hcp_make_average_dataset
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"