hcp_long_freesurfer#

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

hcp_long_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.

--parsubjects (int, default 1):

How many subjects to run in parallel.

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

Whether to overwrite existing data (yes) or not (no). Note that previous data is deleted before the run, so in the case of a failed command run, previous results are lost.

--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.

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

Name of the longitudinal template.

--hcp_no_t2w:

Set this flag to process without T2w. Disabled by default.

--hcp_seed (int):

The recon-all seed value.

--hcp_parallel_mode (str, default "BUILTIN"):

Parallelization execution mode, one of FSLSUB, BUILTIN, NONE.

--hcp_fslsub_queue (str, default ""):

FSLSUB queue name.

--hcp_max_jobs (int, default -1):

Maximum number of concurrent processes in BUILTIN mode. Set to -1 to auto-detect.

--hcp_start_stage (str, default "TEMPLATE"):
One of:

  • TEMPLATE,

  • TIMEPOINTS.

--hcp_end_stage (str, default "TIMEPOINTS"):
One of:

  • TEMPLATE,

  • TIMEPOINTS.

Output files

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

Notes

hcp_long_freesurfer parameter mapping:

QuNex parameter

HCPpipelines parameter

hcp_longitudinal_template

longitudinal-template

hcp_no_t2w

use-T2w

hcp_fs_seed

seed

hcp_parallel_mode

parallel-mode

hcp_fslsub_queue

fslsub-queue

hcp_max_jobs

max-jobs

hcp_start_stage

start-stage

hcp_end_stage

end-stage

Examples

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