3dMVM: Inappropriate coding in test No.1!

mironside · October 24, 2022, 9:28pm

Hello gang et al,

Apologies for the noob question but I can’t figure out what I have coded inappropriately in my 3dMVM.
Thanks so much for all of your time and this great resource!

Best,
Maria


3dMVM \
-prefix 3dMVM.FC.PlusvMinus.65Dep.130DepAnx \
 -jobs 20  \
 -num_glt 13  \
 -gltLabel 1 'R2EvR1' -gltCode 1 'run : 1*R2E -1*R1' \
 -gltLabel 2 'R2LvR1' -gltCode 2 'run : 1*R2L -1*R1' \
 -gltLabel 3 'R3EvR1' -gltCode 3 'run : 1*R3E -1*R1' \
 -gltLabel 4 'R3LvR1' -gltCode 4 'run : 1*R3L -1*R1' \
 -gltLabel 5 'R4EvR3L' -gltCode 5 'run : 1*R4E -1*R3L' \
 -gltLabel 6 'R4LvR3L' -gltCode 6 'run : 1*R4L -1*R3L' \
 -gltLabel 7 'DvDA_R1' -gltCode 7 'group : 1*DepAnx -1*Dep run : 1*R1' \
 -gltLabel 8 'DvDA_R2E' -gltCode 8 'group : 1*DepAnx -1*Dep run : 1*R2E' \
 -gltLabel 9 'DvDA_R2L' -gltCode 9 'group : 1*DepAnx -1*Dep run : 1*R2L' \
 -gltLabel 10 'DvDA_R3E' -gltCode 10 'group : 1*DepAnx -1*Dep run : 1*R3E' \
 -gltLabel 11 'DvDA_R3L' -gltCode 11 'group : 1*DepAnx -1*Dep run : 1*R3L' \
 -gltLabel 12 'DvDA_R4E' -gltCode 12 'group : 1*DepAnx -1*Dep run : 1*R4E' \
 -gltLabel 13 'DvDA_R4L' -gltCode 13 'group : 1*DepAnx -1*Dep run : 1*R4L' \
 -num_glf 6  \
 -glfLabel 1 'DvDA_R2EvR1' -glfCode 1 'group : 1*DepAnx -1*Dep run : 1*R2E -1*R1' \
 -glfLabel 2 'DvDA_R2LvR1' -glfCode 2 'group : 1*DepAnx -1*Dep run : 1*R2L -1*R1' \
 -glfLabel 3 'DvDA_R3EvR1' -glfCode 3 'group : 1*DepAnx -1*Dep run : 1*R3E -1*R1' \
 -glfLabel 4 'DvDA_R3LvR1' -glfCode 4 'group : 1*DepAnx -1*Dep run : 1*R3L -1*R1' \
 -glfLabel 5 'DvDA_R4EvR3L' -glfCode 5 'group : 1*DepAnx -1*Dep run : 1*R4E -1*R3L' \
 -glfLabel 6 'DvDA_R4LvR3L' -glfCode 6 'group : 1*DepAnx -1*Dep run : 1*R4L -1*R3L' \
 -dataTable \
 Subj group run InputFile \
 AA438 DepAnx '[R1]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AA438/T0/__FC/stats.AA438-T0-__FC.scaled+tlrc'[PlusvMinusR1_GLT#0_Coef]' \
 AA438 DepAnx '[R2E]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AA438/T0/__FC/stats.AA438-T0-__FC.scaled+tlrc'[PlusvMinusEarlyR2_GLT#0_Coef]' \
 AA438 DepAnx '[R2L]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AA438/T0/__FC/stats.AA438-T0-__FC.scaled+tlrc'[PlusvMinusLateR2_GLT#0_Coef]' \
 AA438 DepAnx '[R3E]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AA438/T0/__FC/stats.AA438-T0-__FC.scaled+tlrc'[PlusvMinusEarlyR3_GLT#0_Coef]' \
 AA438 DepAnx '[R3L]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AA438/T0/__FC/stats.AA438-T0-__FC.scaled+tlrc'[PlusvMinusLateR3_GLT#0_Coef]' \
 AA438 DepAnx '[R4E]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AA438/T0/__FC/stats.AA438-T0-__FC.scaled+tlrc'[PlusvMinusEarlyR4_GLT#0_Coef]' \
 AA438 DepAnx '[R4L]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AA438/T0/__FC/stats.AA438-T0-__FC.scaled+tlrc'[PlusvMinusLateR4_GLT#0_Coef]' \
 AB903 Dep '[R1]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AB903/T0/__FC/stats.AB903-T0-__FC.scaled+tlrc'[PlusvMinusR1_GLT#0_Coef]' \
 AB903 Dep '[R2E]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AB903/T0/__FC/stats.AB903-T0-__FC.scaled+tlrc'[PlusvMinusEarlyR2_GLT#0_Coef]' \
 AB903 Dep '[R2L]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AB903/T0/__FC/stats.AB903-T0-__FC.scaled+tlrc'[PlusvMinusLateR2_GLT#0_Coef]' \
 AB903 Dep '[R3E]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AB903/T0/__FC/stats.AB903-T0-__FC.scaled+tlrc'[PlusvMinusEarlyR3_GLT#0_Coef]' \
 AB903 Dep '[R3L]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AB903/T0/__FC/stats.AB903-T0-__FC.scaled+tlrc'[PlusvMinusLateR3_GLT#0_Coef]' \
 AB903 Dep '[R4E]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AB903/T0/__FC/stats.AB903-T0-__FC.scaled+tlrc'[PlusvMinusEarlyR4_GLT#0_Coef]' \
 AB903 Dep '[R4L]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AB903/T0/__FC/stats.AB903-T0-__FC.scaled+tlrc'[PlusvMinusLateR4_GLT#0_Coef]' \

