dataTable is not rectangular

jwaltz · January 24, 2018, 1:25am

Hi-

When I run the script below, I get the following message:

Error in if (len%%wd != 0) errex.AFNI(paste(“The content under -dataTable is not rectangular !”, :
argument is of length zero
Calls: process.MVM.opts
Execution halted
Pessig_3dMVM_DXxPEVALxPEMAGxASI.sh: 13: Pessig_3dMVM_DXxPEVALxPEMAGxASI.sh: -wsVars: not found
Pessig_3dMVM_DXxPEVALxPEMAGxASI.sh: 15: Pessig_3dMVM_DXxPEVALxPEMAGxASI.sh: -jobs: not found

As far as I can see, my dataTable is rectangular (27 controls and 26 patients, but 3dMVM can handle unequal sample sizes, right?

Thanks.

#! bin/sh

cd /data/brutus_data12/jwaltz/pessig/pessig_new/group.results.binary

name1=‘[BigPosPE_TSs#0_Coef]’
name2=‘[BigNegPE_TSs#0_Coef]’
name3=‘[SmallPosPE_TSs#0_Coef]’
name4=‘[SmallNegPE_TSs#0_Coef]’

3dMVM -prefix Pessig_DXxPEVALxPEMAGxASI.3dMVM
-mask ./mask_group+tlrc.
-bsVars "GroupASItot" \
-wsVars 'PEvalPEmag’
-qVars ASItot \
-jobs 16
-dataTable
Subj Group PEval PEMag ASItot InputFile
12352 HV Pos Large 0 ./stats.BigSmallPEs_IndividMed.12352+tlrc.${name1}
12405 HV Pos Large 0 ./stats.BigSmallPEs_IndividMed.12405+tlrc.${name1}
12541 HV Pos Large 0 ./stats.BigSmallPEs_IndividMed.12541+tlrc.${name1}
12546 HV Pos Large 8 ./stats.BigSmallPEs_IndividMed.12546+tlrc.${name1}
12568 HV Pos Large 13 ./stats.BigSmallPEs_IndividMed.12568+tlrc.${name1}
12594 HV Pos Large 0 ./stats.BigSmallPEs_IndividMed.12594+tlrc.${name1}
12669 HV Pos Large 1 ./stats.BigSmallPEs_IndividMed.12669+tlrc.${name1}
12670 HV Pos Large 2 ./stats.BigSmallPEs_IndividMed.12670+tlrc.${name1}
12671 HV Pos Large 21 ./stats.BigSmallPEs_IndividMed.12671+tlrc.${name1}
12675 HV Pos Large 6 ./stats.BigSmallPEs_IndividMed.12675+tlrc.${name1}
12677 HV Pos Large 2 ./stats.BigSmallPEs_IndividMed.12677+tlrc.${name1}
12678 HV Pos Large 2 ./stats.BigSmallPEs_IndividMed.12678+tlrc.${name1}
12684 HV Pos Large 10 ./stats.BigSmallPEs_IndividMed.12684+tlrc.${name1}
12693 HV Pos Large 10 ./stats.BigSmallPEs_IndividMed.12693+tlrc.${name1}
12700 HV Pos Large 5 ./stats.BigSmallPEs_IndividMed.12700+tlrc.${name1}
12706 HV Pos Large 1 ./stats.BigSmallPEs_IndividMed.12706+tlrc.${name1}
12730 HV Pos Large 16 ./stats.BigSmallPEs_IndividMed.12730+tlrc.${name1}
12733 HV Pos Large 9 ./stats.BigSmallPEs_IndividMed.12733+tlrc.${name1}
12734 HV Pos Large 0 ./stats.BigSmallPEs_IndividMed.12734+tlrc.${name1}
12735 HV Pos Large 5 ./stats.BigSmallPEs_IndividMed.12735+tlrc.${name1}
12752 HV Pos Large 7 ./stats.BigSmallPEs_IndividMed.12752+tlrc.${name1}
12758 HV Pos Large 14 ./stats.BigSmallPEs_IndividMed.12758+tlrc.${name1}
12770 HV Pos Large 1 ./stats.BigSmallPEs_IndividMed.12770+tlrc.${name1}
13018 HV Pos Large 6 ./stats.BigSmallPEs_IndividMed.13018+tlrc.${name1}
