do this with 200+images).
Secondly, I have previously used the GUI and when I tried to register the IC components to standard space, it failed. The components were quite convincing in terms of networks, but some blobs were outside the brain when overlayed on the mean image. I am a bit concerned that I am perhaps missing some vital steps in terms of putting the data (whether it is the 4D images or the IC components) in the right space - registration of the components into standard space did not work at all!
Many thanks
Sarah
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