Hi
Very observant ;) When you call melodic from the GUI, the masking is done in preprocessing, you should find a line
$FSLDIR/bin/fslmaths prefiltered_func_data -mas mask prefiltered_func_data_thresh
in the log file. Therefore, once the melodic command line gets active it no longer needs bet (--nobet) and can simply threshold based on intensity (--bgthreshold=10)
hth
Christian
On 23 Sep 2012, at 14:31, Andi Heckel <[log in to unmask]> wrote:
> Dear FSL experts,
>
> I have a question regarding masking under Melodic (Multi-Session temporal concatenation).
>
> In our case, the FoVs of the bold images differ a bit across subjects (with e.g. parts of the cerebellum cut away in some subjects).
>
> According to "report_log.html" as produced by the Melodic GUI, an intersection mask seems to be created applying "fslmaths -Tmin" on the merged
> individual brain-masks.
>
> However, this group mask does not appear in the subsequent melodic call:
>
> /usr/local/fsl/bin/melodic -i .filelist -o groupmelodic.ica -v --nobet --bgthreshold=10 --tr=3.330 --report --guireport=../../report.html --bgimage=bg_image -d 0 --mmthresh=0.5 -a concat
>
> Doesn't it make sense to add the intersection mask to this command line using melodic's --mask switch in order to exclude anatomy that is not present in all input volumes ? ( ... --mask=mask.nii.gz ... )
>
> Moreover, if the --nobet option is omitted, would melodic create such a group (intersection) mask in "-a concat" mode ?
>
> Kind regards,
> andi
>
>
>
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