Hi Javanray,the command you ran so far (fslview $FSLDIR/data/standard/MNI152_T1_2mm groupmelodic_fix.ica/melodic_IC -l "Red-Yellow" -b 4,15 &)
shows you the group components that you created with melodic (the -l "Red-Yellow" -b 4,15 is just setting a default colour and range for display).
To decide which dr_stage3_… files you want to look at you need to decide 2 things:
1) among the 30 components you have in your melodic_IC file (you can see them changing “Volume” in the bottom left of fslview), you need to decide which are your components of interest (some of them will look like the resting state networks commonly described in literature, some other will be artefacts, e.g. motion artefact, white matter etc.). For example, let’s assume you are interested in components 2, 5 and 6.
2) from the design matrix you set up before calling dual regression (e.g. design.amt / design.con) you need to identify the contrast of interest for your question. For example, let’s say your first contrast is Autism > Controls and second contrast is Autism < Controls.
To see the spatial differences between the two groups in functional connectivity in your networks of interest, you’ll need to look at the following images:
Contrast 1 (Autism > Controls)
dr_stage3_ic0002_tfce_corrp_tstat1.nii.gz
dr_stage3_ic0005_tfce_corrp_tstat1.nii.gz
dr_stage3_ic0006_tfce_corrp_tstat1.nii.gz
Contrast 2 (Autism < Controls)
dr_stage3_ic0002_tfce_corrp_tstat2.nii.gz
dr_stage3_ic0005_tfce_corrp_tstat2.nii.gz
dr_stage3_ic0006_tfce_corrp_tstat2.nii.gz
Best,
Ludovica
—
Ludovica Griffanti, PhD
Analysis Postdoctoral Research Assistant
Oxford Centre for Functional MRI of the Brain (FMRIB)
Nuffield Department of Clinical Neurosciences, University of Oxford
John Radcliffe Hospital
Oxford, OX3 9DU, UK
email:
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Dear Dr.Griffanti,
Thanks for your helpful answer.
I want to look at the spatial differences in functional connectivity within resting state networks to see the difference between Autism and Controls group,
I have read the (http://fsl.fmrib.ox.ac.uk/fslcourse/lectures/practicals/melodic/index.html) , it seems I have done the same procedure.
Then I ran the following code to view the results from the dual regression analysis : (fslview $FSLDIR/data/standard/MNI152_T1_2mm groupmelodic_fix.ica/melodic_IC -l "Red-Yellow" -b 4,15 &) but don't know about the " -b 4,15" part, what does it do?
Then I added the two files it says. Now I don't know whether I have to add all the 30 (dr_stage3_ic00??_tfce_corrp_tstat4.nii.gz) files I have, or not?
The other question is, what does it show and how should I find out the difference between the two groups with this?
Your clarification and collaboration are fully appreciated.
Javanray.
