Dear team,
I'm writing to ask how to use MELODIC to calculate group differences.
For background, we collected resting-state fMRI datasets from two groups of mice (training vs control). Then, we wanted to compare the difference in the ICA components between the two groups.
We input all datasets and used the following command:
melodic -i ${filelist} -o ${OUT_PATH}/groupICA.ica -v --nobet --tr=${TR} --report --guireport=./report/report.html --bgimage=${TEMPLATE} --mmthre sh=0.5 -a concat -m ${GRP_MASK} -d ${IC_NUM} --Sdes=${DESIGN_mat} --Scon=${DESIGN_con} --Ostats –Oorig
we added '--Sdes=${DESIGN_mat} --Scon=${DESIGN_con}' as design matrix and contrast across subject domain.
Example of design matrix:
/NumWaves 2
/NumPoints 10
/Matrix
1 0
1 0
1 0
1 0
1 0
0 1
0 1
0 1
0 1
0 1
Example of contrast:
1 -1
-1 1
After running the command, we got the groupICA.ica folder.
Here are our questions:
1. Did we use the command correctly to measure the group difference, or should we use Dual regression?
2. If the command was correct, does the 'melodic_IC.nii.gz' file in the output folder contains the between-group comparison z map for each component or just the common components detected in both groups?
Thank you in advance!
Kind regards,
Zengmin
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