Here is the script. I ran a paired ttest between two conditions and included a covariate.
3dttest++ -prefix /imaging/Analysis/Ttest_Feb2022/FeelvsNat_Neg -paired \
-setA Feel_Neg \
1422 /imaging/1422/1422.results/Feel_Bad_Resp+tlrc.BRIK \
1423 /imaging/1423/1423.results/Feel_Bad_Resp+tlrc.BRIK \
1425 /imaging/1425/1425.results/Feel_Bad_Resp+tlrc.BRIK \
1426 /imaging/1426/1426_giantmove.results/Feel_Bad_Resp+tlrc.BRIK \
1428 /imaging/1428/1428.results/Feel_Bad_Resp+tlrc.BRIK \
1433 /imaging/1433/1433_giantmove.results/Feel_Bad_Resp+tlrc.BRIK \
1438 /imaging/1438/1438.results/Feel_Bad_Resp+tlrc.BRIK \
1439 /imaging/1439/1439.results/Feel_Bad_Resp+tlrc.BRIK \
1443 /imaging/1443/1443.results/Feel_Bad_Resp+tlrc.BRIK \
1444 /imaging/1444/1444.results/Feel_Bad_Resp+tlrc.BRIK \
1448 /imaging/1448/1448.results/Feel_Bad_Resp+tlrc.BRIK \
1451 /imaging/1451/1451.results/Feel_Bad_Resp+tlrc.BRIK \
1452 /imaging/1452/1452.results/Feel_Bad_Resp+tlrc.BRIK \
1453 /imaging/1453/1453.results/Feel_Bad_Resp+tlrc.BRIK \
1459 /imaging/1459/1459.results/Feel_Bad_Resp+tlrc.BRIK \
1477 /imaging/1477/1477.results/Feel_Bad_Resp+tlrc.BRIK \
1478 /imaging/1478/1478.results/Feel_Bad_Resp+tlrc.BRIK \
1479 /imaging/1479/1479_giantmove.results/Feel_Bad_Resp+tlrc.BRIK \
1480 /imaging/1480/1480.results/Feel_Bad_Resp+tlrc.BRIK \
1486 /imaging/1486/1486.results/Feel_Bad_Resp+tlrc.BRIK \
1489 /imaging/1489/1489.results/Feel_Bad_Resp+tlrc.BRIK \
1490 /imaging/1490/1490.results/Feel_Bad_Resp+tlrc.BRIK \
1491 /imaging/1491/1491.results/Feel_Bad_Resp+tlrc.BRIK \
1431 /imaging/1431/1431.results/Feel_Bad_Resp+tlrc.BRIK \
1432 /imaging/1432/1432.results/Feel_Bad_Resp+tlrc.BRIK \
1437 /imaging/1437/1437.results/Feel_Bad_Resp+tlrc.BRIK \
1440 /imaging/1440/1440.results/Feel_Bad_Resp+tlrc.BRIK \
1441 /imaging/1441/1441.results/Feel_Bad_Resp+tlrc.BRIK \
1442 /imaging/1442/1442_giantmove.results/Feel_Bad_Resp+tlrc.BRIK \
1445 /imaging/1445/1445.results/Feel_Bad_Resp+tlrc.BRIK \
1447 /imaging/1447/1447.results/Feel_Bad_Resp+tlrc.BRIK \
1454 /imaging/1454/1454_giantmove.results/Feel_Bad_Resp+tlrc.BRIK \
1455 /imaging/1455/1455.results/Feel_Bad_Resp+tlrc.BRIK \
1456 /imaging/1456/1456.results/Feel_Bad_Resp+tlrc.BRIK \
1460 /imaging/1460/1460.results/Feel_Bad_Resp+tlrc.BRIK \
1462 /imaging/1462/1462.results/Feel_Bad_Resp+tlrc.BRIK \
1463 /imaging/1463/1463.results/Feel_Bad_Resp+tlrc.BRIK \
1464 /imaging/1464/1464.results/Feel_Bad_Resp+tlrc.BRIK \
1465 /imaging/1465/1465.results/Feel_Bad_Resp+tlrc.BRIK \
1467 /imaging/1467/1467.results/Feel_Bad_Resp+tlrc.BRIK \
1468 /imaging/1468/1468.results/Feel_Bad_Resp+tlrc.BRIK \
1469 /imaging/1469/1469.results/Feel_Bad_Resp+tlrc.BRIK \
1471 /imaging/1471/1471_giantmove.results/Feel_Bad_Resp+tlrc.BRIK \
1474 /imaging/1474/1474.results/Feel_Bad_Resp+tlrc.BRIK \
1481 /imaging/1481/1481.results/Feel_Bad_Resp+tlrc.BRIK \
1482 /imaging/1482/1482.results/Feel_Bad_Resp+tlrc.BRIK \
