Hello,

We are attempting to perform a context-dependent connectivity analyses, and after looking at the output of the Decon_stat file we became concerned something was going wrong. I have attached a screen shot of the bucket “1028_br.fanat_Ramyg_fe.drdns_stat+orig.BRIK” overlay and I will attempt to describe the problem.

When looking at the interaction sub-bricks [27]&[28] everything appears fine. However, the seed region sub-bricks [29]&[30] looks out-of-whack. The data aligns well with the anatomical, but it shows up as having an enormous amount of activity throughout the top 3 quarters of brain-slices (almost like a blob). What might be causing this? Or is the problem that I’m looking at the data at stages that is meaningless?

My next steps are to perform:
3dcalc -a 1028_br.fanat_Ramyg_fe.drdns_stat+orig'[29]' -b 1028_br.fanat_Ramyg_fe.drdns_stat+orig'[27]' -expr 'ispositive(b)*sqrt(a)-isnegative(b)*sqrt(a)' -prefix Corr_1028_Ramyg_feware

3dcalc -a Corr_1028_Ramyg_feware+orig -expr 'log((1+a)/(1-a))/2' -prefix Corr_1028_Ramyg_feware_Z

I also pasted a copy of the script we used to generate the connectivity bucket file below.

Thanks,
Steve




Script for 1028 connectivity





adwarp -dxyz 2 -apar BR_1028_192.ANATwarp+tlrc -dpar 'pb04.1028.r01.warp+orig' -prefix 1028r1.drdnss_norm

adwarp -dxyz 2 -apar BR_1028_192.ANATwarp+tlrc -dpar 'pb04.1028.r02.warp+orig' -prefix 1028r2.drdnss_norm

adwarp -dxyz 2 -apar BR_1028_192.ANATwarp+tlrc -dpar 'pb04.1028.r03.warp+orig' -prefix 1028r3.drdnss_norm

adwarp -dxyz 2 -apar BR_1028_192.ANATwarp+tlrc -dpar 'pb04.1028.r04.warp+orig' -prefix 1028r4.drdnss_norm
adwarp -dxyz 2 -apar BR_1028_192.ANATwarp+tlrc -dpar 'pb04.1028.r05.warp+orig' -prefix 1028r5.drdnss_norm

adwarp -dxyz 2 -apar BR_1028_192.ANATwarp+tlrc -dpar 'pb04.1028.r06.warp+orig' -prefix 1028r6.drdnss_norm



3dmaskave -mask /media/Linux/BR_RT_locked/Group/mask_amygmask_FeAwareVnoAware_N16_01+tlrc -mrange 1 1 1028r1.drdnss_norm+tlrc > 1028r1_Ramyg_feware_Seed.1D

3dmaskave -mask /media/Linux/BR_RT_locked/Group/mask_amygmask_FeAwareVnoAware_N16_01+tlrc -mrange 1 1 1028r2.drdnss_norm+tlrc > 1028r2_Ramyg_feware_Seed.1D

3dmaskave -mask /media/Linux/BR_RT_locked/Group/mask_amygmask_FeAwareVnoAware_N16_01+tlrc -mrange 1 1 1028r3.drdnss_norm+tlrc > 1028r3_Ramyg_feware_Seed.1D

3dmaskave -mask /media/Linux/BR_RT_locked/Group/mask_amygmask_FeAwareVnoAware_N16_01+tlrc -mrange 1 1 1028r4.drdnss_norm+tlrc > 1028r4_Ramyg_feware_Seed.1D

3dmaskave -mask /media/Linux/BR_RT_locked/Group/mask_amygmask_FeAwareVnoAware_N16_01+tlrc -mrange 1 1 1028r5.drdnss_norm+tlrc > 1028r5_Ramyg_feware_Seed.1D

3dmaskave -mask /media/Linux/BR_RT_locked/Group/mask_amygmask_FeAwareVnoAware_N16_01+tlrc -mrange 1 1 1028r6.drdnss_norm+tlrc > 1028r6_Ramyg_feware_Seed.1D

