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
> 
> 
>