preprocess_mice#

qx_mice.process_mice.preprocess_mice(sinfo, options, overwrite=False, thread=0)#

preprocess_mice [... processing options]

Runs the QuNex mice preprocessing command.

Warning

Successful preparation of mice data for preprocessing encompasses:

  • data import,

  • setup_mice,

  • create_session_info,

  • create_batch.

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.

--bias_field_correction (str, default 'yes'):

Whether to perform bias field correction, yes/no.

--melodic_anatfile (str, default 'qx_library/etc/mice_pipelines/EPI_braine'):

Path to the melodic anat file, without the extension, e.g. without .nii.gz.

--fix_rdata (str, default 'qx_library/etc/mice_pipelines/zerbi_2015_neuroimage.RData'):

Path to the RData file used by fix.

--fix_threshold (int, default 2):

Fix ICA treshold.

--fix_no_motion_cleanup:

A flag for disabling cleanup of motion confounds. Disabled by default.

--fix_aggressive_cleanup:

A flag for performing aggressive cleanup. Disabled by default.

--mice_highpass (float, default '0.01'):

The value of the highpass filter.

--mice_lowpass (float, default '0.25'):

The value of the lowpass filter.

--mice_volumes (int, default 900):

Number of volumes.

--flirt_ref (str, default 'qx_library/etc/mice_pipelines/EPI_template.nii.gz'):

Path to the template file.

Output files

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

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

Examples

qunex preprocess_mice \
    --sessionsfolder="/data/mice_study/sessions" \
    --sessions="/data/mice_study/processsing/batch.txt"