* 14 voxels survive the mask




1dcat 1028r1_Ramyg_feware_Seed.1D'[0]' > 1028_Ramyg_feware1_Seed.1D

1dcat 1028r2_Ramyg_feware_Seed.1D'[0]' > 1028_Ramyg_feware2_Seed.1D

1dcat 1028r3_Ramyg_feware_Seed.1D'[0]' > 1028_Ramyg_feware3_Seed.1D

1dcat 1028r4_Ramyg_feware_Seed.1D'[0]' > 1028_Ramyg_feware4_Seed.1D

1dcat 1028r5_Ramyg_feware_Seed.1D'[0]' > 1028_Ramyg_feware5_Seed.1D

1dcat 1028r6_Ramyg_feware_Seed.1D'[0]' > 1028_Ramyg_feware6_Seed.1D



3dDetrend -polort 2 -prefix 1028r1_Ramyg_feware_SeedR.1D 1028_Ramyg_feware1_Seed.1D\'

3dDetrend -polort 2 -prefix 1028r2_Ramyg_feware_SeedR.1D 1028_Ramyg_feware2_Seed.1D\'

3dDetrend -polort 2 -prefix 1028r3_Ramyg_feware_SeedR.1D 1028_Ramyg_feware3_Seed.1D\'

3dDetrend -polort 2 -prefix 1028r4_Ramyg_feware_SeedR.1D 1028_Ramyg_feware4_Seed.1D\'

3dDetrend -polort 2 -prefix 1028r5_Ramyg_feware_SeedR.1D 1028_Ramyg_feware5_Seed.1D\'

3dDetrend -polort 2 -prefix 1028r6_Ramyg_feware_SeedR.1D 1028_Ramyg_feware6_Seed.1D\'



1dtranspose 1028r1_Ramyg_feware_SeedR.1D 1028r1_Ramyg_feware_Seed_ts.1D

1dtranspose 1028r2_Ramyg_feware_SeedR.1D 1028r2_Ramyg_feware_Seed_ts.1D

1dtranspose 1028r3_Ramyg_feware_SeedR.1D 1028r3_Ramyg_feware_Seed_ts.1D

1dtranspose 1028r4_Ramyg_feware_SeedR.1D 1028r4_Ramyg_feware_Seed_ts.1D

1dtranspose 1028r5_Ramyg_feware_SeedR.1D 1028r5_Ramyg_feware_Seed_ts.1D

1dtranspose 1028r6_Ramyg_feware_SeedR.1D 1028r6_Ramyg_feware_Seed_ts.1D



1dUpsample 12 1028r1_Ramyg_feware_Seed_ts.1D > 1028r1_Upsamp_Ramyg_feware_Seed_tss.1D

1dUpsample 12 1028r2_Ramyg_feware_Seed_ts.1D > 1028r2_Upsamp_Ramyg_feware_Seed_tss.1D

1dUpsample 12 1028r3_Ramyg_feware_Seed_ts.1D > 1028r3_Upsamp_Ramyg_feware_Seed_tss.1D

1dUpsample 12 1028r4_Ramyg_feware_Seed_ts.1D > 1028r4_Upsamp_Ramyg_feware_Seed_tss.1D

1dUpsample 12 1028r5_Ramyg_feware_Seed_ts.1D > 1028r5_Upsamp_Ramyg_feware_Seed_tss.1D

1dUpsample 12 1028r6_Ramyg_feware_Seed_ts.1D > 1028r6_Upsamp_Ramyg_feware_Seed_tss.1D



waver -dt 0.25 -GAM -inline 1@1 > GammaHR.1D



3dTfitter -RHS 1028r1_Upsamp_Ramyg_feware_Seed_tss.1D -FALTUNG GammaHR.1D 1028r1_Ramyg_feware_Seed_Neur 012 0

3dTfitter -RHS 1028r2_Upsamp_Ramyg_feware_Seed_tss.1D -FALTUNG GammaHR.1D 1028r2_Ramyg_feware_Seed_Neur 012 0

3dTfitter -RHS 1028r3_Upsamp_Ramyg_feware_Seed_tss.1D -FALTUNG GammaHR.1D 1028r3_Ramyg_feware_Seed_Neur 012 0

3dTfitter -RHS 1028r4_Upsamp_Ramyg_feware_Seed_tss.1D -FALTUNG GammaHR.1D 1028r4_Ramyg_feware_Seed_Neur 012 0