1484 /imaging/1484/1484.results/Feel_Bad_Resp+tlrc.BRIK \
-setB Nat_Neg \
1422 /imaging/1422/1422.results/Nat_neg_Resp+tlrc.BRIK \
1423 /imaging/1423/1423.results/Nat_neg_Resp+tlrc.BRIK \
1425 /imaging/1425/1425.results/Nat_neg_Resp+tlrc.BRIK \
1426 /imaging/1426/1426_giantmove.results/Nat_neg_Resp+tlrc.BRIK \
1428 /imaging/1428/1428.results/Nat_neg_Resp+tlrc.BRIK \
1433 /imaging/1433/1433_giantmove.results/Nat_neg_Resp+tlrc.BRIK \
1438 /imaging/1438/1438.results/Nat_neg_Resp+tlrc.BRIK \
1439 /imaging/1439/1439.results/Nat_neg_Resp+tlrc.BRIK \
1443 /imaging/1443/1443.results/Nat_neg_Resp+tlrc.BRIK \
1444 /imaging/1444/1444.results/Nat_neg_Resp+tlrc.BRIK \
1448 /imaging/1448/1448.results/Nat_neg_Resp+tlrc.BRIK \
1451 /imaging/1451/1451.results/Nat_neg_Resp+tlrc.BRIK \
1452 /imaging/1452/1452.results/Nat_neg_Resp+tlrc.BRIK \
1453 /imaging/1453/1453.results/Nat_neg_Resp+tlrc.BRIK \
1459 /imaging/1459/1459.results/Nat_neg_Resp+tlrc.BRIK \
1477 /imaging/1477/1477.results/Nat_neg_Resp+tlrc.BRIK \
1478 /imaging/1478/1478.results/Nat_neg_Resp+tlrc.BRIK \
1479 /imaging/1479/1479_giantmove.results/Nat_neg_Resp+tlrc.BRIK \
1480 /imaging/1480/1480.results/Nat_neg_Resp+tlrc.BRIK \
1486 /imaging/1486/1486.results/Nat_neg_Resp+tlrc.BRIK \
1489 /imaging/1489/1489.results/Nat_neg_Resp+tlrc.BRIK \
1490 /imaging/1490/1490.results/Nat_neg_Resp+tlrc.BRIK \
1491 /imaging/1491/1491.results/Nat_neg_Resp+tlrc.BRIK \
1431 /imaging/1431/1431.results/Nat_neg_Resp+tlrc.BRIK \
1432 /imaging/1432/1432.results/Nat_neg_Resp+tlrc.BRIK \
1437 /imaging/1437/1437.results/Nat_neg_Resp+tlrc.BRIK \
1440 /imaging/1440/1440.results/Nat_neg_Resp+tlrc.BRIK \
1441 /imaging/1441/1441.results/Nat_neg_Resp+tlrc.BRIK \
1442 /imaging/1442/1442_giantmove.results/Nat_neg_Resp+tlrc.BRIK \
1445 /imaging/1445/1445.results/Nat_neg_Resp+tlrc.BRIK \
1447 /imaging/1447/1447.results/Nat_neg_Resp+tlrc.BRIK \
1454 /imaging/1454/1454_giantmove.results/Nat_neg_Resp+tlrc.BRIK \
1455 /imaging/1455/1455.results/Nat_neg_Resp+tlrc.BRIK \
1456 /imaging/1456/1456.results/Nat_neg_Resp+tlrc.BRIK \
1460 /imaging/1460/1460.results/Nat_neg_Resp+tlrc.BRIK \
1462 /imaging/1462/1462.results/Nat_neg_Resp+tlrc.BRIK \
1463 /imaging/1463/1463.results/Nat_neg_Resp+tlrc.BRIK \
1464 /imaging/1464/1464.results/Nat_neg_Resp+tlrc.BRIK \
1465 /imaging/1465/1465.results/Nat_neg_Resp+tlrc.BRIK \
1467 /imaging/1467/1467.results/Nat_neg_Resp+tlrc.BRIK \
1468 /imaging/1468/1468.results/Nat_neg_Resp+tlrc.BRIK \
1469 /imaging/1469/1469.results/Nat_neg_Resp+tlrc.BRIK \
1471 /imaging/1471/1471_giantmove.results/Nat_neg_Resp+tlrc.BRIK \
1474 /imaging/1474/1474.results/Nat_neg_Resp+tlrc.BRIK \
1481 /imaging/1481/1481.results/Nat_neg_Resp+tlrc.BRIK \
1482 /imaging/1482/1482.results/Nat_neg_Resp+tlrc.BRIK \
1484 /imaging/1484/1484.results/Nat_neg_Resp+tlrc.BRIK \
-covariates /imaging/Analysis/TTest_Oct5_2021/Covariate/ICU_All