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.
This is the Dimon command I use. It correctly leaves the HEAD/BRIK files in the -gert_outdir. You may want to play around with the -GERT_Reco -gert_create_dataset commands and their location on the command.
Just to add to Colm’s good example, there are 2 things that go wrong in your example, though Dimon could be updated to handle them.
One is that the GERT_Reco scripts use a simple ‘mkdir’ command to make directories. If intermediate directories are needed, that would fail. It can be updated to include the -p option.
The other is specifying a NIFTI prefix is not reconciled with outdir and -gert_write_as_nifti.
I will fix both of those things and run a new build tonight.
Updates for that are available, as of AFNI version AFNI_18.3.16.
Thanks,
rick
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