Hi AFNI experts,
I would like to revive this thread because I couldn't find an answer on the message board except for this one.
Just like above, I am comparing two groups (20 controls vs 13 patients), including one covariate (age), using 3dMEMA. The output has t-stats for the between-group comparison as well as for the group that was entered first (patients as I'm interested in controls-patients) but is missing the t-stats for the second group. Just like above, the missing t-stat is in the third sub-brick. As expected, the beta map of the group missing the t-stats looks very similar to the output of 3dttest++ for that group (as do the maps for group 1 and between-group comparison). So 3dMEMA seems to have run fine except for the missing t-stats.
So I tried other options and found that once I switch the groups or take out the covariate in the original grouping, the problem disappears. While I can switch the sign to see the contrast of choice, I'm wondering why this is? How would NaNs come about?!
Thanks a lot!
Nic
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Error message for the 3rd sub-brick:
[schwarz@PBPSYCPC509D-1 1.mema]$ ./mema_cmd
Covariates will be centered around their respective means
Have lop$centerType 0
Have lop$centerType2 1
[1] "-----------------"
[1] "Totally 50 slices in the volume data."
[1] "Starting to analyze data slice-wise. Running progression shown below:"
[1] "-----------------"
Z slice # 1 done: 07/29/14 16:22:27.204
Z slice # 2 done: 07/29/14 16:22:30.343
.
.
.
Z slice # 49 done: 07/29/14 18:28:10.775
Z slice # 50 done: 07/29/14 18:28:14.114
Warning message:
In sqrt(resList$se[2]^2 - resList$se[1]^2) : NaNs produced
[1] "Analysis finished: 07/29/14 18:28:14.119"
[1] "#++++++++++++++++++++++++++++++++++++++++++++"
[1] 1
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Sep 30 2013) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset visual_CvsP+orig
+ Changed dataset view type and filenames.
+ created 6 FDR curves in dataset header
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Sep 30 2013) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset visual_CvsP_ICC+orig
+ Changed dataset view type and filenames.
++ 3drefit processed 1 datasets
++ 3drefit: AFNI version=AFNI_2011_12_21_1014 (Sep 30 2013) [64-bit]
++ Authored by: RW Cox
++ Processing AFNI dataset visual_CvsP_resZ+orig
+ Changed dataset view type and filenames.
+ created 33 FDR curves in dataset header
++ 3drefit processed 1 datasets
[1] ""
++ 3dcalc: AFNI version=AFNI_2011_12_21_1014 (Sep 30 2013) [64-bit]
++ Authored by: A cast of thousands
*+ WARNING: output sub-brick 3 is all zeros!
++ Output dataset ./visual_CvsP_masked+tlrc.BRIK
3dMEMA cmd:
3dMEMA -prefix visual_CvsP -groups patients controls -set patients \
2165 ../../../group.visual/96TRs/2165.results/stats.2165_REML+tlrc'[visual#0_Coef]' ../../../group.visual/96TRs/2165.results/stats.2165_REML+tlrc'[visual#0_Tstat]' \
2253 ../../../group.visual/96TRs/2253.results.anti/stats.2253_REML+tlrc'[visual#0_Coef]' ../../../group.visual/96TRs/2253.results.anti/stats.2253_REML+tlrc'[visual#0_Tstat]' \
2326 ../../../group.visual/96TRs/2326.results/stats.2326_REML+tlrc'[visual#0_Coef]' ../../../group.visual/96TRs/2326.results/stats.2326_REML+tlrc'[visual#0_Tstat]' \
.
.
.
-set control \
2133 ../../../group.visual/96TRs/2133.results/stats.2133_REML+tlrc'[visual#0_Coef]' ../../../group.visual/96TRs/2133.results/stats.2133_REML+tlrc'[visual#0_Tstat]' \
2141 ../../../group.visual/96TRs/2141.results/stats.2141_REML+tlrc'[visual#0_Coef]' ../../../group.visual/96TRs/2141.results/stats.2141_REML+tlrc'[visual#0_Tstat]' \
2147 ../../../group.visual/96TRs/2147.results/stats.2147_REML+tlrc'[visual#0_Coef]' ../../../group.visual/96TRs/2147.results/stats.2147_REML+tlrc'[visual#0_Tstat]' \
.
.
.
-model_outliers -residual_Z -HKtest -missing_data 0 -covariates cov_age.1D -covariates_center mean -covariates_model center=same slope=different
Covariate Table:
subj age
2165 60
2253 59
2326 81
.
.
.
2133 73
2141 64
2147 53
.
.
.
