AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

|
October 28, 2020 11:33AM
Hello. I have been trying to run 3dLME script but it is not working. The error says:

"Error in if (len%%wd != 0) errex.AFNI(paste("The content under -dataTable is not rectangular !", : argument is of length zero
Calls: process.LME.opts
Execution halted
./GM_script.sh: line 2: -mask: command not found
./GM_script.sh: line 3: -model: command not found
./GM_script.sh: line 4: -ranEff: command not found
./GM_script.sh: line 5: -SS_type: command not found
./GM_script.sh: line 6: -qVars: command not found
./GM_script.sh: line 7: -num_glt: command not found
and so on until the last line of the script.

It seems to me that there is some kind of problem with the first line but I have no idea what it could be. I will be most grateful for help with this issue. I attach below the full script.

3dLME -prefix GM_VBM_chrono_tod.nii -jobs 4 \
-mask mask.nii \
-model 'chronotype*time*sex+age+TIV' \
-ranEff '~1' \
-SS_type 3 \
-qVars 'age,TIV' \
-num_glt 6 \
-gltLabel 1 'E-M' -gltCode 1 'time : 1*evening -1*morning' \
-gltLabel 2 'EC_E-M' -gltCode 2 'chronotype : 1*EC time: 1*evening -1*morning' \
-gltLabel 3 'LC_E-M' -gltCode 3 'chronotype : 1*LC time: 1*evening -1*morning' \
-gltLabel 4 'M_LC-EC' -gltCode 4 'time : 1*morning chronotype : 1*LC -1*EC' \
-gltLabel 5 'E_LC-EC' -gltCode 5 'time : 1*evening chronotype : 1*LC -1*EC' \
-gltLabel 6 'Avg_LC-EC' -gltCode 6 'time : 1*morning & 1*evening chronotype : 1*LC -1*EC & 1*LC -1*EC' \
-dataTable \
Subj chronotype time sex age TIV InputFile \
sub02 EC morning M 33 1502 /morning/smoothed_mwp1sub-02_T1w_RO.nii \
sub04 EC morning F 26 1429 /morning/smoothed_mwp1sub-04_T1w_RO.nii \
sub07 EC morning M 27 1592 /morning/smoothed_mwp1sub-07_T1w_RO.nii \
sub08 EC morning F 22 1308 /morning/smoothed_mwp1sub-08_T1w_RO.nii \
sub14 EC morning F 26 1456 /morning/smoothed_mwp1sub-14_T1w_RO.nii \
sub15 EC morning F 22 1408 /morning/smoothed_mwp1sub-15_T1w_RO.nii \
sub16 EC morning F 22 1687 /morning/smoothed_mwp1sub-16_T1w_RO.nii \
sub17 EC morning M 23 1719 /morning/smoothed_mwp1sub-17_T1w_RO.nii \
sub18 EC morning M 23 1657 /morning/smoothed_mwp1sub-18_T1w_RO.nii \
sub19 EC morning F 35 1396 /morning/smoothed_mwp1sub-19_T1w_RO.nii \
sub20 LC morning M 20 1655 /morning/smoothed_mwp1sub-20_T1w_RO.nii \
sub21 LC morning M 22 1547 /morning/smoothed_mwp1sub-21_T1w_RO.nii \
sub22 LC morning F 22 1420 /morning/smoothed_mwp1sub-22_T1w_RO.nii \
sub26 LC morning F 24 1430 /morning/smoothed_mwp1sub-26_T1w_RO.nii \
sub29 LC morning F 20 1428 /morning/smoothed_mwp1sub-29_T1w_RO.nii \
sub38 LC morning F 24 1505 /morning/smoothed_mwp1sub-38_T1w_RO.nii \
sub39 LC morning F 33 1313 /morning/smoothed_mwp1sub-39_T1w_RO.nii \
sub40 LC morning M 25 1721 /morning/smoothed_mwp1sub-40_T1w_RO.nii \
sub41 LC morning M 21 1646 /morning/smoothed_mwp1sub-41_T1w_RO.nii \
sub42 LC morning F 22 1355 /morning/smoothed_mwp1sub-42_T1w_RO.nii \