3dTfitter -RHS 1028r5_Upsamp_Ramyg_feware_Seed_tss.1D -FALTUNG GammaHR.1D 1028r5_Ramyg_feware_Seed_Neur 012 0

3dTfitter -RHS 1028r6_Upsamp_Ramyg_feware_Seed_tss.1D -FALTUNG GammaHR.1D 1028r6_Ramyg_feware_Seed_Neur 012 0



1dtranspose 1028r1_Ramyg_feware_Seed_Neur.1D 1028r1_Ramyg_feware_Seed_Neur_ts.1D

1dtranspose 1028r2_Ramyg_feware_Seed_Neur.1D 1028r2_Ramyg_feware_Seed_Neur_ts.1D

1dtranspose 1028r3_Ramyg_feware_Seed_Neur.1D 1028r3_Ramyg_feware_Seed_Neur_ts.1D

1dtranspose 1028r4_Ramyg_feware_Seed_Neur.1D 1028r4_Ramyg_feware_Seed_Neur_ts.1D

1dtranspose 1028r5_Ramyg_feware_Seed_Neur.1D 1028r5_Ramyg_feware_Seed_Neur_ts.1D

1dtranspose 1028r6_Ramyg_feware_Seed_Neur.1D 1028r6_Ramyg_feware_Seed_Neur_ts.1D

waver -dt 0.25 -GAM -gamb 8.6 -gamc 0.547 -gamd 0 -peak 1 -numout 1548 -input FeAware.txt'{0..1547}' > 1028r1.FeAware.1D
waver -dt 0.25 -GAM -gamb 8.6 -gamc 0.547 -gamd 0 -peak 1 -numout 1548 -input FeAware.txt'{1548..3095}' > 1028r2.FeAware.1D
waver -dt 0.25 -GAM -gamb 8.6 -gamc 0.547 -gamd 0 -peak 1 -numout 1548 -input FeAware.txt'{3096..4643}' > 1028r3.FeAware.1D
waver -dt 0.25 -GAM -gamb 8.6 -gamc 0.547 -gamd 0 -peak 1 -numout 1548 -input FeAware.txt'{4644..6191}' > 1028r4.FeAware.1D
waver -dt 0.25 -GAM -gamb 8.6 -gamc 0.547 -gamd 0 -peak 1 -numout 1548 -input FeAware.txt'{6192..7739}' > 1028r5.FeAware.1D
waver -dt 0.25 -GAM -gamb 8.6 -gamc 0.547 -gamd 0 -peak 1 -numout 1548 -input FeAware.txt'{7740..9287}' > 1028r6.FeAware.1D

1deval -a 1028r1_Ramyg_feware_Seed_Neur_ts.1D -b 1028r1.FeAware.1D -expr 'a*b' > 1028r1_InterRamyg_feware_neu.1D
1deval -a 1028r2_Ramyg_feware_Seed_Neur_ts.1D -b 1028r2.FeAware.1D -expr 'a*b' > 1028r2_InterRamyg_feware_neu.1D
1deval -a 1028r3_Ramyg_feware_Seed_Neur_ts.1D -b 1028r3.FeAware.1D -expr 'a*b' > 1028r3_InterRamyg_feware_neu.1D
1deval -a 1028r4_Ramyg_feware_Seed_Neur_ts.1D -b 1028r4.FeAware.1D -expr 'a*b' > 1028r4_InterRamyg_feware_neu.1D
1deval -a 1028r5_Ramyg_feware_Seed_Neur_ts.1D -b 1028r5.FeAware.1D -expr 'a*b' > 1028r5_InterRamyg_feware_neu.1D
1deval -a 1028r6_Ramyg_feware_Seed_Neur_ts.1D -b 1028r6.FeAware.1D -expr 'a*b' > 1028r6_InterRamyg_feware_neu.1D

