preprocess_mice
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"