Hi
the other mask should have been used - can you please send the log.txt
file to see what's going on.
christian
On 14 Nov 2007, at 10:12, Ilya Veer wrote:
> Hi Christian,
>
> Thanks for your swift reply! Indeed, all the components are inside the
> mask saved in the groupmelodic.ica folder. However, this mask seems to
> be based on the structural images from each subject because the entire
> standard brain falls within this mask. This could explain why the
> spatial pattern of several components exceeded the boundaries of
> some of
> the subjects' functional data... Another mask is saved in the parent
> directory, though, which does seem to be the mean mask based on the
> functional images (top of the brain is not included as expected). Why
> isn't this mask being used, rather than the one in groupmelodic.ica?
>
> Thanks!
>
> Ilya.
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
> Behalf Of Christian F. Beckmann
> Sent: Tuesday, November 13, 2007 5:48 PM
> To: [log in to unmask]
> Subject: Re: [FSL] mean group mask in melodic
>
> Hi
>
> the mask melodic uses does get saved in the groupmelodic.ica folder -
> there certainly should not be any voxels within any of the components
> outside this mask. Wrt fsl_glm : just use the -c option and supply
> a .con file generated by the Feat or the Glm setup program. Have
> forgotten to list -c in the command line help, will be added to the
> next release
> hth
> christian
>
> On 13 Nov 2007, at 16:23, Ilya Veer wrote:
>
>> Hi,
>>
>> I have a question regarding multi-session temporal concatenation in
>> Melodic. The top of the brain is not scanned in about one third of
>> my subjects. A mean mask, including voxels that are present in all
>> subjects, is correctly generated by melodic. However, several
>> components found in the group ica do show a spatial pattern
>> exceeding this mask. Does melodic not take the mask information into
>> account? Should I therefore only look at components with spatial
>> patterns within the borders of the mean mask or maybe use fslroi
>> beforehand to exclude these voxels? Any suggestions would be greatly
>> appreciated.
>>
>> Second, I tried the fsl_glm command to redo post-stats on the
>> melodic subject modes (melodic_Smodes) using another design matrix
>> and other contrasts. However, I could not find a way to include a
>> contrast file. How does one do this using the fsl_glm command?
>>
>> Many thanks in advance!
>>
>> Ilya Veer
>> Leiden Institute for Brain and Cognition
>>
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