Dear FSL experts,
We ran MELODIC on our resting state data using multi-session temporal concatenation followed by dual regression analysis including randomise.
We had conducted an unpaired t-test in randomise comparing two groups (16 controls versus 16 patients).
Contrasts:
1.000000e+00 -1.000000e+00
-1.000000e+00 1.000000e+00
1.000000e+00 0.000000e+00
0.000000e+00 1.000000e+00
Now we would like to threshold the statistics maps from randomise using Gaussian gamma mixture model as was done by Nicola Filippini “Distinct patterns of brain activity in young carriers of the APOE-��4 allele”
I have being trying to figure out how to apply that threshold but I could not find a solution and the only one post that I found in the archives on this topic does not have answer for its last question. (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1009&L=FSL&P=R17502&1=FSL&9=A&I=3&J=on&X=565E91456B012C3733&Y=lojicas%40yahoo.com&d=No+Match%3BMatch%3BMatches&z=4)
My guess is that I have to apply the following steps:
1) To convert the tstast maps from randomise to zmaps we can use the following commands righ?:
fslmaths dr_stage3_ic00*_tstat1.nii.gz -mul 0 -add 1 grot.nii
ttoz grot.nii dr_stage3_ic00*_tstat1.nii.g <dof>
Where DOFs are the number of the subjects included in the analysis minus the number of explanatory variable (EVs) in my design, Is that right?
2) After that we would get the zstat1 map and I know I have apply GGMM using the second type of usage of melodic but I am not sure how to set up melodic. I was thinking we would run melodic as I described below:
melodic –i bg_image (dummy option) --ICs=4d_zmaps_from_randomise_tstat1_or_tstat2 --mix=melodic_mix_33X32.txt (dummy mixing matrix) -o outputname -v --report –Ostats
If not, Could you please explain to me how to set up melodic?
Do I have to use a design matrix and a design contrast options in melodic, if so What are the designs and the "tstat images" (4d_zmaps_from_randomise: tstat1_and_tstat2 or tstat3 and Tstat4) that I have to use?
3) once when we have the zstat1 maps thresholded, Can we apply the following command?
fslmaths thresh_zstat1.nii -ztop pmap1.nii
obtaining the uncorrected p images, which can be use as a input in FDR, right???
I know how valuable is your time, I really appreciate any hint on this
Thank you so much in advance
Lorena
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