sub43 LC morning M 23 1623 /morning/smoothed_mwp1sub-43_T1w_RO.nii \
sub44 LC morning F 25 1490 /morning/smoothed_mwp1sub-44_T1w_RO.nii \
sub46 LC morning F 25 1503 /morning/smoothed_mwp1sub-46_T1w_RO.nii \
sub47 EC morning F 25 1522 /morning/smoothed_mwp1sub-47_T1w_RO.nii \
sub48 EC morning M 24 1702 /morning/smoothed_mwp1sub-48_T1w_RO.nii \
sub49 EC morning M 21 1359 /morning/smoothed_mwp1sub-49_T1w_RO.nii \
sub50 LC morning F 22 1633 /morning/smoothed_mwp1sub-50_T1w_RO.nii \
sub51 LC morning F 20 1457 /morning/smoothed_mwp1sub-51_T1w_RO.nii \
sub52 LC morning M 25 1683 /morning/smoothed_mwp1sub-52_T1w_RO.nii \
sub53 EC morning F 31 1472 /morning/smoothed_mwp1sub-53_T1w_RO.nii \
sub54 EC morning F 22 1462 /morning/smoothed_mwp1sub-54_T1w_RO.nii \
sub55 LC morning M 22 1877 /morning/smoothed_mwp1sub-55_T1w_RO.nii \
sub56 LC morning F 22 1805 /morning/smoothed_mwp1sub-56_T1w_RO.nii \
sub57 LC morning F 23 1424 /morning/smoothed_mwp1sub-57_T1w_RO.nii \
sub58 LC morning F 24 1480 /morning/smoothed_mwp1sub-58_T1w_RO.nii \
sub59 LC morning M 21 1420 /morning/smoothed_mwp1sub-59_T1w_RO.nii \
sub60 LC morning F 30 1597 /morning/smoothed_mwp1sub-60_T1w_RO.nii \
sub61 LC morning F 22 1420 /morning/smoothed_mwp1sub-61_T1w_RO.nii \
sub62 LC morning M 25 1538 /morning/smoothed_mwp1sub-62_T1w_RO.nii \
sub63 LC morning F 26 1589 /morning/smoothed_mwp1sub-63_T1w_RO.nii \
sub64 LC morning F 24 1462 /morning/smoothed_mwp1sub-64_T1w_RO.nii \
sub65 LC morning M 20 1414 /morning/smoothed_mwp1sub-65_T1w_RO.nii \
sub66 LC morning M 26 1727 /morning/smoothed_mwp1sub-66_T1w_RO.nii \
sub67 LC morning F 22 1503 /morning/smoothed_mwp1sub-67_T1w_RO.nii \
sub68 LC morning F 28 1578 /morning/smoothed_mwp1sub-68_T1w_RO.nii \
sub69 EC morning M 31 1696 /morning/smoothed_mwp1sub-69_T1w_RO.nii \
sub70 EC morning F 21 1653 /morning/smoothed_mwp1sub-70_T1w_RO.nii \
sub72 LC morning F 21 1427 /morning/smoothed_mwp1sub-72_T1w_RO.nii \
sub73 EC morning F 26 1568 /morning/smoothed_mwp1sub-73_T1w_RO.nii \
sub74 EC morning F 23 1362 /morning/smoothed_mwp1sub-74_T1w_RO.nii \
sub75 EC morning F 21 1310 /morning/smoothed_mwp1sub-75_T1w_RO.nii \
sub76 EC morning M 20 1591 /morning/smoothed_mwp1sub-76_T1w_RO.nii \
sub77 EC morning M 24 1571 /morning/smoothed_mwp1sub-77_T1w_RO.nii \
sub78 LC morning F 22 1357 /morning/smoothed_mwp1sub-78_T1w_RO.nii \
sub79 EC morning M 26 1753 /morning/smoothed_mwp1sub-79_T1w_RO.nii \
sub80 EC morning F 22 1707 /morning/smoothed_mwp1sub-80_T1w_RO.nii \
sub81 EC morning F 29 1669 /morning/smoothed_mwp1sub-81_T1w_RO.nii \
sub82 EC morning F 21 1661 /morning/smoothed_mwp1sub-82_T1w_RO.nii \
sub83 EC morning F 31 1419 /morning/smoothed_mwp1sub-83_T1w_RO.nii \
sub84 EC morning F 22 1297 /morning/smoothed_mwp1sub-84_T1w_RO.nii \
sub85 EC morning F 20 1436 /morning/smoothed_mwp1sub-85_T1w_RO.nii \
sub86 EC morning F 22 1558 /morning/smoothed_mwp1sub-86_T1w_RO.nii \
sub87 EC morning M 31 1751 /morning/smoothed_mwp1sub-87_T1w_RO.nii \
sub89 EC morning M 23 1509 /morning/smoothed_mwp1sub-89_T1w_RO.nii \
