3dLMEr coding

AFNI Message Board
1

AFNI version info (afni -ver):AFNI_26.0.10

Hi afni experts,

I'm a bit unclear how to code my design for 3dLMEr

2 Groups (19 Control, 15 pt) x 5 Blocks of a task (repeated measure) + 2 Covariates: Age and Sex

I have to add Scanner as a covariate as 5/19 Control were scanned on a different scanner/protocol

I added a column for the variable Scanner in dataTable with A and B

So which one is the right code:

3dLMEr \
-prefix LMEr_5bl \
-model "Group*Block+Sex+Age+Scanner+(1|Subj)" \
-qVars "Age" \

or

3dLMEr \
-prefix LMEr_5bl \
-model "Group*Block+Sex+Age+Scanner+(1|Subj)+(1|Scanner)" \
-qVars "Age" \

or

3dLMEr \
-prefix LMEr_5bl \
-model "Group*Block+Sex+Age+Scanner+(1|Subj)+(1|Subj:Scanner)" \
-qVars "Age" \

thanks

-pb

2

Could you provide more information about your data structure? How many scanners are involved? Was the data for each participant collected across all scanners?

Gang Chen

3

Hi Gang,

I put my whole script below (I didn't see how I could attach it)
There are 2 scanners, well in fact it's the same scanner, but at some point there was a major upgrade to the hardware and software.
All subjects were scanned once, some were scanned with the 1st scanner (14/19 controls and 15/15 patients), others with the 2nd scanner (5/19 controls).

Maybe I didn't pose the problem correctly in my initial question.
The goal here is to check if BOLD differs between the 14 and the 5 controls. So I thought (the reviewer too), to treat the 2 scanners as some kind of variable (eg, covariate) in the analysis. But maybe using a covariate is not correct.