waver -GAM -peak 1 -TR 0.25 -input 1028r1_InterRamyg_feware_neu.1D -numout 1548 > 1028r1_InterRamyg_feware_ts.1D
waver -GAM -peak 1 -TR 0.25 -input 1028r2_InterRamyg_feware_neu.1D -numout 1548 > 1028r2_InterRamyg_feware_ts.1D
waver -GAM -peak 1 -TR 0.25 -input 1028r3_InterRamyg_feware_neu.1D -numout 1548 > 1028r3_InterRamyg_feware_ts.1D
waver -GAM -peak 1 -TR 0.25 -input 1028r4_InterRamyg_feware_neu.1D -numout 1548 > 1028r4_InterRamyg_feware_ts.1D
waver -GAM -peak 1 -TR 0.25 -input 1028r5_InterRamyg_feware_neu.1D -numout 1548 > 1028r5_InterRamyg_feware_ts.1D
waver -GAM -peak 1 -TR 0.25 -input 1028r6_InterRamyg_feware_neu.1D -numout 1548 > 1028r6_InterRamyg_feware_ts.1D


cat 1028r1_InterRamyg_feware_ts.1D 1028r2_InterRamyg_feware_ts.1D 1028r3_InterRamyg_feware_ts.1D 1028r4_InterRamyg_feware_ts.1D 1028r5_InterRamyg_feware_ts.1D 1028r6_InterRamyg_feware_ts.1D > 1028.drcs_InterRamyg_fewaremask_ts.1D

cat 1028r1_Ramyg_feware_Seed_ts.1D 1028r2_Ramyg_feware_Seed_ts.1D 1028r3_Ramyg_feware_Seed_ts.1D 1028r4_Ramyg_feware_Seed_ts.1D 1028r5_Ramyg_feware_Seed_ts.1D 1028r6_Ramyg_feware_Seed_ts.1D > 1028.drcs_SeedRamyg_fewaremask_ts.1D

1dcat 1028.drcs_InterRamyg_fewaremask_ts.1D'{0..$(12)}' > 1028.drcs_InterRamyg_fewaremask_NEWts.1D



3dDeconvolve -input pb04.1028*warp+orig.BRIK -num_stimts 15 -local_times -polort A -allzero_OK -GOFORIT 5 -stim_times_AM1 1 FD_F.txt 'dmBLOCK' -stim_label 1 'FD_F' -stim_times_AM1 2 FD_D.txt 'dmBLOCK' -stim_label 2 'FD_D' -stim_times_AM1 3 FD_B.txt 'dmBLOCK' -stim_label 3 'FD_B' -stim_times_AM1 4 DN_D.txt 'dmBLOCK' -stim_label 4 'DN_D' -stim_times_AM1 5 DN_N.txt 'dmBLOCK' -stim_label 5 'DN_N' -stim_times_AM1 6 DN_B.txt 'dmBLOCK' -stim_label 6 'DN_B' -stim_times_AM1 7 FN_F.txt 'dmBLOCK' -stim_label 7 'FN_F' -stim_times_AM1 8 FN_N.txt 'dmBLOCK' -stim_label 8 'FN_N' -stim_times_AM1 9 FN_B.txt 'dmBLOCK' -stim_label 9 'FN_B' -stim_times_AM1 10 D_D.txt 'dmBLOCK' -stim_label 10 'D_D' -stim_times_AM1 11 F_F.txt 'dmBLOCK' -stim_label 11 'F_F' -stim_times_AM1 12 N_N.txt 'dmBLOCK' -stim_label 12 'N_N' -stim_times_AM1 13 Error.txt 'dmBLOCK' -stim_label 13 'Er' -stim_file 14 1028.drcs_InterRamyg_fewaremask_NEWts.1D -stim_label 14 '1028.INTER.Ramyg.Femask' -stim_file 15 1028.drcs_SeedRamyg_fewaremask_ts.1D -stim_label 15 '1028.SEED.Ramyg.Femask'-fout -tout -full_first -bucket 1028_br.fanat_Ramyg_fe.drdns_stat



3dcalc -a 1028_br.fanat_Ramyg_fe.drdns_stat+orig'[29]' -b 1028_br.fanat_Ramyg_fe.drdns_stat+orig'[27]' -expr 'ispositive(b)*sqrt(a)-isnegative(b)*sqrt(a)' -prefix Corr_1028_Ramyg_feware

3dcalc -a Corr_1028_Ramyg_feware+orig -expr 'log((1+a)/(1-a))/2' -prefix Corr_1028_Ramyg_feware_Z

adwarp -dxyz 2 -apar BR_1028_192.ANATwarp+tlrc -dpar 'Corr_1028_Ramyg_feware_Z+orig' -prefix Corr_1028_Ramyg_feware_ZZ