Hi
that's because these things have nothing to do with command line melodic. The GUI will do many things (related to pre-processing of the functional data and registrations mainly) that use generic fsl tools like fslmaths, bet etc. Check the log files to see what tools are being called. The structural data is an example of a GUI input that is not being passed on to the command line tool but is being used in the pre-ICA processing.
Once all data has been pre-processed, the GUI will call command-line melodic to do the actual ICA processing. That entire command line call is to be found in the log directory. When calling melodic with the --help option you should find the output directory as the first optional argument...
The -Ostats option on the command line corresponds to the 'output full stats folder' in the GUI, so no need to call the command line version. In order to get individual volumes simply run fslsplit on melodic_IC, which contains all the unthresholded maps as a single 4D file.
hth
Christian
On 23 Jul 2012, at 19:33, Gregory Kirk wrote:
> unhelpfully melodic does not output to the command line the command that is run to run
> a job submitted by the gui. i am confussed as many of the options to select
> in the gui such as output directory and structural image to use are not listed as options
> with melodic --help.
>
> one reason why i want to run command line is that i wish to use the option --Ostats
> to see if this will output volume maps for each of the components to use them for quantitative comparisons
> with connectivity from fiber tracking.
>
> greg
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