hcp_make_average_dataset

qx_utilities.hcp.process_hcp.hcp_make_average_dataset(sessions, sessionids, options, overwrite=True, thread=0)

hcp_make_average_dataset [... processing options]

hcp_mad [... processing options]

Runs the HCP make average dataset pipeline (MakeAverageDataset.sh).

Warning

The code expects the HCP minimal preprocessing pipeline to be executed.

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.

--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_surface_atlas_dir (str, default '${HCPPIPEDIR}/global/templates/standard_mesh_atlases'):

Path to the location of the standard surfaces.

--hcp_grayordinates_dir (str, default '${HCPPIPEDIR}/global/templates/91282_Greyordinates'):

Path to the location of the standard grayorinates space.

--hcp_hiresmesh (int, default 164):

High resolution mesh node count.

--hcp_lowresmeshes (int, default 32):

Low resolution meshes node count. To provide more values separate them with commas.

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

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

--hcp_pregradient_smoothing (int, default 1):

Sigma of the pregradient smoothing.

--hcp_mad_regname (str, default 'MSMALL'):

Name of the registration.

--hcp_mad_videen_maps (str, default 'corrThickness,thickness,MyelinMap_BC,SmoothedMyelinMap_BC'):

Maps you want to use for the videen palette.

--hcp_mad_greyscale_maps (str, default 'sulc,curvature'):

Maps you want to use for the greyscale palette.

--hcp_mad_distortion_maps (str, default 'SphericalDistortion,ArealDistortion,EdgeDistortion'):

Distortion maps.

--hcp_mad_gradient_maps (str, default 'MyelinMap_BC,SmoothedMyelinMap_BC,corrThickness'):

Maps you want to compute the gradient on.

--hcp_mad_std_maps (str, default 'sulc@curvature,corrThickness,thickness,MyelinMap_BC'):

Maps you want to compute the standard deviation on.

--hcp_mad_multi_maps (str, default 'NONE'):

Maps with more than one map (column) that cannot be merged and must be averaged.

Output files

A group folder with outputs is created inside the QuNex's session folder.

Notes

Mapping of QuNex parameters onto HCP ASL pipeline parameters:

Below is a detailed specification about how QuNex parameters are mapped onto the HCP ASL parameters.

QuNex parameter	HCP ASL parameter
hcp_gdcoeffs	grads
hcp_asl_mtname	mtname
hcp_asl_territories_atlas	territories_atlas
hcp_asl_territories_labels	territories_labels
hcp_asl_use_t1	use_t1
hcp_asl_nobandingcorr	nobandingcorr
hcp_asl_interpolation	interpolation
hcp_asl_cores	cores

Examples

A run with the default set of parameters:

qunex hcp_make_average_dataset \
    --sessionsfolder="<path_to_study_folder>/sessions" \
    --batchfile="<path_to_study_folder>/processing/batch.txt" \
    --hcp_outgroupname="hcp_group"