sub91 LC morning M 25 1588 /morning/smoothed_mwp1sub-91_T1w_RO.nii \
sub92 LC morning M 23 1644 /morning/smoothed_mwp1sub-92_T1w_RO.nii \
sub93 LC morning F 23 1466 /morning/smoothed_mwp1sub-93_T1w_RO.nii \
sub95 LC morning F 24 1314 /morning/smoothed_mwp1sub-95_T1w_RO.nii \
sub99 EC morning M 22 1708 /morning/smoothed_mwp1sub-99_T1w_RO.nii \
sub102 EC morning M 26 1470 /morning/smoothed_mwp1sub-102_T1w_RO.nii \
sub103 EC morning M 24 1693 /morning/smoothed_mwp1sub-103_T1w_RO.nii \
sub104 EC morning F 21 1427 /morning/smoothed_mwp1sub-104_T1w_RO.nii \
sub105 EC morning F 22 1744 /morning/smoothed_mwp1sub-105_T1w_RO.nii \
sub106 LC morning M 31 1756 /morning/smoothed_mwp1sub-106_T1w_RO.nii \
sub02 EC evening M 33 1498 /evening/smoothed_mwp1sub-02_T1w_RO.nii \
sub04 EC evening F 26 1428 /evening/smoothed_mwp1sub-04_T1w_RO.nii \
sub07 EC evening M 27 1590 /evening/smoothed_mwp1sub-07_T1w_RO.nii \
sub08 EC evening F 22 1319 /evening/smoothed_mwp1sub-08_T1w_RO.nii \
sub14 EC evening F 26 1458 /evening/smoothed_mwp1sub-14_T1w_RO.nii \
sub15 EC evening F 22 1405 /evening/smoothed_mwp1sub-15_T1w_RO.nii \
sub16 EC evening F 22 1680 /evening/smoothed_mwp1sub-16_T1w_RO.nii \
sub17 EC evening M 23 1717 /evening/smoothed_mwp1sub-17_T1w_RO.nii \
sub18 EC evening M 23 1650 /evening/smoothed_mwp1sub-18_T1w_RO.nii \
sub19 EC evening F 35 1401 /evening/smoothed_mwp1sub-19_T1w_RO.nii \
sub20 LC evening M 20 1650 /evening/smoothed_mwp1sub-20_T1w_RO.nii \
sub21 LC evening M 22 1554 /evening/smoothed_mwp1sub-21_T1w_RO.nii \
sub22 LC evening F 22 1433 /evening/smoothed_mwp1sub-22_T1w_RO.nii \
sub26 LC evening F 24 1423 /evening/smoothed_mwp1sub-26_T1w_RO.nii \
sub29 LC evening F 20 1422 /evening/smoothed_mwp1sub-29_T1w_RO.nii \
sub38 LC evening F 24 1518 /evening/smoothed_mwp1sub-38_T1w_RO.nii \
sub39 LC evening F 33 1307 /evening/smoothed_mwp1sub-39_T1w_RO.nii \
sub40 LC evening M 25 1722 /evening/smoothed_mwp1sub-40_T1w_RO.nii \
sub41 LC evening M 21 1644 /evening/smoothed_mwp1sub-41_T1w_RO.nii \
sub42 LC evening F 22 1356 /evening/smoothed_mwp1sub-42_T1w_RO.nii \
sub43 LC evening M 23 1637 /evening/smoothed_mwp1sub-43_T1w_RO.nii \
sub44 LC evening F 25 1484 /evening/smoothed_mwp1sub-44_T1w_RO.nii \
sub46 LC evening F 25 1501 /evening/smoothed_mwp1sub-46_T1w_RO.nii \
sub47 EC evening F 25 1502 /evening/smoothed_mwp1sub-47_T1w_RO.nii \
sub48 EC evening M 24 1701 /evening/smoothed_mwp1sub-48_T1w_RO.nii \
sub49 EC evening M 21 1363 /evening/smoothed_mwp1sub-49_T1w_RO.nii \
sub50 LC evening F 22 1650 /evening/smoothed_mwp1sub-50_T1w_RO.nii \
sub51 LC evening F 20 1464 /evening/smoothed_mwp1sub-51_T1w_RO.nii \
sub52 LC evening M 25 1684 /evening/smoothed_mwp1sub-52_T1w_RO.nii \
sub53 EC evening F 31 1481 /evening/smoothed_mwp1sub-53_T1w_RO.nii \
sub54 EC evening F 22 1446 /evening/smoothed_mwp1sub-54_T1w_RO.nii \
sub55 LC evening M 22 1869 /evening/smoothed_mwp1sub-55_T1w_RO.nii \
sub56 LC evening F 22 1810 /evening/smoothed_mwp1sub-56_T1w_RO.nii \