3dLMEr
-prefix LMEr_5bl_19HV15CFS_AgeSexScan
-model "Group*Block+Sex+AgeCentered+Scanner+(1|Subj)+(1|Scanner)"
-qVars "AgeCentered"
-mask Atlas_AllBrain_MECFS_35mm+tlrc
-dataTable
Subj Group Block Age Sex AgeCentered Scanner InputFile
CFS_101 HV bl1 42 M -0.1 A
stats.CFS_101_${dset_CFS}+tlrc'['1']'
CFS_101 HV bl2 42 M -0.1 A stats.CFS_101_${dset_CFS}+tlrc'['4']'
CFS_101 HV bl3 42 M -0.1 A stats.CFS_101_${dset_CFS}+tlrc'['7']'
CFS_101 HV bl4 42 M -0.1 A stats.CFS_101_${dset_CFS}+tlrc'['10']'
CFS_101 HV bl5 42 M -0.1 A stats.CFS_101_${dset_CFS}+tlrc'['13']'
CFS_102 HV bl1 61 F 18.9 A stats.CFS_102_${dset_CFS}+tlrc'['1']'
CFS_102 HV bl2 61 F 18.9 A stats.CFS_102_${dset_CFS}+tlrc'['4']'
CFS_102 HV bl3 61 F 18.9 A stats.CFS_102_${dset_CFS}+tlrc'['7']'
CFS_102 HV bl4 61 F 18.9 A stats.CFS_102_${dset_CFS}+tlrc'['10']'
CFS_102 HV bl5 61 F 18.9 A stats.CFS_102_${dset_CFS}+tlrc'['13']'
CFS_109 HV bl1 20 F -22.1 A stats.CFS_109_${dset_CFS}+tlrc'['1']'
CFS_109 HV bl2 20 F -22.1 A stats.CFS_109_${dset_CFS}+tlrc'['4']'
CFS_109 HV bl3 20 F -22.1 A stats.CFS_109_${dset_CFS}+tlrc'['7']'
CFS_109 HV bl4 20 F -22.1 A stats.CFS_109_${dset_CFS}+tlrc'['10']'
CFS_109 HV bl5 20 F -22.1 A stats.CFS_109_${dset_CFS}+tlrc'['13']'
CFS_110 HV bl1 54 F 11.9 A stats.CFS_110_${dset_CFS}+tlrc'['1']'
CFS_110 HV bl2 54 F 11.9 A stats.CFS_110_${dset_CFS}+tlrc'['4']'
CFS_110 HV bl3 54 F 11.9 A stats.CFS_110_${dset_CFS}+tlrc'['7']'
CFS_110 HV bl4 54 F 11.9 A stats.CFS_110_${dset_CFS}+tlrc'['10']'
CFS_110 HV bl5 54 F 11.9 A stats.CFS_110_${dset_CFS}+tlrc'['13']'
CFS_111 HV bl1 21 M -21.1 A stats.CFS_111_${dset_CFS111}+tlrc'['1']'
CFS_111 HV bl2 21 M -21.1 A stats.CFS_111_${dset_CFS111}+tlrc'['4']'
CFS_111 HV bl3 21 M -21.1 A stats.CFS_111_${dset_CFS111}+tlrc'['7']'
CFS_111 HV bl4 21 M -21.1 A stats.CFS_111_${dset_CFS111}+tlrc'['10']'
CFS_111 HV bl5 21 M -21.1 A stats.CFS_111_${dset_CFS111}+tlrc'['13']'
CFS_112 HV bl1 56 M 13.9 A stats.CFS_112_${dset_CFS}+tlrc'['1']'
CFS_112 HV bl2 56 M 13.9 A stats.CFS_112_${dset_CFS}+tlrc'['4']'
CFS_112 HV bl3 56 M 13.9 A stats.CFS_112_${dset_CFS}+tlrc'['7']'
CFS_112 HV bl4 56 M 13.9 A stats.CFS_112_${dset_CFS}+tlrc'['10']'
CFS_112 HV bl5 56 M 13.9 A stats.CFS_112_${dset_CFS}+tlrc'['13']'
CFS_113 HV bl1 36 M -6.1 A stats.CFS_113_${dset_CFS}+tlrc'['1']'
CFS_113 HV bl2 36 M -6.1 A stats.CFS_113_${dset_CFS}+tlrc'['4']'
CFS_113 HV bl3 36 M -6.1 A stats.CFS_113_${dset_CFS}+tlrc'['7']'
CFS_113 HV bl4 36 M -6.1 A stats.CFS_113_${dset_CFS}+tlrc'['10']'
CFS_113 HV bl5 36 M -6.1 A stats.CFS_113_${dset_CFS}+tlrc'['13']'
CFS_120 HV bl1 53 F 10.9 A stats.CFS_120_${dset_CFS}+tlrc'['1']'
CFS_120 HV bl2 53 F 10.9 A stats.CFS_120_${dset_CFS}+tlrc'['4']'
CFS_120 HV bl3 53 F 10.9 A stats.CFS_120_${dset_CFS}+tlrc'['7']'
CFS_120 HV bl4 53 F 10.9 A stats.CFS_120_${dset_CFS}+tlrc'['10']'
CFS_120 HV bl5 53 F 10.9 A stats.CFS_120_${dset_CFS}+tlrc'['13']'
