afni.nimh.nih.gov

Dear all,

I am trying to design a 2x3 repeated measure design for a within subject study where we have three interventions as condition and the resting state fMRI performed pre and post intervention. I want to calculate the time (pre vs post) and intervention( 3types: control,low and high) interactions.I also wanted to assess that between intervention (pre-post differences with respect to a seed region). For this purpose, I created two scripts: one with using 3dANOVA3 type 4 and another using 3dMVM. could you please have a look at both command-line scripts and let me know if there any further changes required.

3dANOVA3 script:
3dANOVA3 -type 4 \
-alevels 2 \
-blevels 3 \
-clevels 15 \
-dset 1 1 1 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON02/ses-5/sub-BEACON02_ses-5_AMY_bil.nii.gz \
-dset 1 1 2 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON03/ses-5/sub-BEACON03_ses-5_AMY_bil.nii.gz \
-dset 1 1 3 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON04/ses-5/sub-BEACON04_ses-5_AMY_bil.nii.gz \
-dset 1 1 4 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON06/ses-5/sub-BEACON06_ses-5_AMY_bil.nii.gz \
-dset 1 1 5 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON07/ses-5/sub-BEACON07_ses-5_AMY_bil.nii.gz \
-dset 1 1 6 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON08/ses-5/sub-BEACON08_ses-5_AMY_bil.nii.gz \
-dset 1 1 7 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON09/ses-5/sub-BEACON09_ses-5_AMY_bil.nii.gz \
-dset 1 1 8 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON13/ses-5/sub-BEACON13_ses-5_AMY_bil.nii.gz \
-dset 1 1 9 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON14/ses-5/sub-BEACON14_ses-5_AMY_bil.nii.gz \
-dset 1 1 10 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON15/ses-5/sub-BEACON15_ses-5_AMY_bil.nii.gz \
-dset 1 1 11 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON16/ses-5/sub-BEACON16_ses-5_AMY_bil.nii.gz \
-dset 1 1 12 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON18/ses-5/sub-BEACON18_ses-5_AMY_bil.nii.gz \
-dset 1 1 13 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON19/ses-5/sub-BEACON19_ses-5_AMY_bil.nii.gz \
-dset 1 1 14 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON21/ses-5/sub-BEACON21_ses-5_AMY_bil.nii.gz \
-dset 1 1 15 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON23/ses-5/sub-BEACON23_ses-5_AMY_bil.nii.gz \
-dset 1 2 1 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON02/ses-3/sub-BEACON02_ses-3_AMY_bil.nii.gz \
-dset 1 2 2 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON03/ses-3/sub-BEACON03_ses-3_AMY_bil.nii.gz \
-dset 1 2 3 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON04/ses-3/sub-BEACON04_ses-3_AMY_bil.nii.gz \
-dset 1 2 4 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON06/ses-3/sub-BEACON06_ses-3_AMY_bil.nii.gz \
-dset 1 2 5 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON07/ses-3/sub-BEACON07_ses-3_AMY_bil.nii.gz \
-dset 1 2 6 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON08/ses-3/sub-BEACON08_ses-3_AMY_bil.nii.gz \
-dset 1 2 7 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON09/ses-3/sub-BEACON09_ses-3_AMY_bil.nii.gz \
-dset 1 2 8 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON13/ses-3/sub-BEACON13_ses-3_AMY_bil.nii.gz \
-dset 1 2 9 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON14/ses-3/sub-BEACON14_ses-3_AMY_bil.nii.gz \
-dset 1 2 10 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON15/ses-3/sub-BEACON15_ses-3_AMY_bil.nii.gz \
-dset 1 2 11 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON16/ses-3/sub-BEACON16_ses-3_AMY_bil.nii.gz \
-dset 1 2 12 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON18/ses-3/sub-BEACON18_ses-3_AMY_bil.nii.gz \
-dset 1 2 13 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON19/ses-3/sub-BEACON19_ses-3_AMY_bil.nii.gz \
-dset 1 2 14 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON21/ses-3/sub-BEACON21_ses-3_AMY_bil.nii.gz \
-dset 1 2 15 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON23/ses-3/sub-BEACON23_ses-3_AMY_bil.nii.gz \
-dset 1 3 1 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON02/ses-1/sub-BEACON02_ses-1_AMY_bil.nii.gz \
-dset 1 3 2 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON03/ses-1/sub-BEACON03_ses-1_AMY_bil.nii.gz \
-dset 1 3 3 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON04/ses-1/sub-BEACON04_ses-1_AMY_bil.nii.gz \
-dset 1 3 4 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON06/ses-1/sub-BEACON06_ses-1_AMY_bil.nii.gz \
-dset 1 3 5 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON07/ses-1/sub-BEACON07_ses-1_AMY_bil.nii.gz \
-dset 1 3 6 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON08/ses-1/sub-BEACON08_ses-1_AMY_bil.nii.gz \
-dset 1 3 7 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON09/ses-1/sub-BEACON09_ses-1_AMY_bil.nii.gz \
-dset 1 3 8 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON13/ses-1/sub-BEACON13_ses-1_AMY_bil.nii.gz \
-dset 1 3 9 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON14/ses-1/sub-BEACON14_ses-1_AMY_bil.nii.gz \
-dset 1 3 10 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON15/ses-1/sub-BEACON15_ses-1_AMY_bil.nii.gz \
-dset 1 3 11 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON16/ses-1/sub-BEACON16_ses-1_AMY_bil.nii.gz \
-dset 1 3 12 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON18/ses-1/sub-BEACON18_ses-1_AMY_bil.nii.gz \
-dset 1 3 13 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON19/ses-1/sub-BEACON19_ses-1_AMY_bil.nii.gz \
