hcp_long_post_freesurfer#

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

hcp_long_post_freesurfer [... processing options]

hcp_lpfs [... 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_prefs_template_res (float, default set from imaging data):

The resolution (in mm) of the structural images templates to use in the preFS step. Note: it should match the resolution of the acquired structural images. If no value is provided, QuNex will try to use the imaging data to set a sensible default value. It will notify you about which setting it used, you should pay attention to this piece of information and manually overwrite the default if something is off.

--hcp_prefs_t1template (str, default ""):

Path to the T1 template to be used by PreFreeSurfer. By default the used template is determined through the resolution provided by the hcp_prefs_template_res parameter.

--hcp_prefs_t1templatebrain (str, default ""):

Path to the T1 brain template to be used by PreFreeSurfer. By default the used template is determined through the resolution provided by the hcp_prefs_template_res parameter.

--hcp_prefs_t1template2mm (str, default ""):

Path to the T1 2mm template to be used by PreFreeSurfer. By default the used template is HCP's MNI152_T1_2mm.nii.gz.

--hcp_prefs_t2template (str, default ""):

Path to the T2 template to be used by PreFreeSurfer. By default the used template is determined through the resolution provided by the hcp_prefs_template_res parameter.

--hcp_prefs_t2templatebrain (str, default ""):

Path to the T2 brain template to be used by PreFreeSurfer. By default the used template is determined through the resolution provided by the hcp_prefs_template_res parameter.

--hcp_prefs_t2template2mm (str, default ""):

Path to the T2 2mm template to be used by PreFreeSurfer. By default the used template is HCP's MNI152_T2_2mm.nii.gz.

--hcp_prefs_templatemask (str, default ""):

Path to the template mask to be used by PreFreeSurfer. By default the used template mask is determined through the resolution provided by the hcp_prefs_template_res parameter.

--hcp_prefs_template2mmmask (str, default ""):

Path to the template mask to be used by PreFreeSurfer. By default the used 2mm template mask is HCP's MNI152_T1_2mm_brain_mask_dil.nii.gz.

--hcp_prefs_fnirtconfig (str, default ""):

Path to the used FNIRT config. Set to the HCP's T1_2_MNI152_2mm.cnf by default.

--hcp_freesurfer_labels (str, default "${HCPPIPEDIR}/global/config/FreeSurferAllLut.txt"):

Path to the location of the FreeSurfer look up table file.

--hcp_surfatlasdir (str, HCP "standard_mesh_atlases"):

Surface atlas directory.

--hcp_grayordinatesres (int, default 2):

The resolution of the volume part of the grayordinate representation in mm.

--hcp_grayordinatesdir (str, default HCP "91282_Greyordinates"):

Grayordinates space directory.

--hcp_subcortgraylabels (str, default HCP "FreeSurferSubcorticalLabelTableLut.txt"):

The location of FreeSurferSubcorticalLabelTableLut.txt.

--hcp_refmyelinmaps (str, default HCP "Conte69.MyelinMap_BC.164k_fs_LR.dscalar.nii"):

Group myelin map to use for bias correction.

--hcp_hiresmesh (int, default 164):

The number of vertices for the high resolution mesh of each hemisphere (in thousands).

--hcp_lowresmesh (int, default 32):

The number of vertices for the low resolution mesh of each hemisphere (in thousands).

--hcp_regname (str, default "MSMSulc"):

The registration used, FS or MSMSulc.

--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 "PREP-T"):
One of:
  • PREP-T (PostFSPrepLong build template, skip timepoint

    processing),

  • POSTFS-TP1 (PostFreeSurfer timepoint stage 1),

  • POSTFS-T (PostFreesurfer template),

  • POSTFS-TP2 (PostFreesurfer timepoint stage 2).

--hcp_end_stage (str, default "POSTFS-TP2"):
One of:
  • PREP-T (PostFSPrepLong build template, skip timepoint

    processing),

  • POSTFS-TP1 (PostFreeSurfer timepoint stage 1),

  • POSTFS-T (PostFreesurfer template),

  • POSTFS-TP2 (PostFreesurfer timepoint stage 2).

Output files

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

Notes

hcp_long_post_freesurfer parameter mapping:

QuNex parameter

HCPpipelines parameter

hcp_longitudinal_template

longitudinal_template

hcp_prefs_t1template

t1template

hcp_prefs_t1templatebrain

t1templatebrain

hcp_prefs_t1template2mm

t1template2mm

hcp_prefs_t2template

t2template

hcp_prefs_t2templatebrain

t2templatebrain

hcp_prefs_t2template2mm

t2template2mm

hcp_prefs_templatemask

templatemask

hcp_prefs_template2mmmask

template2mmmask

hcp_prefs_fnirtconfig

fnirtconfig

hcp_freesurfer_labels

freesurferlabels

hcp_surfatlasdir

surfatlasdir

hcp_grayordinatesres

grayordinatesres

hcp_grayordinatesdir

grayordinatesdir

hcp_subcortgraylabels

subcortgraylabels

hcp_refmyelinmaps

refmyelinmaps

hcp_hiresmesh

hiresmesh

hcp_lowresmesh

lowresmesh

hcp_regname

regname

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_post_freesurfer \
    --sessionsfolder="<path_to_study_folder>/sessions" \
    --batchfile="<path_to_study_folder>/processing/batch.txt"