Hi there,
I am running the melodic command without masking since the images are already preprocessed (betted) and are in standard space. See command example below:
melodic -i melodic_input_subject_ADOs_new_line_NMI.txt -o melodic_ados_all_NMI -a concat --nomask --nobet --mmthresh=0.5 --tr=3 --report -v --Oall
I noticed that the brain extracted fmri data (the warped and the ones in native space) are non-zero outside the brain resulting in analyses being carried out outside the brain.
I looked at the masks that I got from feat preprocessing, and they are bigger that the brain, matching the non-zero space outside the brains. So I can't really use those, and the MNI mask may not match our population. Manual thresholding is also not a good idea I guess.
So first, is this a statistical disadvantage (ie more voxels to compare)? and has anyone have had similar problems and how to deal with them.
Thanks very much in advance!
Torsten
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