-dset 1 3 14 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON21/ses-1/sub-BEACON21_ses-1_AMY_bil.nii.gz \
-dset 1 3 15 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON23/ses-1/sub-BEACON23_ses-1_AMY_bil.nii.gz \
-dset 2 1 1 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON02/ses-6/sub-BEACON02_ses-6_AMY_bil.nii.gz \
-dset 2 1 2 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON03/ses-6/sub-BEACON03_ses-6_AMY_bil.nii.gz \
-dset 2 1 3 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON04/ses-6/sub-BEACON04_ses-6_AMY_bil.nii.gz \
-dset 2 1 4 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON06/ses-6/sub-BEACON06_ses-6_AMY_bil.nii.gz \
-dset 2 1 5 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON07/ses-6/sub-BEACON07_ses-6_AMY_bil.nii.gz \
-dset 2 1 6 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON08/ses-6/sub-BEACON08_ses-6_AMY_bil.nii.gz \
-dset 2 1 7 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON09/ses-6/sub-BEACON09_ses-6_AMY_bil.nii.gz \
-dset 2 1 8 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON13/ses-6/sub-BEACON13_ses-6_AMY_bil.nii.gz \
-dset 2 1 9 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON14/ses-6/sub-BEACON14_ses-6_AMY_bil.nii.gz \
-dset 2 1 10 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON15/ses-6/sub-BEACON15_ses-6_AMY_bil.nii.gz \
-dset 2 1 11 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON16/ses-6/sub-BEACON16_ses-6_AMY_bil.nii.gz \
-dset 2 1 12 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON18/ses-6/sub-BEACON18_ses-6_AMY_bil.nii.gz \
-dset 2 1 13 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON19/ses-6/sub-BEACON19_ses-6_AMY_bil.nii.gz \
-dset 2 1 14 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON21/ses-6/sub-BEACON21_ses-6_AMY_bil.nii.gz \
-dset 2 1 15 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON23/ses-6/sub-BEACON23_ses-6_AMY_bil.nii.gz \
-dset 2 2 1 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON02/ses-4/sub-BEACON02_ses-4_AMY_bil.nii.gz \
-dset 2 2 2 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON03/ses-4/sub-BEACON03_ses-4_AMY_bil.nii.gz \
-dset 2 2 3 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON04/ses-4/sub-BEACON04_ses-4_AMY_bil.nii.gz \
-dset 2 2 4 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON06/ses-4/sub-BEACON06_ses-4_AMY_bil.nii.gz \
-dset 2 2 5 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON07/ses-4/sub-BEACON07_ses-4_AMY_bil.nii.gz \
-dset 2 2 6 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON08/ses-4/sub-BEACON08_ses-4_AMY_bil.nii.gz \
-dset 2 2 7 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON09/ses-4/sub-BEACON09_ses-4_AMY_bil.nii.gz \
-dset 2 2 8 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON13/ses-4/sub-BEACON13_ses-4_AMY_bil.nii.gz \
-dset 2 2 9 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON14/ses-4/sub-BEACON14_ses-4_AMY_bil.nii.gz \
-dset 2 2 10 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON15/ses-4/sub-BEACON15_ses-4_AMY_bil.nii.gz \
-dset 2 2 11 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON16/ses-4/sub-BEACON16_ses-4_AMY_bil.nii.gz \
-dset 2 2 12 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON18/ses-4/sub-BEACON18_ses-4_AMY_bil.nii.gz \
-dset 2 2 13 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON19/ses-4/sub-BEACON19_ses-4_AMY_bil.nii.gz \
-dset 2 2 14 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON21/ses-4/sub-BEACON21_ses-4_AMY_bil.nii.gz \
-dset 2 2 15 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON23/ses-4/sub-BEACON23_ses-4_AMY_bil.nii.gz \
-dset 2 3 1 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON02/ses-2/sub-BEACON02_ses-2_AMY_bil.nii.gz \
-dset 2 3 2 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON03/ses-2/sub-BEACON03_ses-2_AMY_bil.nii.gz \
-dset 2 3 3 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON04/ses-2/sub-BEACON04_ses-2_AMY_bil.nii.gz \
-dset 2 3 4 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON06/ses-2/sub-BEACON06_ses-2_AMY_bil.nii.gz \
-dset 2 3 5 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON07/ses-2/sub-BEACON07_ses-2_AMY_bil.nii.gz \
-dset 2 3 6 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON08/ses-2/sub-BEACON08_ses-2_AMY_bil.nii.gz \
-dset 2 3 7 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON09/ses-2/sub-BEACON09_ses-2_AMY_bil.nii.gz \
-dset 2 3 8 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON13/ses-2/sub-BEACON13_ses-2_AMY_bil.nii.gz \
-dset 2 3 9 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON14/ses-2/sub-BEACON14_ses-2_AMY_bil.nii.gz \
-dset 2 3 10 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON15/ses-2/sub-BEACON15_ses-2_AMY_bil.nii.gz \
-dset 2 3 11 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON16/ses-2/sub-BEACON16_ses-2_AMY_bil.nii.gz \
-dset 2 3 12 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON18/ses-2/sub-BEACON18_ses-2_AMY_bil.nii.gz \
-dset 2 3 13 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON19/ses-2/sub-BEACON19_ses-2_AMY_bil.nii.gz \
-dset 2 3 14 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON21/ses-2/sub-BEACON21_ses-2_AMY_bil.nii.gz \
-dset 2 3 15 /media/fmrilab/Storage11/BEACON/Marvin/ICA_CompCor_smoothed/sub-BEACON23/ses-2/sub-BEACON23_ses-2_AMY_bil.nii.gz \
-fa time \
-fb condition \
-fab time*cond \
-adiff 1 2 prevspost \
-bdiff 1 2 contvsL \
-bdiff 1 3 contvsH \
-bdiff 2 3 lvsH \
-bcontr -0.5 1 -0.5 LvscontH \
-bcontr 1 -0.5 -0.5 contvsLH \
-aBcontr 1 -1 : 1 precontvspostcont \
-aBcontr 1 -1 : 2 prelowvspostlow \
-aBcontr 1 -1 : 3 prehighvsposthigh \
-bucket BEACON_anova