13067 HV Pos Large 6 ./stats.BigSmallPEs_IndividMed.13067+tlrc.${name1}
13095 HV Pos Large 3 ./stats.BigSmallPEs_IndividMed.13095+tlrc.${name1}
13096 HV Pos Large 0 ./stats.BigSmallPEs_IndividMed.13096+tlrc.${name1}
12380 SZ Pos Large 14 ./stats.BigSmallPEs_IndividMed.12380+tlrc.${name1}
12390 SZ Pos Large 27 ./stats.BigSmallPEs_IndividMed.12390+tlrc.${name1}
12425 SZ Pos Large 14 ./stats.BigSmallPEs_IndividMed.12425+tlrc.${name1}
12463 SZ Pos Large 1 ./stats.BigSmallPEs_IndividMed.12463+tlrc.${name1}
12468 SZ Pos Large 6 ./stats.BigSmallPEs_IndividMed.12468+tlrc.${name1}
12481 SZ Pos Large 18 ./stats.BigSmallPEs_IndividMed.12481+tlrc.${name1}
12505 SZ Pos Large 8 ./stats.BigSmallPEs_IndividMed.12505+tlrc.${name1}
12609 SZ Pos Large 7 ./stats.BigSmallPEs_IndividMed.12609+tlrc.${name1}
12614 SZ Pos Large 12 ./stats.BigSmallPEs_IndividMed.12614+tlrc.${name1}
12616 SZ Pos Large 22 ./stats.BigSmallPEs_IndividMed.12616+tlrc.${name1}
12645 SZ Pos Large 3 ./stats.BigSmallPEs_IndividMed.12645+tlrc.${name1}
12679 SZ Pos Large 14 ./stats.BigSmallPEs_IndividMed.12679+tlrc.${name1}
12787 SZ Pos Large 0 ./stats.BigSmallPEs_IndividMed.12787+tlrc.${name1}
12790 SZ Pos Large 0 ./stats.BigSmallPEs_IndividMed.12790+tlrc.${name1}
12833 SZ Pos Large 17 ./stats.BigSmallPEs_IndividMed.12833+tlrc.${name1}
12834 SZ Pos Large 11 ./stats.BigSmallPEs_IndividMed.12834+tlrc.${name1}
12863 SZ Pos Large 1 ./stats.BigSmallPEs_IndividMed.12863+tlrc.${name1}
12864 SZ Pos Large 15 ./stats.BigSmallPEs_IndividMed.12864+tlrc.${name1}
12874 SZ Pos Large 8 ./stats.BigSmallPEs_IndividMed.12874+tlrc.${name1}
12882 SZ Pos Large 10 ./stats.BigSmallPEs_IndividMed.12882+tlrc.${name1}
12900 SZ Pos Large 11 ./stats.BigSmallPEs_IndividMed.12900+tlrc.${name1}
12906 SZ Pos Large 20 ./stats.BigSmallPEs_IndividMed.12906+tlrc.${name1}
12953 SZ Pos Large 6 ./stats.BigSmallPEs_IndividMed.12953+tlrc.${name1}
12962 SZ Pos Large 18 ./stats.BigSmallPEs_IndividMed.12962+tlrc.${name1}
13063 SZ Pos Large 10 ./stats.BigSmallPEs_IndividMed.13063+tlrc.${name1}
13125 SZ Pos Large 25 ./stats.BigSmallPEs_IndividMed.13125+tlrc.${name1}
12352 HV Neg Large 0 ./stats.BigSmallPEs_IndividMed.12352+tlrc.${name2}
12405 HV Neg Large 0 ./stats.BigSmallPEs_IndividMed.12405+tlrc.${name2}
12541 HV Neg Large 0 ./stats.BigSmallPEs_IndividMed.12541+tlrc.${name2}
12546 HV Neg Large 8 ./stats.BigSmallPEs_IndividMed.12546+tlrc.${name2}
12568 HV Neg Large 13 ./stats.BigSmallPEs_IndividMed.12568+tlrc.${name2}
12594 HV Neg Large 0 ./stats.BigSmallPEs_IndividMed.12594+tlrc.${name2}
12669 HV Neg Large 1 ./stats.BigSmallPEs_IndividMed.12669+tlrc.${name2}
12670 HV Neg Large 2 ./stats.BigSmallPEs_IndividMed.12670+tlrc.${name2}