CFS_122 HV bl1 40 M -2.1 A stats.CFS_122_${dset_CFS}+tlrc'['1']'
CFS_122 HV bl2 40 M -2.1 A stats.CFS_122_${dset_CFS}+tlrc'['4']'
CFS_122 HV bl3 40 M -2.1 A stats.CFS_122_${dset_CFS}+tlrc'['7']'
CFS_122 HV bl4 40 M -2.1 A stats.CFS_122_${dset_CFS}+tlrc'['10']'
CFS_122 HV bl5 40 M -2.1 A stats.CFS_122_${dset_CFS}+tlrc'['13']'
CFS_123 HV bl1 36 M -6.1 A stats.CFS_123_${dset_CFS}+tlrc'['1']'
CFS_123 HV bl2 36 M -6.1 A stats.CFS_123_${dset_CFS}+tlrc'['4']'
CFS_123 HV bl3 36 M -6.1 A stats.CFS_123_${dset_CFS}+tlrc'['7']'
CFS_123 HV bl4 36 M -6.1 A stats.CFS_123_${dset_CFS}+tlrc'['10']'
CFS_123 HV bl5 36 M -6.1 A stats.CFS_123_${dset_CFS}+tlrc'['13']'
CFS_124 HV bl1 26 M -16.1 A stats.CFS_124_${dset_CFS}+tlrc'['1']'
CFS_124 HV bl2 26 M -16.1 A stats.CFS_124_${dset_CFS}+tlrc'['4']'
CFS_124 HV bl3 26 M -16.1 A stats.CFS_124_${dset_CFS}+tlrc'['7']'
CFS_124 HV bl4 26 M -16.1 A stats.CFS_124_${dset_CFS}+tlrc'['10']'
CFS_124 HV bl5 26 M -16.1 A stats.CFS_124_${dset_CFS}+tlrc'['13']'
TDT_101 HV bl1 53 M 10.9 A stats.TDT_101_${dset_CFS}+tlrc'['1']'
TDT_101 HV bl2 53 M 10.9 A stats.TDT_101_${dset_CFS}+tlrc'['4']'
TDT_101 HV bl3 53 M 10.9 A stats.TDT_101_${dset_CFS}+tlrc'['7']'
TDT_101 HV bl4 53 M 10.9 A stats.TDT_101_${dset_CFS}+tlrc'['10']'
TDT_101 HV bl5 53 M 10.9 A stats.TDT_101_${dset_CFS}+tlrc'['13']'
TDT_105 HV bl1 42 M -0.1 A stats.TDT_105_${dset_CFS}+tlrc'['1']'
TDT_105 HV bl2 42 M -0.1 A stats.TDT_105_${dset_CFS}+tlrc'['4']'
TDT_105 HV bl3 42 M -0.1 A stats.TDT_105_${dset_CFS}+tlrc'['7']'
TDT_105 HV bl4 42 M -0.1 A stats.TDT_105_${dset_CFS}+tlrc'['10']'
TDT_105 HV bl5 42 M -0.1 A stats.TDT_105_${dset_CFS}+tlrc'['13']'
TDT_107 HV bl1 51 M 8.9 A stats.TDT_107_${dset_CFS}+tlrc'['1']'
TDT_107 HV bl2 51 M 8.9 A stats.TDT_107_${dset_CFS}+tlrc'['4']'
TDT_107 HV bl3 51 M 8.9 A stats.TDT_107_${dset_CFS}+tlrc'['7']'
TDT_107 HV bl4 51 M 8.9 A stats.TDT_107_${dset_CFS}+tlrc'['10']'
TDT_107 HV bl5 51 M 8.9 A stats.TDT_107_${dset_CFS}+tlrc'['13']'
890002 HV bl1 23 F -19.1 B stats.890002_${dset_PASC}+tlrc'['1']'
890002 HV bl2 23 F -19.1 B stats.890002_${dset_PASC}+tlrc'['4']'
890002 HV bl3 23 F -19.1 B stats.890002_${dset_PASC}+tlrc'['7']'
890002 HV bl4 23 F -19.1 B stats.890002_${dset_PASC}+tlrc'['10']'
890002 HV bl5 23 F -19.1 B stats.890002_${dset_PASC}+tlrc'['13']'
890004 HV bl1 25 M -17.1 B stats.890004_${dset_PASC}+tlrc'['1']'
890004 HV bl2 25 M -17.1 B stats.890004_${dset_PASC}+tlrc'['4']'
890004 HV bl3 25 M -17.1 B stats.890004_${dset_PASC}+tlrc'['7']'
890004 HV bl4 25 M -17.1 B stats.890004_${dset_PASC}+tlrc'['10']'
890004 HV bl5 25 M -17.1 B stats.890004_${dset_PASC}+tlrc'['13']'
890012 HV bl1 44 M 1.9 B stats.890012_${dset_PASC}+tlrc'['1']'
890012 HV bl2 44 M 1.9 B stats.890012_${dset_PASC}+tlrc'['4']'
890012 HV bl3 44 M 1.9 B stats.890012_${dset_PASC}+tlrc'['7']'
890012 HV bl4 44 M 1.9 B stats.890012_${dset_PASC}+tlrc'['10']'
