3dMVM matrix issue

bjaso · May 15, 2018, 1:18am

I’m trying to run 3dMVM and I cannot understand the error I am receiving. After a lot of googling it appears that it might be an issue with R so I updated my R packages but to no avail. Any ideas how I can fix this error?
This is the script I’m running:
3dMVM -prefix ‘MVM_attempt.nii’
-bsVars ‘Group:condition’
-qVars ‘age,FD’
-num_glt 3
-gltLabel 1 HC_recurrent -gltCode 1 ‘Group : 1HC - 1RC condition : 1rest’
-gltLabel 2 HC_single -gltCode 2 'Group : 1HC - 1SN condition : 1rest’
-gltLabel 3 single_recur -gltCode 3 ‘Group : 1SN - 1RC condition : 1*rest’
-dataTable @table5.txt

And the table looks like this:
Subj age FD condition Group Inputfile
28185 26 0.0774 rest HC /Users/Profile/Desktop/imaging/all/28185_mssd_final.nii.gz
28352 23 0.1481 rest HC /Users/Profile/Desktop/imaging/all/28352_mssd_final.nii.gz
33747 26 0.0976 rest HC /Users/Profile/Desktop/imaging/all/33747_mssd_final.nii.gz
37112 35 0.1282 rest HC /Users/Profile/Desktop/imaging/all/37112_mssd_final.nii.gz
38520 62 0.1003 rest HC /Users/Profile/Desktop/imaging/all/38520_mssd_final.nii.gz
38623 42 0.1139 rest HC /Users/Profile/Desktop/imaging/all/38623_mssd_final.nii.gz
38731 21 0.1024 rest HC /Users/Profile/Desktop/imaging/all/38731_mssd_final.nii.gz
39041 60 0.0957 rest HC /Users/Profile/Desktop/imaging/all/39041_mssd_final.nii.gz
39159 18 0.0884 rest HC /Users/Profile/Desktop/imaging/all/39159_mssd_final.nii.gz
39168 50 0.2882 rest HC /Users/Profile/Desktop/imaging/all/39168_mssd_final.nii.gz
39218 26 0.1046 rest HC /Users/Profile/Desktop/imaging/all/39218_mssd_final.nii.gz
39331 59 0.0823 rest HC /Users/Profile/Desktop/imaging/all/39331_mssd_final.nii.gz
39353 52 0.1087 rest HC /Users/Profile/Desktop/imaging/all/39353_mssd_final.nii.gz
39393 49 0.1332 rest HC /Users/Profile/Desktop/imaging/all/39393_mssd_final.nii.gz
39431 33 0.0834 rest HC /Users/Profile/Desktop/imaging/all/39431_mssd_final.nii.gz
39432 59 0.1066 rest HC /Users/Profile/Desktop/imaging/all/39432_mssd_final.nii.gz
39635 53 0.1144 rest HC /Users/Profile/Desktop/imaging/all/39635_mssd_final.nii.gz
39669 61 0.0729 rest HC /Users/Profile/Desktop/imaging/all/39669_mssd_final.nii.gz
39686 21 0.1883 rest HC /Users/Profile/Desktop/imaging/all/39686_mssd_final.nii.gz
39820 57 0.1370 rest HC /Users/Profile/Desktop/imaging/all/39820_mssd_final.nii.gz
39895 50 0.1445 rest HC /Users/Profile/Desktop/imaging/all/39895_mssd_final.nii.gz
39974 60 0.1948 rest HC /Users/Profile/Desktop/imaging/all/39974_mssd_final.nii.gz
40383 52 0.1244 rest HC /Users/Profile/Desktop/imaging/all/40383_mssd_final.nii.gz
40461 52 0.1258 rest HC /Users/Profile/Desktop/imaging/all/40461_mssd_final.nii.gz
40524 25 0.1216 rest HC /Users/Profile/Desktop/imaging/all/40524_mssd_final.nii.gz
40525 43 0.1335 rest HC /Users/Profile/Desktop/imaging/all/40525_mssd_final.nii.gz
40573 27 0.1313 rest HC /Users/Profile/Desktop/imaging/all/40573_mssd_final.nii.gz
40628 20 0.1263 rest HC /Users/Profile/Desktop/imaging/all/40628_mssd_final.nii.gz
40757 49 0.1294 rest HC /Users/Profile/Desktop/imaging/all/40757_mssd_final.nii.gz
40944 35 0.1497 rest HC /Users/Profile/Desktop/imaging/all/40944_mssd_final.nii.gz
43384 21 0.0969 rest HC /Users/Profile/Desktop/imaging/all/43384_mssd_final.nii.gz
43450 22 0.0727 rest HC /Users/Profile/Desktop/imaging/all/43450_mssd_final.nii.gz