12671 HV Neg Large 21 ./stats.BigSmallPEs_IndividMed.12671+tlrc.${name2}
12675 HV Neg Large 6 ./stats.BigSmallPEs_IndividMed.12675+tlrc.${name2}
12677 HV Neg Large 2 ./stats.BigSmallPEs_IndividMed.12677+tlrc.${name2}
12678 HV Neg Large 2 ./stats.BigSmallPEs_IndividMed.12678+tlrc.${name2}
12684 HV Neg Large 10 ./stats.BigSmallPEs_IndividMed.12684+tlrc.${name2}
12693 HV Neg Large 10 ./stats.BigSmallPEs_IndividMed.12693+tlrc.${name2}
12700 HV Neg Large 5 ./stats.BigSmallPEs_IndividMed.12700+tlrc.${name2}
12706 HV Neg Large 1 ./stats.BigSmallPEs_IndividMed.12706+tlrc.${name2}
12730 HV Neg Large 16 ./stats.BigSmallPEs_IndividMed.12730+tlrc.${name2}
12733 HV Neg Large 9 ./stats.BigSmallPEs_IndividMed.12733+tlrc.${name2}
12734 HV Neg Large 0 ./stats.BigSmallPEs_IndividMed.12734+tlrc.${name2}
12735 HV Neg Large 5 ./stats.BigSmallPEs_IndividMed.12735+tlrc.${name2}
12752 HV Neg Large 7 ./stats.BigSmallPEs_IndividMed.12752+tlrc.${name2}
12758 HV Neg Large 14 ./stats.BigSmallPEs_IndividMed.12758+tlrc.${name2}
12770 HV Neg Large 1 ./stats.BigSmallPEs_IndividMed.12770+tlrc.${name2}
13018 HV Neg Large 6 ./stats.BigSmallPEs_IndividMed.13018+tlrc.${name2}
13067 HV Neg Large 6 ./stats.BigSmallPEs_IndividMed.13067+tlrc.${name2}
13095 HV Neg Large 3 ./stats.BigSmallPEs_IndividMed.13095+tlrc.${name2}
13096 HV Neg Large 0 ./stats.BigSmallPEs_IndividMed.13096+tlrc.${name2}
12380 SZ Neg Large 14 ./stats.BigSmallPEs_IndividMed.12380+tlrc.${name2}
12390 SZ Neg Large 27 ./stats.BigSmallPEs_IndividMed.12390+tlrc.${name2}
12425 SZ Neg Large 14 ./stats.BigSmallPEs_IndividMed.12425+tlrc.${name2}
12463 SZ Neg Large 1 ./stats.BigSmallPEs_IndividMed.12463+tlrc.${name2}
12468 SZ Neg Large 6 ./stats.BigSmallPEs_IndividMed.12468+tlrc.${name2}
12481 SZ Neg Large 18 ./stats.BigSmallPEs_IndividMed.12481+tlrc.${name2}
12505 SZ Neg Large 8 ./stats.BigSmallPEs_IndividMed.12505+tlrc.${name2}
12609 SZ Neg Large 7 ./stats.BigSmallPEs_IndividMed.12609+tlrc.${name2}
12614 SZ Neg Large 12 ./stats.BigSmallPEs_IndividMed.12614+tlrc.${name2}
12616 SZ Neg Large 22 ./stats.BigSmallPEs_IndividMed.12616+tlrc.${name2}
12645 SZ Neg Large 3 ./stats.BigSmallPEs_IndividMed.12645+tlrc.${name2}
12679 SZ Neg Large 14 ./stats.BigSmallPEs_IndividMed.12679+tlrc.${name2}
12787 SZ Neg Large 0 ./stats.BigSmallPEs_IndividMed.12787+tlrc.${name2}
12790 SZ Neg Large 0 ./stats.BigSmallPEs_IndividMed.12790+tlrc.${name2}
12833 SZ Neg Large 17 ./stats.BigSmallPEs_IndividMed.12833+tlrc.${name2}
12834 SZ Neg Large 11 ./stats.BigSmallPEs_IndividMed.12834+tlrc.${name2}
12863 SZ Neg Large 1 ./stats.BigSmallPEs_IndividMed.12863+tlrc.${name2}
12864 SZ Neg Large 15 ./stats.BigSmallPEs_IndividMed.12864+tlrc.${name2}
12874 SZ Neg Large 8 ./stats.BigSmallPEs_IndividMed.12874+tlrc.${name2}