sub57 LC evening F 23 1424 /evening/smoothed_mwp1sub-57_T1w_RO.nii \
sub58 LC evening F 24 1479 /evening/smoothed_mwp1sub-58_T1w_RO.nii \
sub59 LC evening M 21 1415 /evening/smoothed_mwp1sub-59_T1w_RO.nii \
sub60 LC evening F 30 1590 /evening/smoothed_mwp1sub-60_T1w_RO.nii \
sub61 LC evening F 22 1420 /evening/smoothed_mwp1sub-61_T1w_RO.nii \
sub62 LC evening M 25 1520 /evening/smoothed_mwp1sub-62_T1w_RO.nii \
sub63 LC evening F 26 1594 /evening/smoothed_mwp1sub-63_T1w_RO.nii \
sub64 LC evening F 24 1467 /evening/smoothed_mwp1sub-64_T1w_RO.nii \
sub65 LC evening M 20 1417 /evening/smoothed_mwp1sub-65_T1w_RO.nii \
sub66 LC evening M 26 1728 /evening/smoothed_mwp1sub-66_T1w_RO.nii \
sub67 LC evening F 22 1494 /evening/smoothed_mwp1sub-67_T1w_RO.nii \
sub68 LC evening F 28 1593 /evening/smoothed_mwp1sub-68_T1w_RO.nii \
sub69 EC evening M 31 1697 /evening/smoothed_mwp1sub-69_T1w_RO.nii \
sub70 EC evening F 21 1654 /evening/smoothed_mwp1sub-70_T1w_RO.nii \
sub72 LC evening F 21 1433 /evening/smoothed_mwp1sub-72_T1w_RO.nii \
sub73 EC evening F 26 1572 /evening/smoothed_mwp1sub-73_T1w_RO.nii \
sub74 EC evening F 23 1373 /evening/smoothed_mwp1sub-74_T1w_RO.nii \
sub75 EC evening F 21 1307 /evening/smoothed_mwp1sub-75_T1w_RO.nii \
sub76 EC evening M 20 1594 /evening/smoothed_mwp1sub-76_T1w_RO.nii \
sub77 EC evening M 24 1579 /evening/smoothed_mwp1sub-77_T1w_RO.nii \
sub78 LC evening F 22 1350 /evening/smoothed_mwp1sub-78_T1w_RO.nii \
sub79 EC evening M 26 1759 /evening/smoothed_mwp1sub-79_T1w_RO.nii \
sub80 EC evening F 22 1698 /evening/smoothed_mwp1sub-80_T1w_RO.nii \
sub81 EC evening F 29 1664 /evening/smoothed_mwp1sub-81_T1w_RO.nii \
sub82 EC evening F 21 1656 /evening/smoothed_mwp1sub-82_T1w_RO.nii \
sub83 EC evening F 31 1407 /evening/smoothed_mwp1sub-83_T1w_RO.nii \
sub84 EC evening F 22 1297 /evening/smoothed_mwp1sub-84_T1w_RO.nii \
sub85 EC evening F 20 1438 /evening/smoothed_mwp1sub-85_T1w_RO.nii \
sub86 EC evening F 22 1555 /evening/smoothed_mwp1sub-86_T1w_RO.nii \
sub87 EC evening M 31 1746 /evening/smoothed_mwp1sub-87_T1w_RO.nii \
sub89 EC evening M 23 1520 /evening/smoothed_mwp1sub-89_T1w_RO.nii \
sub91 LC evening M 25 1594 /evening/smoothed_mwp1sub-91_T1w_RO.nii \
sub92 LC evening M 23 1638 /evening/smoothed_mwp1sub-92_T1w_RO.nii \
sub93 LC evening F 23 1462 /evening/smoothed_mwp1sub-93_T1w_RO.nii \
sub95 LC evening F 24 1311 /evening/smoothed_mwp1sub-95_T1w_RO.nii \
sub99 EC evening M 22 1716 /evening/smoothed_mwp1sub-99_T1w_RO.nii \
sub102 EC evening M 26 1468 /evening/smoothed_mwp1sub-102_T1w_RO.nii \
sub103 EC evening M 24 1696 /evening/smoothed_mwp1sub-103_T1w_RO.nii \
sub104 EC evening F 21 1434 /evening/smoothed_mwp1sub-104_T1w_RO.nii \
sub105 EC evening F 22 1732 /evening/smoothed_mwp1sub-105_T1w_RO.nii \
sub106 LC evening M 31 1754 /evening/smoothed_mwp1sub-106_T1w_RO.nii
Subject Author Posted

3dLME issue

lavr October 28, 2020 11:33AM

Re: 3dLME issue

gang October 28, 2020 11:51AM

Re: 3dLME issue

lavr October 28, 2020 01:46PM