I have some questions about the results of 3dMVM and 3dFDR. After running 3dMVM code as bellow.
-prefix SpeechMVM \
-bsVars "Group*Age" \
-qVars "Age,MoCA" \
-num_glt 1 \
-gltLabel 1 S_vs_C -gltCode 1 'Group : -1*Contr 1*Singr' \
Subj Group Age MoCA InputFile \
S002 Singr 70 26 S002.rs.SpeechSeederrts.nii''\
S003 Contr 61 27 S003.rs.SpeechSeederrts.nii''\
I got 16 sub-bricks named ‘(Intercept) F’, ‘Group F’ , … They all named as “XXX F”. When I review the results, which sub-brick should I put as a Threshold? Or my code is wrong? Besides, does the q-value mean FDR correction is included?
I also ran a 3dFDR code on the MVM results.
3dFDR -input SpeechMVM_Risk+tlrc. -prefix SpeechFDR01 -new
All 16 sub-bricks are named as “FDRz: XXX”. There is no q value. I don’t know how to report it either.
Xiyue, the output from 3dMVM should automatically contain the information to assign the FDR values, which would show up under the threshold bar on the AFNI GUI. Thus, you do not need to run a separate 3dFDR command.
Do I need to set the thresholds? The 16 sub-bricks all named as “XXX F”. Or I should leave the threshold blank?
I don’t really understand your question. Again, the FDR information is already embedded in the output of 3dMVM, and you don’t need to do anything. When you visualize the results, the FDR value will show up when you set a threshold on the AFNI GUI.
My question is that should I put the same # on the ULay and OLay options? As shown in this screenshot.
should I put the same # on the ULay and OLay options?
For F-statistic, use the same sub-brick for OLay and Thr (ULay is typically for anatomical data). For t- or z-statistic, set OLay with the effect estimates (e.g., beta) and Thr with the statistic sub-brick.
Sorry for ask you again and again…
I ran another 3dMVM with 4 -gltCode. The code is shown as bellow:
-prefix Speech_glt3 \
-bsVars "Group*Age*Risk" \
-qVars "Age,Risk" \
-num_glt 4 \
-gltLabel 1 Group -gltCode 1 'Group : 1*Singr -1*Contr' \
-gltLabel 2 Risk -gltCode 2 'Risk : 1*Singr -1*Contr' \
-gltLabel 3 GroupRisk -gltCode 3 'Group : 1*Singr -1*Contr Risk:' \
-gltLabel 4 GroupAge -gltCode 4 'Group : 1*Singr -1*Contr Age:' \
Subj Group Age Sex Risk InputFile \
S002 Singr 70 1 1 S002.rs.SpeechSeederrts.nii''\
And I got #14 GroupAge and #15 GroupAge t. Is it correct to put #14 on OLay and #15 on Thr?
I got #14 GroupAge and #15 GroupAge t. Is it correct to put #14 on OLay and #15 on Thr?
Yes, I do recommend such specification.