create_study
create_study#
- qx_utilities.general.utilities.create_study(studyfolder=None, folders=None)#
create_study studyfolder=<path to study base folder> [folders=$TOOLS/python/python/qx_utilities/templates/study_folders_default.txt]
Creates the base study folder structure.
Parameters
- --studyfolder (str):
The path to the study folder to be generated.
- --folders (str, default $TOOLS/python/python/qx_utilities/templates/study_folders_default.txt):
Path to the file which defines the subfolder structure.
Notes
Creates the base folder at the provided path location and the study folders. By default $TOOLS/python/python/qx_utilities/templates/study_folders_default.txt will be used for subfolder specification. The default structure is:
<studyfolder> ├── analysis │ └── scripts ├── processing │ ├── logs │ │ ├── batchlogs │ │ ├── comlogs │ │ ├── runchecks │ │ └── runlogs │ ├── lists │ ├── scripts │ └── scenes │ └── QC │ ├── T1w │ ├── T2w │ ├── myelin │ ├── BOLD │ └── DWI ├── info │ ├── demographics │ ├── tasks │ ├── stimuli │ ├── bids │ └── hcpls └── sessions ├── inbox │ ├── MR │ ├── EEG │ ├── BIDS │ ├── HCPLS │ ├── behavior │ ├── concs │ └── events ├── archive │ ├── MR │ ├── EEG │ ├── BIDS │ ├── HCPLS │ └── behavior ├── specs └── QC
Do note that the command will create all the missing folders in which the specified study is to reside. The command also prepares template batch_example.txt and pipeline example mapping files in <studyfolder>/sessions/specs folder. Finally, it creates a .qunexstudy file in the <studyfolder> to identify it as a study basefolder.
Examples
qunex create_study \ --studyfolder=/Volumes/data/studies/WM.v4