map_mice_data
map_mice_data#
- qx_mice.process_mice.map_mice_data(sinfo, options, overwrite=False, thread=0)#
map_mice_data [... processing options]
Runs the command to prepare a QuNex study for mice preprocessing.
Warning
Preprocessed mica data is required.
Parameters
- --batchfile (str, default ''):
The batch.txt file with all the sessions information.
- --sessionsfolder (str, default '.'):
The path to the study/sessions folder, where the imaging data is supposed to go.
- --bolds (str, default ''):
Which bold images to process. You can select bolds through their number, name or task (e.g. rest), you can chain multiple conditions together by providing a comma separated list.
- --parsessions (int, default 1):
How many sessions to run in parallel.
- --parelements (int, default 1):
How many elements (e.g. bolds) to run in parallel.
- --overwrite (str, default 'no'):
Whether to overwrite target files that already exist (yes) or not (no).
- --logfolder (str, default ''):
The path to the folder where runlogs and comlogs are to be stored, if other than default.
- --log (str, default 'keep'):
Whether to keep ('keep') or remove ('remove') the temporary logs once jobs are completed. When a comma or pipe ('|') separated list is given, the log will be created at the first provided location and then linked or copied to other locations. The valid locations are:
Output files
The results of this step will be present in the functional folder in the sessions's root:
study └─ sessions ├─ session1 | └─ functional └─ session2 └─ functional
Examples
qunex map_mice_data \ --sessionsfolder="/data/mice_study/sessions" \ --sessions="/data/mice_study/processsing/batch.txt"