Hi,
I have run the GICA again without design.mat and design.con files and don't
find any significant differences in the output, other than what you would
expect from running MELODIC twice - a minor reordering of components and
that the melodic call logged in logs/gica referred to the design files in
the 'with' case, as you would expect:
/usr/local/fsl/bin/melodic -i .filelist -o groupmelodic.ica -v --nobet
--bgthreshold=3 --tr=1.0 --report --guireport=../../report.html
--bgimage=bg_image -
-mmthresh=0.5 -a concat --Sdes=[path-to-design-mats]/design.mat
--Scon=[path-to-design-mats]/design.con
Is it correct to leave the two temporal design options blank? Do I need to
select a particular output stats option? The FEAT version number is 3.05.
The MELODIC manual promises ".. if a contrast matrix was specified, the
table will also contain Z-statistics and p-values for all the contrasts.".
Should these be (despite the absence of single-subject cons) the group
comparisons that I am interested in and specified in the design matrices?
Thanks in advance,
Simon.
On Thu, 2 Oct 2008 08:24:45 +0100, Steve Smith <[log in to unmask]> wrote:
>Hi - that all sounds correct - having selected those design.mat
>and .con files in the MELODIC GUI you should see extra information
>using them appear in the web-page component reports - did you not get
>that?
>
>Cheers.
>
>
>On 1 Oct 2008, at 13:40, Simon Robinson wrote:
>
>> Hi,
>>
>> I would like to compare the level and distribution of activation in
>> RSNs
>> between patient and control groups. I have followed previous FSL
>> archive
>> threads on this topic, but it seems that those related to ICA
>> performed on
>> subject's data individually (with the single-session ICA option),
>> mostly
>> with pre v3 versions of MELODIC. If possible I would like to avoid the
>> labour and risk of misidentification involved in a template-matching
>> approach to identifying which component corresponds to which RSN in
>> each
>> subject (as in (Greicius, 2004) for the Default Mode), particularly
>> as I
>> would like to look at a number of RSNs.
>>
>> My question is whether it is possible to perform an intergroup
>> comparison
>> using one of MELODIC's group ICA approaches (either temporal
>> concatenation
>> or Tensor ICA). Some previous threads and manual entries suggest
>> that it is,
>> but I can't see how to do this in practice (or how it would work in
>> the
>> absence of back-projected single-subject responses).
>>
>> I was encourage by the MELODIC post-stats tab roll-over dialogue
>>
>> "If you are doing multi-session/multi-subjects ICA, you can also
>> optionally
>> select a subject "design.mat" model and "design.con" contrast
>> file ... These
>> will be used by MELODIC in ordering the ICA components, and in
>> providing
>> richer reporting information about the multiple sessions/subjects."
>>
>> and
>>
>> Steve Smith's answer Item #012747 "One of the new features in this
>> version
>> of MELODIC is the ability to put in temporal and/or subject models,
>> which
>> MELODIC then uses at the "post-ICA" stage to help you interpret the
>> components. All you have to do is to create a FEAT-style model and
>> contrast
>> file and enter this into the MELODIC GUI, and it will use this for
>> you."
>>
>> I ran a GICA for controls and patients using temporal concatenation
>> and
>> included design.mat and design.con files (defined using Glm) in the
>> MELODIC
>> post-stats GUI. My design looks like the following (as in
>> Christian's post
>> #011963 - reply to Peter Fried - only reduced from 15 controls and
>> patients
>> to 4 for brevity)
>>
>> group EV1 EV2
>> controls patients Title EV1 EV2
>> s1 1 1 0 | C1 controls mean 1 0
>> s2 1 1 0 | C2 patients mean 0 1
>> s3 1 1 0 | C3 C > P 1 -1
>> s4 1 1 0 | C4 P > C -1 1
>> s5 2 0 1 |
>> s6 2 0 1 |
>> s7 2 0 1 |
>> s8 2 0 1 |
>>
>> MELODIC didn't seem to use them - at least nothing is registered in
>> the log
>> after the writing out of the groupmelodic.*. Can you tell me if it's
>> possible to compare two groups in a GICA, and if so, how?
>>
>> Thanks in advance,
>>
>> Simon.
>>
>> --
>> Simon Robinson, Ph.D.
>> Postdoctoral Researcher
>> Functional NeuroImaging Laboratory
>> Center for Mind/Brain Sciences
>> Via delle Regole 101 - 38060 Mattarello (TN)
>> Italy
>>
>
>
>---------------------------------------------------------------------------
>Stephen M. Smith, Professor of Biomedical Engineering
>Associate Director, Oxford University FMRIB Centre
>
>FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
>+44 (0) 1865 222726 (fax 222717)
>[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
>---------------------------------------------------------------------------
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