12882 SZ Neg Large 10 ./stats.BigSmallPEs_IndividMed.12882+tlrc.${name2}
12900 SZ Neg Large 11 ./stats.BigSmallPEs_IndividMed.12900+tlrc.${name2}
12906 SZ Neg Large 20 ./stats.BigSmallPEs_IndividMed.12906+tlrc.${name2}
12953 SZ Neg Large 6 ./stats.BigSmallPEs_IndividMed.12953+tlrc.${name2}
12962 SZ Neg Large 18 ./stats.BigSmallPEs_IndividMed.12962+tlrc.${name2}
13063 SZ Neg Large 10 ./stats.BigSmallPEs_IndividMed.13063+tlrc.${name2}
13125 SZ Neg Large 25 ./stats.BigSmallPEs_IndividMed.13125+tlrc.${name2}
12352 HV Pos Small 0 ./stats.BigSmallPEs_IndividMed.12352+tlrc.${name3}
12405 HV Pos Small 0 ./stats.BigSmallPEs_IndividMed.12405+tlrc.${name3}
12541 HV Pos Small 0 ./stats.BigSmallPEs_IndividMed.12541+tlrc.${name3}
12546 HV Pos Small 8 ./stats.BigSmallPEs_IndividMed.12546+tlrc.${name3}
12568 HV Pos Small 13 ./stats.BigSmallPEs_IndividMed.12568+tlrc.${name3}
12594 HV Pos Small 0 ./stats.BigSmallPEs_IndividMed.12594+tlrc.${name3}
12669 HV Pos Small 1 ./stats.BigSmallPEs_IndividMed.12669+tlrc.${name3}
12670 HV Pos Small 2 ./stats.BigSmallPEs_IndividMed.12670+tlrc.${name3}
12671 HV Pos Small 21 ./stats.BigSmallPEs_IndividMed.12671+tlrc.${name3}
12675 HV Pos Small 6 ./stats.BigSmallPEs_IndividMed.12675+tlrc.${name3}
12677 HV Pos Small 2 ./stats.BigSmallPEs_IndividMed.12677+tlrc.${name3}
12678 HV Pos Small 2 ./stats.BigSmallPEs_IndividMed.12678+tlrc.${name3}
12684 HV Pos Small 10 ./stats.BigSmallPEs_IndividMed.12684+tlrc.${name3}
12693 HV Pos Small 10 ./stats.BigSmallPEs_IndividMed.12693+tlrc.${name3}
12700 HV Pos Small 5 ./stats.BigSmallPEs_IndividMed.12700+tlrc.${name3}
12706 HV Pos Small 1 ./stats.BigSmallPEs_IndividMed.12706+tlrc.${name3}
12730 HV Pos Small 16 ./stats.BigSmallPEs_IndividMed.12730+tlrc.${name3}
12733 HV Pos Small 9 ./stats.BigSmallPEs_IndividMed.12733+tlrc.${name3}
12734 HV Pos Small 0 ./stats.BigSmallPEs_IndividMed.12734+tlrc.${name3}
12735 HV Pos Small 5 ./stats.BigSmallPEs_IndividMed.12735+tlrc.${name3}
12752 HV Pos Small 7 ./stats.BigSmallPEs_IndividMed.12752+tlrc.${name3}
12758 HV Pos Small 14 ./stats.BigSmallPEs_IndividMed.12758+tlrc.${name3}
12770 HV Pos Small 1 ./stats.BigSmallPEs_IndividMed.12770+tlrc.${name3}
13018 HV Pos Small 6 ./stats.BigSmallPEs_IndividMed.13018+tlrc.${name3}
13067 HV Pos Small 6 ./stats.BigSmallPEs_IndividMed.13067+tlrc.${name3}
13095 HV Pos Small 3 ./stats.BigSmallPEs_IndividMed.13095+tlrc.${name3}
13096 HV Pos Small 0 ./stats.BigSmallPEs_IndividMed.13096+tlrc.${name3}
12380 SZ Pos Small 14 ./stats.BigSmallPEs_IndividMed.12380+tlrc.${name3}
12390 SZ Pos Small 27 ./stats.BigSmallPEs_IndividMed.12390+tlrc.${name3}
12425 SZ Pos Small 14 ./stats.BigSmallPEs_IndividMed.12425+tlrc.${name3}
12463 SZ Pos Small 1 ./stats.BigSmallPEs_IndividMed.12463+tlrc.${name3}