890012 HV bl5 44 M 1.9 B stats.890012_${dset_PASC}+tlrc'['13']'
890022 HV bl1 61 M 18.9 B stats.890022_${dset_PASC2}+tlrc'['1']'
890022 HV bl2 61 M 18.9 B stats.890022_${dset_PASC2}+tlrc'['4']'
890022 HV bl3 61 M 18.9 B stats.890022_${dset_PASC2}+tlrc'['7']'
890022 HV bl4 61 M 18.9 B stats.890022_${dset_PASC2}+tlrc'['10']'
890022 HV bl5 61 M 18.9 B stats.890022_${dset_PASC2}+tlrc'['13']'
511004 HV bl1 56 M 13.9 B stats.511004_${dset_GWI}+tlrc'['1']'
511004 HV bl2 56 M 13.9 B stats.511004_${dset_GWI}+tlrc'['4']'
511004 HV bl3 56 M 13.9 B stats.511004_${dset_GWI}+tlrc'['7']'
511004 HV bl4 56 M 13.9 B stats.511004_${dset_GWI}+tlrc'['10']'
511004 HV bl5 56 M 13.9 B stats.511004_${dset_GWI}+tlrc'['13']'
CFS_302 CFS bl1 49 M 9.5 A stats.CFS_302_${dset_CFS}+tlrc'['1']'
CFS_302 CFS bl2 49 M 9.5 A stats.CFS_302_${dset_CFS}+tlrc'['4']'
CFS_302 CFS bl3 49 M 9.5 A stats.CFS_302_${dset_CFS}+tlrc'['7']'
CFS_302 CFS bl4 49 M 9.5 A stats.CFS_302_${dset_CFS}+tlrc'['10']'
CFS_302 CFS bl5 49 M 9.5 A stats.CFS_302_${dset_CFS}+tlrc'['13']'
CFS_303 CFS bl1 51 F 11.5 A stats.CFS_303_${dset_CFS}+tlrc'['1']'
CFS_303 CFS bl2 51 F 11.5 A stats.CFS_303_${dset_CFS}+tlrc'['4']'
CFS_303 CFS bl3 51 F 11.5 A stats.CFS_303_${dset_CFS}+tlrc'['7']'
CFS_303 CFS bl4 51 F 11.5 A stats.CFS_303_${dset_CFS}+tlrc'['10']'
CFS_303 CFS bl5 51 F 11.5 A stats.CFS_303_${dset_CFS}+tlrc'['13']'
CFS_304 CFS bl1 46 M 6.5 A stats.CFS_304_${dset_CFS}+tlrc'['1']'
CFS_304 CFS bl2 46 M 6.5 A stats.CFS_304_${dset_CFS}+tlrc'['4']'
CFS_304 CFS bl3 46 M 6.5 A stats.CFS_304_${dset_CFS}+tlrc'['7']'
CFS_304 CFS bl4 46 M 6.5 A stats.CFS_304_${dset_CFS}+tlrc'['10']'
CFS_304 CFS bl5 46 M 6.5 A stats.CFS_304_${dset_CFS}+tlrc'['13']'
CFS_305 CFS bl1 38 F -1.5 A stats.CFS_305_${dset_CFS}+tlrc'['1']'
CFS_305 CFS bl2 38 F -1.5 A stats.CFS_305_${dset_CFS}+tlrc'['4']'
CFS_305 CFS bl3 38 F -1.5 A stats.CFS_305_${dset_CFS}+tlrc'['7']'
CFS_305 CFS bl4 38 F -1.5 A stats.CFS_305_${dset_CFS}+tlrc'['10']'
CFS_305 CFS bl5 38 F -1.5 A stats.CFS_305_${dset_CFS}+tlrc'['13']'
CFS_316 CFS bl1 44 F 4.5 A stats.CFS_316_${dset_CFS}+tlrc'['1']'
CFS_316 CFS bl2 44 F 4.5 A stats.CFS_316_${dset_CFS}+tlrc'['4']'
CFS_316 CFS bl3 44 F 4.5 A stats.CFS_316_${dset_CFS}+tlrc'['7']'
CFS_316 CFS bl4 44 F 4.5 A stats.CFS_316_${dset_CFS}+tlrc'['10']'
CFS_316 CFS bl5 44 F 4.5 A stats.CFS_316_${dset_CFS}+tlrc'['13']'
CFS_319 CFS bl1 19 F -20.5 A stats.CFS_319_${dset_CFS}+tlrc'['1']'
CFS_319 CFS bl2 19 F -20.5 A stats.CFS_319_${dset_CFS}+tlrc'['4']'
CFS_319 CFS bl3 19 F -20.5 A stats.CFS_319_${dset_CFS}+tlrc'['7']'
CFS_319 CFS bl4 19 F -20.5 A stats.CFS_319_${dset_CFS}+tlrc'['10']'
CFS_319 CFS bl5 19 F -20.5 A stats.CFS_319_${dset_CFS}+tlrc'['13']'
CFS_320 CFS bl1 37 M -2.5 A stats.CFS_320_${dset_CFS}+tlrc'['1']'
CFS_320 CFS bl2 37 M -2.5 A stats.CFS_320_${dset_CFS}+tlrc'['4']'
CFS_320 CFS bl3 37 M -2.5 A stats.CFS_320_${dset_CFS}+tlrc'['7']'
