hcp_longitudinal_freesurfer
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>"