12468 SZ Pos Small 6 ./stats.BigSmallPEs_IndividMed.12468+tlrc.${name3}
12481 SZ Pos Small 18 ./stats.BigSmallPEs_IndividMed.12481+tlrc.${name3}
12505 SZ Pos Small 8 ./stats.BigSmallPEs_IndividMed.12505+tlrc.${name3}
12609 SZ Pos Small 7 ./stats.BigSmallPEs_IndividMed.12609+tlrc.${name3}
12614 SZ Pos Small 12 ./stats.BigSmallPEs_IndividMed.12614+tlrc.${name3}
12616 SZ Pos Small 22 ./stats.BigSmallPEs_IndividMed.12616+tlrc.${name3}
12645 SZ Pos Small 3 ./stats.BigSmallPEs_IndividMed.12645+tlrc.${name3}
12679 SZ Pos Small 14 ./stats.BigSmallPEs_IndividMed.12679+tlrc.${name3}
12787 SZ Pos Small 0 ./stats.BigSmallPEs_IndividMed.12787+tlrc.${name3}
12790 SZ Pos Small 0 ./stats.BigSmallPEs_IndividMed.12790+tlrc.${name3}
12833 SZ Pos Small 17 ./stats.BigSmallPEs_IndividMed.12833+tlrc.${name3}
12834 SZ Pos Small 11 ./stats.BigSmallPEs_IndividMed.12834+tlrc.${name3}
12863 SZ Pos Small 1 ./stats.BigSmallPEs_IndividMed.12863+tlrc.${name3}
12864 SZ Pos Small 15 ./stats.BigSmallPEs_IndividMed.12864+tlrc.${name3}
12874 SZ Pos Small 8 ./stats.BigSmallPEs_IndividMed.12874+tlrc.${name3}
12882 SZ Pos Small 10 ./stats.BigSmallPEs_IndividMed.12882+tlrc.${name3}
12900 SZ Pos Small 11 ./stats.BigSmallPEs_IndividMed.12900+tlrc.${name3}
12906 SZ Pos Small 20 ./stats.BigSmallPEs_IndividMed.12906+tlrc.${name3}
12953 SZ Pos Small 6 ./stats.BigSmallPEs_IndividMed.12953+tlrc.${name3}
12962 SZ Pos Small 18 ./stats.BigSmallPEs_IndividMed.12962+tlrc.${name3}
13063 SZ Pos Small 10 ./stats.BigSmallPEs_IndividMed.13063+tlrc.${name3}
13125 SZ Pos Small 25 ./stats.BigSmallPEs_IndividMed.13125+tlrc.${name3}
12352 HV Neg Small 0 ./stats.BigSmallPEs_IndividMed.12352+tlrc.${name4}
12405 HV Neg Small 0 ./stats.BigSmallPEs_IndividMed.12405+tlrc.${name4}
12541 HV Neg Small 0 ./stats.BigSmallPEs_IndividMed.12541+tlrc.${name4}
12546 HV Neg Small 8 ./stats.BigSmallPEs_IndividMed.12546+tlrc.${name4}
12568 HV Neg Small 13 ./stats.BigSmallPEs_IndividMed.12568+tlrc.${name4}
12594 HV Neg Small 0 ./stats.BigSmallPEs_IndividMed.12594+tlrc.${name4}
12669 HV Neg Small 1 ./stats.BigSmallPEs_IndividMed.12669+tlrc.${name4}
12670 HV Neg Small 2 ./stats.BigSmallPEs_IndividMed.12670+tlrc.${name4}
12671 HV Neg Small 21 ./stats.BigSmallPEs_IndividMed.12671+tlrc.${name4}
12675 HV Neg Small 6 ./stats.BigSmallPEs_IndividMed.12675+tlrc.${name4}
12677 HV Neg Small 2 ./stats.BigSmallPEs_IndividMed.12677+tlrc.${name4}
12678 HV Neg Small 2 ./stats.BigSmallPEs_IndividMed.12678+tlrc.${name4}
12684 HV Neg Small 10 ./stats.BigSmallPEs_IndividMed.12684+tlrc.${name4}
12693 HV Neg Small 10 ./stats.BigSmallPEs_IndividMed.12693+tlrc.${name4}
12700 HV Neg Small 5 ./stats.BigSmallPEs_IndividMed.12700+tlrc.${name4}