43462 21 0.1084 rest HC /Users/Profile/Desktop/imaging/all/43462_mssd_final.nii.gz
43520 28 0.0792 rest HC /Users/Profile/Desktop/imaging/all/43520_mssd_final.nii.gz
43521 44 0.0968 rest HC /Users/Profile/Desktop/imaging/all/43521_mssd_final.nii.gz
43634 58 0.0901 rest HC /Users/Profile/Desktop/imaging/all/43634_mssd_final.nii.gz
43649 22 0.1415 rest HC /Users/Profile/Desktop/imaging/all/43649_mssd_final.nii.gz
43677 25 0.0753 rest HC /Users/Profile/Desktop/imaging/all/43677_mssd_final.nii.gz
43762 53 0.0746 rest HC /Users/Profile/Desktop/imaging/all/43762_mssd_final.nii.gz
44012 19 0.1118 rest HC /Users/Profile/Desktop/imaging/all/44012_mssd_final.nii.gz
44131 22 0.0977 rest HC /Users/Profile/Desktop/imaging/all/44131_mssd_final.nii.gz
44171 18 0.1341 rest HC /Users/Profile/Desktop/imaging/all/44171_mssd_final.nii.gz
44291 24 0.0806 rest HC /Users/Profile/Desktop/imaging/all/44291_mssd_final.nii.gz
44344 63 0.2118 rest HC /Users/Profile/Desktop/imaging/all/44344_mssd_final.nii.gz
44345 47 0.0840 rest HC /Users/Profile/Desktop/imaging/all/44345_mssd_final.nii.gz
44370 56 0.1147 rest HC /Users/Profile/Desktop/imaging/all/44370_mssd_final.nii.gz
50720 40 0.0972 rest HC /Users/Profile/Desktop/imaging/all/50720_mssd_final.nii.gz
50795 22 0.0974 rest HC /Users/Profile/Desktop/imaging/all/50795_mssd_final.nii.gz
51063 18 0.0857 rest HC /Users/Profile/Desktop/imaging/all/51063_mssd_final.nii.gz
51456 62 0.1923 rest HC /Users/Profile/Desktop/imaging/all/51456_mssd_final.nii.gz
51477 21 0.1761 rest HC /Users/Profile/Desktop/imaging/all/51477_mssd_final.nii.gz
51513 40 0.1228 rest HC /Users/Profile/Desktop/imaging/all/51513_mssd_final.nii.gz
51514 21 0.0989 rest HC /Users/Profile/Desktop/imaging/all/51514_mssd_final.nii.gz
51638 18 0.0894 rest HC /Users/Profile/Desktop/imaging/all/51638_mssd_final.nii.gz
51679 27 0.0839 rest HC /Users/Profile/Desktop/imaging/all/51679_mssd_final.nii.gz
51882 53 0.0842 rest HC /Users/Profile/Desktop/imaging/all/51882_mssd_final.nii.gz
52126 24 0.0802 rest HC /Users/Profile/Desktop/imaging/all/52126_mssd_final.nii.gz
52197 18 0.1670 rest HC /Users/Profile/Desktop/imaging/all/52197_mssd_final.nii.gz
52307 22 0.0803 rest HC /Users/Profile/Desktop/imaging/all/52307_mssd_final.nii.gz
52319 47 0.0867 rest HC /Users/Profile/Desktop/imaging/all/52319_mssd_final.nii.gz
52502 18 0.0909 rest HC /Users/Profile/Desktop/imaging/all/52502_mssd_final.nii.gz
52577 50 0.1079 rest HC /Users/Profile/Desktop/imaging/all/52577_mssd_final.nii.gz
53627 53 0.1601 rest HC /Users/Profile/Desktop/imaging/all/53627_mssd_final.nii.gz
53874 47 0.0875 rest HC /Users/Profile/Desktop/imaging/all/53874_mssd_final.nii.gz
54532 22 0.1647 rest HC /Users/Profile/Desktop/imaging/all/54532_mssd_final.nii.gz
54534 21 0.0676 rest HC /Users/Profile/Desktop/imaging/all/54534_mssd_final.nii.gz
54895 59 0.0909 rest HC /Users/Profile/Desktop/imaging/all/54895_mssd_final.nii.gz
55061 53 0.0830 rest HC /Users/Profile/Desktop/imaging/all/55061_mssd_final.nii.gz
55352 59 0.1127 rest HC /Users/Profile/Desktop/imaging/all/55352_mssd_final.nii.gz
55738 25 0.0788 rest HC /Users/Profile/Desktop/imaging/all/55738_mssd_final.nii.gz
55806 30 0.1189 rest HC /Users/Profile/Desktop/imaging/all/55806_mssd_final.nii.gz
56164 62 0.1117 rest HC /Users/Profile/Desktop/imaging/all/56164_mssd_final.nii.gz
35827 36 0.1230 rest HC /Users/Profile/Desktop/imaging/all/35827_mssd_final.nii.gz
