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