12706 HV Neg Small 1 ./stats.BigSmallPEs_IndividMed.12706+tlrc.${name4}
12730 HV Neg Small 16 ./stats.BigSmallPEs_IndividMed.12730+tlrc.${name4}
12733 HV Neg Small 9 ./stats.BigSmallPEs_IndividMed.12733+tlrc.${name4}
12734 HV Neg Small 0 ./stats.BigSmallPEs_IndividMed.12734+tlrc.${name4}
12735 HV Neg Small 5 ./stats.BigSmallPEs_IndividMed.12735+tlrc.${name4}
12752 HV Neg Small 7 ./stats.BigSmallPEs_IndividMed.12752+tlrc.${name4}
12758 HV Neg Small 14 ./stats.BigSmallPEs_IndividMed.12758+tlrc.${name4}
12770 HV Neg Small 1 ./stats.BigSmallPEs_IndividMed.12770+tlrc.${name4}
13018 HV Neg Small 6 ./stats.BigSmallPEs_IndividMed.13018+tlrc.${name4}
13067 HV Neg Small 6 ./stats.BigSmallPEs_IndividMed.13067+tlrc.${name4}
13095 HV Neg Small 3 ./stats.BigSmallPEs_IndividMed.13095+tlrc.${name4}
13096 HV Neg Small 0 ./stats.BigSmallPEs_IndividMed.13096+tlrc.${name4}
12380 SZ Neg Small 14 ./stats.BigSmallPEs_IndividMed.12380+tlrc.${name4}
12390 SZ Neg Small 27 ./stats.BigSmallPEs_IndividMed.12390+tlrc.${name4}
12425 SZ Neg Small 14 ./stats.BigSmallPEs_IndividMed.12425+tlrc.${name4}
12463 SZ Neg Small 1 ./stats.BigSmallPEs_IndividMed.12463+tlrc.${name4}
12468 SZ Neg Small 6 ./stats.BigSmallPEs_IndividMed.12468+tlrc.${name4}
12481 SZ Neg Small 18 ./stats.BigSmallPEs_IndividMed.12481+tlrc.${name4}
12505 SZ Neg Small 8 ./stats.BigSmallPEs_IndividMed.12505+tlrc.${name4}
12609 SZ Neg Small 7 ./stats.BigSmallPEs_IndividMed.12609+tlrc.${name4}
12614 SZ Neg Small 12 ./stats.BigSmallPEs_IndividMed.12614+tlrc.${name4}
12616 SZ Neg Small 22 ./stats.BigSmallPEs_IndividMed.12616+tlrc.${name4}
12645 SZ Neg Small 3 ./stats.BigSmallPEs_IndividMed.12645+tlrc.${name4}
12679 SZ Neg Small 14 ./stats.BigSmallPEs_IndividMed.12679+tlrc.${name4}
12787 SZ Neg Small 0 ./stats.BigSmallPEs_IndividMed.12787+tlrc.${name4}
12790 SZ Neg Small 0 ./stats.BigSmallPEs_IndividMed.12790+tlrc.${name4}
12833 SZ Neg Small 17 ./stats.BigSmallPEs_IndividMed.12833+tlrc.${name4}
12834 SZ Neg Small 11 ./stats.BigSmallPEs_IndividMed.12834+tlrc.${name4}
12863 SZ Neg Small 1 ./stats.BigSmallPEs_IndividMed.12863+tlrc.${name4}
12864 SZ Neg Small 15 ./stats.BigSmallPEs_IndividMed.12864+tlrc.${name4}
12874 SZ Neg Small 8 ./stats.BigSmallPEs_IndividMed.12874+tlrc.${name4}
12882 SZ Neg Small 10 ./stats.BigSmallPEs_IndividMed.12882+tlrc.${name4}
12900 SZ Neg Small 11 ./stats.BigSmallPEs_IndividMed.12900+tlrc.${name4}
12906 SZ Neg Small 20 ./stats.BigSmallPEs_IndividMed.12906+tlrc.${name4}
12953 SZ Neg Small 6 ./stats.BigSmallPEs_IndividMed.12953+tlrc.${name4}
12962 SZ Neg Small 18 ./stats.BigSmallPEs_IndividMed.12962+tlrc.${name4}
13063 SZ Neg Small 10 ./stats.BigSmallPEs_IndividMed.13063+tlrc.${name4}
13125 SZ Neg Small 25 ./stats.BigSmallPEs_IndividMed.13125+tlrc.${name4}

