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3dFoodie
April 19, 2016 12:03PM
Hello, I am trying to run the 3dMEMA code below. When I try to use the mask listed I get the following error:

Error in if (is.na(size)) { : argument is of length zero
Calls: process.MEMA.opts -> read.AFNI
In addition: Warning messages:
1: In readLines(conhead) : line 1 appears to contain an embedded nul
2: In readLines(conhead) : line 194 appears to contain an embedded nul
3: In readLines(conhead) :
incomplete final line found on 'MNI152_T1_3mm_brain_graymattermask.nii.gz'
Execution halted

When I comment out the line with the mask, I get this error:

** Error:
Bad testName of for group G1
Error: Error parsing input
Execution halted

The second seems to occur in the following lines of 3dMEMA.R:
if (lop$anaType==1 | lop$anaType==2 | lop$anaType==4) {
if (length(lop$testName) != length(lop$grpName)) {
err.AFNI(paste("Bad testName of ", paste(lop$testName, collapse=' '),
"for group",
paste(lop$grpName, collapse=' ')) );
return(NULL);
Although I cannot figure out why lop$testName wouldn't be the same as lop$grpName.

I cannot figure out either error, so any help would be appreciated to move forward with this. Thank you!

This is what I am trying to run:
3dMEMA -prefix CtxEGNG_SPMG3_Fear-Calm_Nogo_STAI_Age_Dx_19BN_23HC_MEMA \
-mask MNI152_T1_3mm_brain_graymattermask.nii.gz \
-jobs 4 \
-covariates STAI_Age_Cov.txt \
-covariates_center STAI=41.52381 Age=22.31915 Dx=0 \
-set Fear-Calm \
BN100 BN100_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN100_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN101 BN101_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN101_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN102 BN102_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN102_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN103 BN103_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN103_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN104 BN104_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN104_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN105 BN105_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN105_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN106 BN106_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN106_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN107 BN107_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN107_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN110 BN110_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN110_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN111 BN111_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN111_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN112 BN112_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN112_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN114 BN114_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN114_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN115 BN115_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN115_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN116 BN116_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN116_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN118 BN118_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN118_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN120 BN120_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN120_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN121 BN121_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN121_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN122 BN122_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN122_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
BN125 BN122_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' BN125_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01717 SC01717_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01717_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01792 SC01792_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01792_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01793 SC01793_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01793_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01818 SC01818_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01818_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01868 SC01868_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01868_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01888 SC01888_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01888_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01890 SC01891_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01890_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01891 SC01891_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01891_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01892 SC01892_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01892_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01893 SC01893_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01893_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01906 SC01906_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01906_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01916 SC01916_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01916_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01922 SC01922_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01922_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01923 SC01923_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01923_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01928 SC01928_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01928_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01943 SC01943_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01943_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01953 SC01953_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01953_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01958 SC01958_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01958_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC01959 SC01959_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC01959_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC02066 SC02066_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC02066_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC02126 SC02126_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC02126_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC02130 SC02130_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC02130_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC02137 SC02137_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC02137_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]' \
SC02144 SC02144_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Coef]' SC02144_CtxEGNG_EmoXResp_Ctx_SPMG3_bucket+tlrc'[Fear-Calm_Nogo_GLT#0_Tstat]'
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Subject Author Posted

3dMEMA Errors

3dFoodie April 19, 2016 12:03PM

Re: 3dMEMA Errors

pbedard April 25, 2016 11:44AM