Hi Jian,
I’d suggest that you’ve encountered the same problem as Manuel: The drive hosting the script temporary directory contents is running out of space. Unfortunately it’s not actually giving a useful error to inform you of such. You can use the -tempdir option when calling the script to manually specify the location of the temporary directory.
It looks like the subsequent errors are arising because you have copy&pasted lines from the terminal output of the script; e.g. from this exerpt:
jian.chen@MCRI.EDU.AU@mcri-n0186:/isilon/data/jianc/ALL/mrtrix/FBA$ Command: mrtransform /isilon/data/jianc/ALL/mrtrix/FBA/upsampled_dwi_mask/C_ALL_065.mif -linear linear_transforms_initial/C_ALL_065.txt -datatype float32 masks_transformed/C_ALL_065_translated.mif
Command:: command not found
, the system sees the following as the instruction that you are trying to execute:
Command: mrtransform /isilon/data/jianc/ALL/mrtrix/FBA/upsampled_dwi_mask/C_ALL_065.mif -linear linear_transforms_initial/C_ALL_065.txt -datatype float32 masks_transformed/C_ALL_065_translated.mif
It’s therefore looking for a program on your system called “Command:”, and can’t find it.
Cheers
Rob