ptaylor · January 24, 2018, 2:21am

I wonder if you need to have double quotes where you use your defined variables?
That is, instead of:


 12352 HV Pos Large 0 ./stats.BigSmallPEs_IndividMed.12352+tlrc.${name1} \

you would have:


 12352 HV Pos Large 0 ./stats.BigSmallPEs_IndividMed.12352+tlrc."${name1}" \

?

Otherwise, I don’t think your squarebrackets in the variable string are being protected. It’s been a while since I’ve used sh/bash, but that is what I would do if it were tcsh.

–pt

jwaltz · January 24, 2018, 4:46am

Hi-

I get the same error, with quotes around the brackets, and if I run it in tcsh. I also did the equivalent of dos2unix to remove possible ^M’s.

Why does it think the dataTable is of length ZERO?

Thanks,

Jim Waltz

Gang · January 24, 2018, 4:55pm

Pessig_3dMVM_DXxPEVALxPEMAGxASI.sh: 13: Pessig_3dMVM_DXxPEVALxPEMAGxASI.sh: -wsVars: not found
Pessig_3dMVM_DXxPEVALxPEMAGxASI.sh: 15: Pessig_3dMVM_DXxPEVALxPEMAGxASI.sh: -jobs: not found

The two lines above indicate that you have at least an extra space after a backslash in one of the first few lines.

jwaltz · January 24, 2018, 5:51pm

Hi-

I discovered that, I am embarrassed to say, and I apologize.

But now I have ANOTHER problem, after the data load:

[1] “Great, test run passed at voxel (35, 63, 50)!”
[1] “Start to compute 101 slices along Z axis. You can monitor the progress”
[1] “and estimate the total run time as shown below.”
[1] “01/24/18 12:45:20.856”
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Warning in install.packages(pkgs_miss, dep = TRUE, repos = “http://watson.nci.nih.gov/cran_mirror/”) :
‘lib = “/usr/local/lib/R/site-library”’ is not writable
Error in install.packages(pkgs_miss, dep = TRUE, repos = “http://watson.nci.nih.gov/cran_mirror/”) :
unable to install packages
Calls: pkgLoad → install.packages
Execution halted

What packages is supposed to be loaded here?

jw

Gang · January 24, 2018, 6:26pm

It looks like that you’re missing some R packages. Try the following command on the terminal before you run the 3dMVM script:

rPkgsInstall -pkgs ALL -site …

Replace the … above with “h t t p://cran.us.r-project.org” (keep the quotes but remove the spaces among h t t p)

The current interface for 3dMVM and 3dLME is notoriously vulnerable to specification errors. Justin Rajendra is developing a script validator that will hopefully alleviate the problem.