Hi
when running melodic from the command line it will perform BET on the
mean functional image (saved using a temporary name) as part of it's
internal processing unless a mask has been supplied or --nobet is used
to force melodic _not_ to run BET. When using the melodic GUI, BET
will be called by the GUI itself as part of the full pre-processing
chain - the subsequent call to the command line version therefore uses
the --nobet option as the data that the GUI passes into the command
line version will be skull stripped already.
hth
Christian
On 29 Jul 2008, at 16:43, Michelle Voss wrote:
> Hi all,
>
> I have been running multi-session tensor-ICA. As inputs I'm using
> skulled 4D volumes with no preprocessing. I run preprocessing and
> bet via the GUI and it skull strips the functional images (the
> filtered_func images are skull stripped). But in the log file when
> it calls melodic, it runs the option --nobet. Just to be sure, this
> is fine right, since the individual functional images are skull
> stripped. As, when I do try to call bet at this stage be re-running
> the log command without this option, I'm not sure what it is running
> bet on? (Calling BET: /usr/local/fsl/bin/bet /var/tmp/tmp.0.ItnKOv /
> var/tmp/tmp.0.ItnKOv_brain -m -f 0.4 > /dev/null )
>
> many thanks,
> Michelle
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