CFS_320 CFS bl4 37 M -2.5 A stats.CFS_320_${dset_CFS}+tlrc'['10']'
CFS_320 CFS bl5 37 M -2.5 A stats.CFS_320_${dset_CFS}+tlrc'['13']'
CFS_321 CFS bl1 26 F -13.5 A stats.CFS_321_${dset_CFS}+tlrc'['1']'
CFS_321 CFS bl2 26 F -13.5 A stats.CFS_321_${dset_CFS}+tlrc'['4']'
CFS_321 CFS bl3 26 F -13.5 A stats.CFS_321_${dset_CFS}+tlrc'['7']'
CFS_321 CFS bl4 26 F -13.5 A stats.CFS_321_${dset_CFS}+tlrc'['10']'
CFS_321 CFS bl5 26 F -13.5 A stats.CFS_321_${dset_CFS}+tlrc'['13']'
CFS_322 CFS bl1 43 M 3.5 A stats.CFS_322_${dset_CFS}+tlrc'['1']'
CFS_322 CFS bl2 43 M 3.5 A stats.CFS_322_${dset_CFS}+tlrc'['4']'
CFS_322 CFS bl3 43 M 3.5 A stats.CFS_322_${dset_CFS}+tlrc'['7']'
CFS_322 CFS bl4 43 M 3.5 A stats.CFS_322_${dset_CFS}+tlrc'['10']'
CFS_322 CFS bl5 43 M 3.5 A stats.CFS_322_${dset_CFS}+tlrc'['13']'
CFS_325 CFS bl1 29 M -10.5 A stats.CFS_325_${dset_CFS}+tlrc'['1']'
CFS_325 CFS bl2 29 M -10.5 A stats.CFS_325_${dset_CFS}+tlrc'['4']'
CFS_325 CFS bl3 29 M -10.5 A stats.CFS_325_${dset_CFS}+tlrc'['7']'
CFS_325 CFS bl4 29 M -10.5 A stats.CFS_325_${dset_CFS}+tlrc'['10']'
CFS_325 CFS bl5 29 M -10.5 A stats.CFS_325_${dset_CFS}+tlrc'['13']'
CFS_327 CFS bl1 32 M -7.5 A stats.CFS_327_${dset_CFS}+tlrc'['1']'
CFS_327 CFS bl2 32 M -7.5 A stats.CFS_327_${dset_CFS}+tlrc'['4']'
CFS_327 CFS bl3 32 M -7.5 A stats.CFS_327_${dset_CFS}+tlrc'['7']'
CFS_327 CFS bl4 32 M -7.5 A stats.CFS_327_${dset_CFS}+tlrc'['10']'
CFS_327 CFS bl5 32 M -7.5 A stats.CFS_327_${dset_CFS}+tlrc'['13']'
TDT_301 CFS bl1 55 F 15.5 A stats.TDT_301_${dset_CFS}+tlrc'['1']'
TDT_301 CFS bl2 55 F 15.5 A stats.TDT_301_${dset_CFS}+tlrc'['4']'
TDT_301 CFS bl3 55 F 15.5 A stats.TDT_301_${dset_CFS}+tlrc'['7']'
TDT_301 CFS bl4 55 F 15.5 A stats.TDT_301_${dset_CFS}+tlrc'['10']'
TDT_301 CFS bl5 55 F 15.5 A stats.TDT_301_${dset_CFS}+tlrc'['13']'
TDT_302 CFS bl1 27 M -12.5 A stats.TDT_302_${dset_CFS}+tlrc'['1']'
TDT_302 CFS bl2 27 M -12.5 A stats.TDT_302_${dset_CFS}+tlrc'['4']'
TDT_302 CFS bl3 27 M -12.5 A stats.TDT_302_${dset_CFS}+tlrc'['7']'
TDT_302 CFS bl4 27 M -12.5 A stats.TDT_302_${dset_CFS}+tlrc'['10']'
TDT_302 CFS bl5 27 M -12.5 A stats.TDT_302_${dset_CFS}+tlrc'['13']'
TDT_303 CFS bl1 44 F 4.5 A stats.TDT_303_${dset_CFS}+tlrc'['1']'
TDT_303 CFS bl2 44 F 4.5 A stats.TDT_303_${dset_CFS}+tlrc'['4']'
TDT_303 CFS bl3 44 F 4.5 A stats.TDT_303_${dset_CFS}+tlrc'['7']'
TDT_303 CFS bl4 44 F 4.5 A stats.TDT_303_${dset_CFS}+tlrc'['10']'
TDT_303 CFS bl5 44 F 4.5 A stats.TDT_303_${dset_CFS}+tlrc'['13']'
TDT_304 CFS bl1 53 M 13.5 A stats.TDT_304_${dset_CFS}+tlrc'['1']'
TDT_304 CFS bl2 53 M 13.5 A stats.TDT_304_${dset_CFS}+tlrc'['4']'
TDT_304 CFS bl3 53 M 13.5 A stats.TDT_304_${dset_CFS}+tlrc'['7']'
TDT_304 CFS bl4 53 M 13.5 A stats.TDT_304_${dset_CFS}+tlrc'['10']'
TDT_304 CFS bl5 53 M 13.5 A stats.TDT_304_${dset_CFS}+tlrc'['13']'

4

One reasonable model in this case is:

-model "Group*Block+Sex+AgeCentered+Scanner+(1|Subj)"

Gang Chen