Hi again, 

Quick update - I found that altering the command line to have "./listfile.csv" instead of "listfile.csv" helped move things along - with a new error message this time. Here's the files that resulted:

customLUT_DiffMagnitude.txt
customLUT_FDRP.txt
customLUT_RawP.txt
distances_scaled.txt
listfile.csv
listfile.csv_commandline.txt
listfile.csv_DiffMagnitude.txt
listfile.csv_diffMesh.txt
listfile.csv_GLM_correctedMean.meta
listfile.csv_mancovaBonferroniP.txt
listfile.csv_mancovaFDRP.txt
listfile.csv_mancovaRawP.txt
listfile.csv_meanAll_uncorrected.meta
listfile.csv_meanAll_uncorrected.vtk
listfile.csv_meanA.meta
listfile.csv_meanB.meta
listfile.csv_normProjections.txt
listfile_DiffMagnitude.txt
listfile_diffMesh.txt
listfile_GLM_correctedMean.meta
listfile_mancovaBonferroniP.txt
listfile_mancovaFDRP.txt
listfile_mancovaRawP.txt
listfile_meanAll_uncorrected.meta
listfile_meanAll_uncorrected.vtk
listfile_meanA.meta
listfile_meanB.meta
listfile_normProjections.txt
transformFiles

...and here's the error (see the very end):

No statistic type selected, defaulting to Hotelling.
Now running nonparametric tests:
Performing MANCOVA permutation testing.
Using 10000 permutations.
Completed MANCOVA permutation testing.
fdr thresh (MANCOVA) is = 0.0027
Runtime was 4 minute(s) and 22 second(s).
Mean_Difference_Min:-1.85594_Max:4.97653
Mean_Difference_Min:-1.85594_Max:4.97653
CreateMRML ./listfile.csv_GroupTest_MRMLscene.mrml -t -f ./transformFiles/TransRawP.tfm -n transRawP -l 1,0,0,0,1,0,0,0,1,10,0,-60 -m -f listfile.csv_meanAll_uncorrected.vtk -n RawP -p transRawP -as RawP -cc customLUT_RawP.txt -q -id RawP -lbl RawP -pos 21.1383,-12.6241,59.2907 -t -f ./transformFiles/TransFDRP.tfm -n transFDRP -l 1,0,0,0,1,0,0,0,1,10,0,-42.9618 -m -f listfile.csv_meanAll_uncorrected.vtk -n FDRP -p transFDRP -as FDRP -cc customLUT_FDRP.txt -q -id FDRP -lbl FDRP -pos 21.1383,-12.6241,42.2524 -t -f ./transformFiles/TransMeanOverlayRight.tfm -n transMeanOverlayRight -l 1,0,0,0,1,0,0,0,1,107.544,0,-25.9236 -m -f listfile.csv_meanA.meta -n MeanAOverlayRight -p transMeanOverlayRight -as MeanAOverlayRight -dc 1,0,0 -op 0.6 -m -f listfile.csv_meanB.meta -n MeanBOverlayRight -p transMeanOverlayRight -as MeanBOverlayRight -dc 0,0,1 -op 0.4 -t -f ./transformFiles/TransMeanOverlayLeft.tfm -n transMeanOverlayLeft -l 1,0,0,0,1,0,0,0,1,-87.5444,0,-25.9236 -m -f listfile.csv_meanA.meta -n MeanAOverlayLeft -p transMeanOverlayLeft -as MeanAOverlayLeft -dc 1,0,0 -op 0.4 -m -f listfile.csv_meanB.meta -n MeanBOverlayLeft -p transMeanOverlayLeft -as MeanBOverlayLeft -dc 0,0,1 -op 0.6 -q -id Overlays -lbl Overlays -pos 31.7074,-12.6241,19.1951 -t -f ./transformFiles/TransMeanRight.tfm -n transMeanRight -l 1,0,0,0,1,0,0,0,1,107.544,0,-8.88534 -m -f listfile.csv_meanA.meta -n MeanRight -p transMeanRight -as MeanRight -dc 1,0,0 -q -id Means -lbl Means -pos 31.7074,-12.6241,2.15689 -t -f ./transformFiles/TransMeanLeft.tfm -n transMeanLeft -l 1,0,0,0,1,0,0,0,1,-87.5444,0,-8.88534 -m -f listfile.csv_meanB.meta -n MeanLeft -p transMeanLeft -as MeanLeft -dc 0,0,1 -t -f ./transformFiles/TransDiffMagnitude.tfm -n transDiffMagnitude -l 1,0,0,0,1,0,0,0,1,10,0,8.15288 -m -f listfile.csv_meanAll_uncorrected.vtk -n DiffMagnitude -p transDiffMagnitude -as DiffMagnitude -cc customLUT_DiffMagnitude.txt -q -id Mean_Difference_Min:-1.85594_Max:4.97653 -lbl Mean_Difference_Min:-1.85594_Max:4.97653 -pos 42.2766,-12.6241,-20.9004 Error: Could not run CreateMRML:
No such file or directory
Error: Could not run CreateMRML:
No such file or directory

...as usual, advise on how best to proceed/troubleshoot would be much appreciated.

Thanks,
Lara