hcp_cortical_thickness

qx_utilities.hcp.hcp_cortical_thickness.hcp_cortical_thickness(sinfo, options, overwrite=False, thread=0)

hcp_cortical_thickness [... processing options]

Runs the curvature-corrected (folding-compensated) cortical thickness step of HCP Pipeline (CorrThick.sh). Computes and saves curvature-corrected thickness, curvatures, regression coefficients, and resampled outputs.

Warning

The code expects the input images to be named and present in the QuNex folder structure. The function will look into folder:

<session id>/hcp/<session id>

for data.

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 logs are to be stored, if other than default.

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

Whether to keep ('keep') or remove ('remove') the temporary logs.

--hcp_corrthick_regnames (str, default 'MSMSulc'):

The desired registration name(s) separated by @, e.g. 'RegName@RegName@RegName@...'.

--hcp_corrthick_hemi (str, default 'B'):

Hemisphere for regression calculation, L=Left, R=Right, or B=Both.

--hcp_corrthick_surf (str, default 'midthickness'):

Surface for regression calculation, white or midthickness.

--hcp_corrthick_patch_size (str, default '6'):

Patch kernel size in millimeters FWHM for regression.

--hcp_corrthick_surf_smooth (str, default '2.14'):

Surface smoothing in millimeters FWHM.

--hcp_corrthick_metric_smooth (str, default '2.52'):

Metric smoothing in millimeters FWHM.

--hcp_corrthick_skip_computation (str, default 'NO'):

Whether to skip computing the curvature-corrected thickness (YES), if it is already available, and just resample it to 164k and 32k, or to compute it (NO).

Output files

The results of this step will be generated and populated in the MNINonLinear folder inside the same session's root hcp folder.

Notes

hcp_cortical_thickness parameter mapping:

QuNex parameter	HCPpipelines parameter
hcp_corrthick_regnames	regnames
hcp_corrthick_hemi	hemi
hcp_corrthick_surf	surf
hcp_corrthick_patch_size	patch-size
hcp_corrthick_surf_smooth	surf-smooth
hcp_corrthick_metric_smooth	metric-smooth
hcp_corrthick_skip_computation	skip-computation

Examples

qunex hcp_cortical_thickness \
    --batchfile=processing/batch.txt \
    --sessionsfolder=sessions \
    --hcp_corrthick_hemi="B" \
    --hcp_corrthick_surf="midthickness"