setup_mice

qx_mice.setup_mice.setup_mice(sinfo, options, overwrite=False, thread=0)

setup_mice [... processing options]

Runs the command to prepare a QuNex study for mice preprocessing.

Warning

Succesfull import of mice data is required to run this command.

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.

--tr (float, default 2.5):

TR of the bold data.

--voxel_increase (int):

The factor by which to increase voxel size. If not provided QuNex will not increase the voxel size.

--orienatation (str, default 'x -y z'):

A string depicting how to fix the orientation. Set to "" to leave orientation as is.

Output files

The results of this step will be present in the mice folder in the sessions's root:

study
└─ sessions
├─ session1
|  └─ mice
└─ session2
    └─ mice

Examples

qunex setup_mice \
    --sessionsfolder='/data/mice_study/sessions' \
    --sessions='/data/mice_study/processsing/batch.txt'

qunex setup_mice \
    --sessionsfolder='/data/mice_study/sessions' \
    --sessions='/data/mice_study/processsing/batch.txt' \
    --sessionids='joe01' \
    --bolds='bold1' \
    --tr='1'