This script was design to erase all outputs, including .log files of a previously run module. You can use this function in case you encounter an error while processing a module, or if you simply want to rerun a module that you have already started or that is completed. Indeed, if the output files of a module already exist, you will not be able to rerun this module before deleting its outputs.
If you want to erase and rerun a core processing module such as
proc_structural you may need to rerun all of its dependent modules, to ensure consistency of interdependent modules!
The basic usage of
micapipe_cleanup requires the same inputs as in mica-pipe.
$ micapipe_cleanup -sub <subject_id> -out <outputDirectory> -bids <BIDS-directory> -ses <session-name> -<module-to-erase>
$ docker micapipe_cleanup
The module(s) you want to erase should be specified with a flag(s) (e.g.
-proc_dwi). Possible optinal arguments are listed below:
||Optional flag that indicates the session name (if omitted, will be managed as a SINGLE session)|
||Deletes volumetric processing derivatives|
||Deletes Freesurfer recon-all processing outputs|
||Deletes post structural volumetric and surface-based processing derivatives|
||Deletes diffusion-weighted image processing derivatives|
||Deletes tractography files and structural connectomes|
||Deletes resting-state funtional MRI processing derivatives|
||Deletes microstructural profile and covariance analysis derivatives|
||Deletes geodesic distance analysis derivatives|