Hi Rick,

I can't seem to figure out how to get the reconstructed output file from Dimon to be written into the folder specified in 'gert_outdir'.

Here is my script:

Dimon -infile_prefix SS22_Structural/e177/s1547/i \
-gert_create_dataset \
-gert_outdir SS22_Structural/Flair \
-gert_to3d_prefix Flair.nii.gz

I run this script in a parent directory (Structural_Scans) that contains the folder SS22_Structural. I am expecting it to create a directory in SS22_Structural called "Flair" and put the output of Dimon in that new directory. It creates the Flair directory in the correct place but it empty. Whatever I try it always writes the files to the current directory (Strucrural_Scans). I get an error at the end of the code that says "mv: No match". I am thinking that the last step where it moves the data is not working for some reason.

Warm regards,
Christine