Hi Becca,
Once you've preprocessed and normalized all of your data to standard space, you could just make a list of your data and enter that list into the command-line version of melodic.
melodic -i list_of_funcs.txt -o output.ica -v --nobet --tr=2 --report --guireport=./report.html -d 25 --mmthresh=0.5 --Ostats -a concat
See the usage for the command and modify the above line to fit your needs.
Cheers,
David
On Feb 8, 2013, at 4:27 PM, becca price wrote:
> Hello,
>
> I am attempting to use Melodic to run a group ICA on images that have already been pre-processed and registered/warped into a standard space (all done in AFNI). Using the GUI, I have turned off all pre-processing but I seem to be unable to turn off the 'standard space' registration step when choosing to do a group dataset analysis. Unfortunately the registration has been failing miserably even after trying multiple different parameter options (e.g., DOFs, etc.) and inputting the same standard space template I used for warping in AFNI. My questions are:
>
> 1) Is there a theoretical problem with skipping registration prior to group ICA when I know the images are already in the same space?
>
> 2) If skipping registration is ok, is there a way to do this using the melodic commandline? The report given to me when using the GUI shows quite a lot of commands that are being run, even when pre-processing options are turned off. What are the commands that would need to be preserved in order to run the group ICA from start to finish?
>
> Thanks very much in advance!
> Becca
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David V. Smith, Ph.D.
Postdoctoral Fellow, Delgado Lab
Department of Psychology
Rutgers University
Newark, NJ 07102
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