another one is 3dMVM as given below:

3dMVM -prefix BEACON_MVM -jobs 12 \
-mask myMask+tlrc \
-bsVars 1 \
-wsVars 'condition*Time' \
-num_glt 9 \
-SC \
-gltLabel 1 control_t0 -gltCode 1 'condition : 1*cont Time : 1*0' \
-gltLabel 2 control_t1 -gltCode 2 'condition : 1*cont Time : 1*1' \
-gltLabel 3 low_t0 -gltCode 3 'condition : 1*low Time : 1*0' \
-gltLabel 4 low_t1 -gltCode 4 'condition : 1*low Time : 1*1' \
-gltLabel 5 high_t0 -gltCode 5 'condition : 1*high Time : 1*0' \
-gltLabel 6 high_t1 -gltCode 6 'condition : 1*high Time : 1*1' \
-gltLabel 7 control_vs_low_t0 -gltCode 7 'condition : 1*cont -1*low Time : 1*1 -1*0' \
-gltLabel 8 control_vs_high_t0 -gltCode 8 'condition : 1*cont -1*high Time : 1*1 -1*0' \
-gltLabel 9 low_vs_high_t0 -gltCode 9 'condition : 1*low -1*high Time : 1*1 -1*0' \
-dataTable @input_BEACON_AMY_both.txt \

Please have a look at both scripts and help me in acheiving my aim.


Best wishes,
~007