Gang · October 25, 2022, 11:39am

Maria, you need to use -bsVars and -wsVars to specify the variable type for “group” and “run”.

mironside · October 26, 2022, 3:27pm

Thanks so much Gang,

I followed the manual to add these but it still isn’t working.
Apologies if I am missing something obvious, I am new to AFNI.

Best,
Maria


3dMVM \
-prefix 3dMVM.FC.PlusvMinus.65Dep.130DepAnx \
 -bsVars 'group' \
 -wsVars 'run' \
 -jobs 20  \
 -num_glt 13  \
 -gltLabel 1 'R2EvR1' -gltCode 1 'run : 1*R2E -1*R1' \
 -gltLabel 2 'R2LvR1' -gltCode 2 'run : 1*R2L -1*R1' \
 -gltLabel 3 'R3EvR1' -gltCode 3 'run : 1*R3E -1*R1' \
 -gltLabel 4 'R3LvR1' -gltCode 4 'run : 1*R3L -1*R1' \
 -gltLabel 5 'R4EvR3L' -gltCode 5 'run : 1*R4E -1*R3L' \
 -gltLabel 6 'R4LvR3L' -gltCode 6 'run : 1*R4L -1*R3L' \
 -gltLabel 7 'DvDA_R1' -gltCode 7 'group : 1*DepAnx -1*Dep run : 1*R1' \
 -gltLabel 8 'DvDA_R2E' -gltCode 8 'group : 1*DepAnx -1*Dep run : 1*R2E' \
 -gltLabel 9 'DvDA_R2L' -gltCode 9 'group : 1*DepAnx -1*Dep run : 1*R2L' \
 -gltLabel 10 'DvDA_R3E' -gltCode 10 'group : 1*DepAnx -1*Dep run : 1*R3E' \
 -gltLabel 11 'DvDA_R3L' -gltCode 11 'group : 1*DepAnx -1*Dep run : 1*R3L' \
 -gltLabel 12 'DvDA_R4E' -gltCode 12 'group : 1*DepAnx -1*Dep run : 1*R4E' \
 -gltLabel 13 'DvDA_R4L' -gltCode 13 'group : 1*DepAnx -1*Dep run : 1*R4L' \
 -num_glf 6  \
 -glfLabel 1 'DvDA_R2EvR1' -glfCode 1 'group : 1*DepAnx -1*Dep run : 1*R2E -1*R1' \
 -glfLabel 2 'DvDA_R2LvR1' -glfCode 2 'group : 1*DepAnx -1*Dep run : 1*R2L -1*R1' \
 -glfLabel 3 'DvDA_R3EvR1' -glfCode 3 'group : 1*DepAnx -1*Dep run : 1*R3E -1*R1' \
 -glfLabel 4 'DvDA_R3LvR1' -glfCode 4 'group : 1*DepAnx -1*Dep run : 1*R3L -1*R1' \
 -glfLabel 5 'DvDA_R4EvR3L' -glfCode 5 'group : 1*DepAnx -1*Dep run : 1*R4E -1*R3L' \
 -glfLabel 6 'DvDA_R4LvR3L' -glfCode 6 'group : 1*DepAnx -1*Dep run : 1*R4L -1*R3L' \
 -dataTable \
 Subj group run InputFile \
 AA438 DepAnx '[R1]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AA438/T0/__FC/stats.AA438-T0-__FC.scaled+tlrc'[PlusvMinusR1_GLT#0_Coef]' \
 AA438 DepAnx '[R2E]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AA438/T0/__FC/stats.AA438-T0-__FC.scaled+tlrc'[PlusvMinusEarlyR2_GLT#0_Coef]' \
 AA438 DepAnx '[R2L]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AA438/T0/__FC/stats.AA438-T0-__FC.scaled+tlrc'[PlusvMinusLateR2_GLT#0_Coef]' \