35840 25 0.1221 rest HC /Users/Profile/Desktop/imaging/all/35840_mssd_final.nii.gz
39391 37 0.1132 rest HC /Users/Profile/Desktop/imaging/all/39391_mssd_final.nii.gz
39560 48 0.1719 rest HC /Users/Profile/Desktop/imaging/all/39560_mssd_final.nii.gz
39607 42 0.2238 rest HC /Users/Profile/Desktop/imaging/all/39607_mssd_final.nii.gz
40599 61 0.1612 rest HC /Users/Profile/Desktop/imaging/all/40599_mssd_final.nii.gz
40678 46 0.0889 rest HC /Users/Profile/Desktop/imaging/all/40678_mssd_final.nii.gz
56098 34 0.1410 rest HC /Users/Profile/Desktop/imaging/all/56098_mssd_final.nii.gz
28380 60 0.0824 rest SN /Users/Profile/Desktop/imaging/all/28380_mssd_final.nii.gz
28552 61 0.0903 rest SN /Users/Profile/Desktop/imaging/all/28552_mssd_final.nii.gz
28694 25 0.1137 rest SN /Users/Profile/Desktop/imaging/all/28694_mssd_final.nii.gz
28754 42 0.1256 rest RC /Users/Profile/Desktop/imaging/all/28754_mssd_final.nii.gz
28929 63 0.1148 rest SN /Users/Profile/Desktop/imaging/all/28929_mssd_final.nii.gz
28995 49 0.1034 rest SN /Users/Profile/Desktop/imaging/all/28995_mssd_final.nii.gz
29126 34 0.0955 rest RC /Users/Profile/Desktop/imaging/all/29126_mssd_final.nii.gz
29303 19 0.0953 rest RC /Users/Profile/Desktop/imaging/all/29303_mssd_final.nii.gz
31605 39 0.1736 rest SN /Users/Profile/Desktop/imaging/all/31605_mssd_final.nii.gz
32007 20 0.0760 rest SN /Users/Profile/Desktop/imaging/all/32007_mssd_final.nii.gz
32876 60 0.1200 rest RC /Users/Profile/Desktop/imaging/all/32876_mssd_final.nii.gz
34854 21 0.1265 rest SN /Users/Profile/Desktop/imaging/all/34854_mssd_final.nii.gz
35606 48 0.1116 rest RC /Users/Profile/Desktop/imaging/all/35606_mssd_final.nii.gz
35943 26 0.1481 rest SN /Users/Profile/Desktop/imaging/all/35943_mssd_final.nii.gz
37421 44 0.1831 rest RC /Users/Profile/Desktop/imaging/all/37421_mssd_final.nii.gz
37545 58 0.1375 rest SN /Users/Profile/Desktop/imaging/all/37545_mssd_final.nii.gz
37767 54 0.1141 rest SN /Users/Profile/Desktop/imaging/all/37767_mssd_final.nii.gz
37848 32 0.1114 rest RC /Users/Profile/Desktop/imaging/all/37848_mssd_final.nii.gz
38115 38 0.1758 rest SN /Users/Profile/Desktop/imaging/all/38115_mssd_final.nii.gz
39257 55 0.1918 rest RC /Users/Profile/Desktop/imaging/all/39257_mssd_final.nii.gz
39276 58 0.1561 rest RC /Users/Profile/Desktop/imaging/all/39276_mssd_final.nii.gz
39685 50 0.1355 rest SN /Users/Profile/Desktop/imaging/all/39685_mssd_final.nii.gz
39699 59 0.1449 rest RC /Users/Profile/Desktop/imaging/all/39699_mssd_final.nii.gz
39755 22 0.1705 rest RC /Users/Profile/Desktop/imaging/all/39755_mssd_final.nii.gz
40151 32 0.0753 rest RC /Users/Profile/Desktop/imaging/all/40151_mssd_final.nii.gz
40580 60 0.0902 rest SN /Users/Profile/Desktop/imaging/all/40580_mssd_final.nii.gz
41540 46 0.1420 rest SN /Users/Profile/Desktop/imaging/all/41540_mssd_final.nii.gz
43617 47 0.1522 rest SN /Users/Profile/Desktop/imaging/all/43617_mssd_final.nii.gz
43704 27 0.0811 rest SN /Users/Profile/Desktop/imaging/all/43704_mssd_final.nii.gz
43998 28 0.0674 rest RC /Users/Profile/Desktop/imaging/all/43998_mssd_final.nii.gz
44130 22 0.1099 rest RC /Users/Profile/Desktop/imaging/all/44130_mssd_final.nii.gz
44405 49 0.1435 rest SN /Users/Profile/Desktop/imaging/all/44405_mssd_final.nii.gz
45589 63 0.1790 rest RC /Users/Profile/Desktop/imaging/all/45589_mssd_final.nii.gz
