hcp_longitudinal_freesurfer

qx_utilities.hcp.process_hcp.hcp_longitudinal_freesurfer(sinfo, subjectids, options, overwrite=False, thread=0)

hcp_longitudinal_freesurfer [... processing options]

hcp_lfs [... processing options]

Runs the HCP Longitudinal FreeSurfer Pipeline (LongitudinalFreeSurferPipeline.sh).

Warning

The code expects the first three HCP preprocessing steps (hcp_pre_freesurfer, hcp_freesurfer and hcp_post_freesurfer) to have been run and finished successfully.

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.

--parsessions (int, default 1):

How many sessions to run in parallel.

--overwrite (str, default 'no'):

Whether to overwrite existing data (yes) or not (no).

--hcp_suffix (str, default ''):

Specifies a suffix to the session id if multiple variants are run, empty otherwise.

--logfolder (str, default ''):

The path to the folder where runlogs and comlogs are to be stored, if other than default.

--log (str, default 'keep'):

Whether to keep ('keep') or remove ('remove') the temporary logs once jobs are completed. When a comma or pipe ('|') separated list is given, the log will be created at the first provided location and then linked or copied to other locations. The valid locations are:

• 'study' (for the default: <study>/processing/logs/comlogs location)

• 'session' (for <sessionid>/logs/comlogs)

• 'hcp' (for <hcp_folder>/logs/comlogs)

• '<path>' (for an arbitrary directory).

--hcp_long_fs_template_id (str, default 'base'):

ID of the base template.

--hcp_long_fs_extra_reconall_base (str, default ''):

A string with extra parameters to pass to Longitudinal FreeSurfer recon-all base template creation. The extra parameters are to be listed in a pipe ('|') separated string. Parameters and their values need to be listed separately. E.g. to pass -norm3diters 3 to reconall, the string has to be: '-norm3diters|3'.

--hcp_long_fs_extra_reconall (str, default ''):

A string with extra parameters to pass to Longitudinal FreeSurfer recon-all processing. The extra parameters are to be listed in a pipe ('|') separated string. Parameters and their values need to be listed separately. E.g. to pass -norm3diters 3 to reconall, the string has to be: '-norm3diters|3'.

Output files

The results of this step will be present in the <study_folder>/<sessions_folder>/<subject_id>.

Notes

hcp_longitudinal_freesurfer parameter mapping:

QuNex parameter	HCPpipelines parameter
hcp_long_fs_template	template
hcp_long_fs_extra_reconall_base	extra-reconall-arg-base
hcp_long_fs_extra_reconall_long	extra-reconall-arg-long

Examples

qunex hcp_longitudinal_freesurfer \
    --sessionsfolder="<path_to_study_folder>/sessions" \
    --batchfile="<path_to_study_folder>/processing/batch.txt" \
    --hcp_long_fs_template_id="<template_id>"