 AA438 DepAnx '[R3E]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AA438/T0/__FC/stats.AA438-T0-__FC.scaled+tlrc'[PlusvMinusEarlyR3_GLT#0_Coef]' \
 AA438 DepAnx '[R3L]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AA438/T0/__FC/stats.AA438-T0-__FC.scaled+tlrc'[PlusvMinusLateR3_GLT#0_Coef]' \
 AA438 DepAnx '[R4E]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AA438/T0/__FC/stats.AA438-T0-__FC.scaled+tlrc'[PlusvMinusEarlyR4_GLT#0_Coef]' \
 AA438 DepAnx '[R4L]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AA438/T0/__FC/stats.AA438-T0-__FC.scaled+tlrc'[PlusvMinusLateR4_GLT#0_Coef]' \
 AB903 Dep '[R1]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AB903/T0/__FC/stats.AB903-T0-__FC.scaled+tlrc'[PlusvMinusR1_GLT#0_Coef]' \
 AB903 Dep '[R2E]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AB903/T0/__FC/stats.AB903-T0-__FC.scaled+tlrc'[PlusvMinusEarlyR2_GLT#0_Coef]' \
 AB903 Dep '[R2L]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AB903/T0/__FC/stats.AB903-T0-__FC.scaled+tlrc'[PlusvMinusLateR2_GLT#0_Coef]' \
 AB903 Dep '[R3E]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AB903/T0/__FC/stats.AB903-T0-__FC.scaled+tlrc'[PlusvMinusEarlyR3_GLT#0_Coef]' \
 AB903 Dep '[R3L]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AB903/T0/__FC/stats.AB903-T0-__FC.scaled+tlrc'[PlusvMinusLateR3_GLT#0_Coef]' \
 AB903 Dep '[R4E]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AB903/T0/__FC/stats.AB903-T0-__FC.scaled+tlrc'[PlusvMinusEarlyR4_GLT#0_Coef]' \
 AB903 Dep '[R4L]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AB903/T0/__FC/stats.AB903-T0-__FC.scaled+tlrc'[PlusvMinusLateR4_GLT#0_Coef]' \
 AC609 DepAnx '[R1]' /media/cephfs/labs/NPC/Analysis/rkuplicki/processing-T1000/results-__FC-fine/AC609/T0/__FC/stats.AC609-T0-__FC.scaled+tlrc'[PlusvMinusR1_GLT#0_Coef]' \

Gang · October 26, 2022, 8:07pm

Maria, do you mind sharing the error message so that I could have a better sense about what’s going on?

My suspicion is that you code the “run” column with square brackets in the labels. However, in your “glt” and “glf” coding, the square brackets are not used. I would drop the square brackets in the “run” column.

A side note: those 6 “glf” lines can be treated as “glt”.

mironside · November 4, 2022, 4:41pm

That works, thank you Gang!