50742 53 0.0787 rest SN /Users/Profile/Desktop/imaging/all/50742_mssd_final.nii.gz
50998 47 0.1323 rest RC /Users/Profile/Desktop/imaging/all/50998_mssd_final.nii.gz
51774 30 0.1448 rest SN /Users/Profile/Desktop/imaging/all/51774_mssd_final.nii.gz
51835 60 0.1811 rest RC /Users/Profile/Desktop/imaging/all/51835_mssd_final.nii.gz
52180 47 0.1460 rest SN /Users/Profile/Desktop/imaging/all/52180_mssd_final.nii.gz
52340 33 0.0793 rest SN /Users/Profile/Desktop/imaging/all/52340_mssd_final.nii.gz
52612 47 0.1258 rest SN /Users/Profile/Desktop/imaging/all/52612_mssd_final.nii.gz
53455 38 0.1418 rest SN /Users/Profile/Desktop/imaging/all/53455_mssd_final.nii.gz
53901 43 0.1380 rest SN /Users/Profile/Desktop/imaging/all/53901_mssd_final.nii.gz
54019 32 0.0658 rest SN /Users/Profile/Desktop/imaging/all/54019_mssd_final.nii.gz
54173 20 0.0911 rest SN /Users/Profile/Desktop/imaging/all/54173_mssd_final.nii.gz
54358 56 0.1166 rest SN /Users/Profile/Desktop/imaging/all/54358_mssd_final.nii.gz
54504 25 0.0860 rest SN /Users/Profile/Desktop/imaging/all/54504_mssd_final.nii.gz
55373 28 0.0859 rest SN /Users/Profile/Desktop/imaging/all/55373_mssd_final.nii.gz
56097 26 0.0873 rest SN /Users/Profile/Desktop/imaging/all/56097_mssd_final.nii.gz
56949 33 0.0866 rest RC /Users/Profile/Desktop/imaging/all/56949_mssd_final.nii.gz
57235 21 0.1033 rest RC /Users/Profile/Desktop/imaging/all/57235_mssd_final.nii.gz
57786 22 0.0780 rest RC /Users/Profile/Desktop/imaging/all/57786_mssd_final.nii.gz
58621 21 0.1304 rest SN /Users/Profile/Desktop/imaging/all/58621_mssd_final.nii.gz
59428 34 0.0928 rest SN /Users/Profile/Desktop/imaging/all/59428_mssd_final.nii.gz
59911 26 0.1045 rest SN /Users/Profile/Desktop/imaging/all/59911_mssd_final.nii.gz
60279 28 0.0792 rest SN /Users/Profile/Desktop/imaging/all/60279_mssd_final.nii.gz
31272 22 0.2261 rest RC /Users/Profile/Desktop/imaging/all/31272_mssd_final.nii.gz
38718 21 0.0864 rest SN /Users/Profile/Desktop/imaging/all/38718_mssd_final.nii.gz
39488 27 0.1453 rest RC /Users/Profile/Desktop/imaging/all/39488_mssd_final.nii.gz
40493 45 0.0929 rest SN /Users/Profile/Desktop/imaging/all/40493_mssd_final.nii.gz
40915 21 0.0922 rest SN /Users/Profile/Desktop/imaging/all/40915_mssd_final.nii.gz
44011 44 0.0905 rest SN /Users/Profile/Desktop/imaging/all/44011_mssd_final.nii.gz
53578 21 0.1108 rest SN /Users/Profile/Desktop/imaging/all/53578_mssd_final.nii.gz

Thank you!
Brittany

Gang · May 15, 2018, 5:36pm

Brittany,

What error message did you get?

A couple of issues:

The space between “-” sign and “1” should be removed in the following three lines:

-gltLabel 1 HC_recurrent -gltCode 1 ‘Group : 1HC - 1RC condition : 1rest’ \
-gltLabel 2 HC_single -gltCode 2 'Group : 1HC - 1SN condition : 1rest’ \
-gltLabel 3 single_recur -gltCode 3 ‘Group : 1SN - 1RC condition : 1*rest’ \

For the following line:

-bsVars ‘Group:condition’ \

is ‘condition’ a between-subjects factor? If so, it should be

-bsVars ‘Group*condition’ \

bjaso · May 15, 2018, 8:51pm

Yikes, sorry! This error message was: Error in glfList[[ii]][sq, jj] ← as.numeric(sepTerms[seq(1, length(sepTerms), :
incorrect number of subscripts on matrix

However, I fixed the spacing issue in the -glt lines and changed the bsvar to just “group” because the condition variable wasn’t necessary for these analyses and it seems to be working just fine now. Thank you!