Modifying IDP Generation - McIntosh-Lab/tvb-ukbb GitHub Wiki

Image-Derived Phenotypes are quantitative metrics generated from various processing steps throughout the pipeline. These IDPs can be found in text files from the IDP_files_<parcellation name> directory within each processed subject directory. Especially important IDPs are featured in the QC Report.

Users may choose to generate new IDPs, set a range of acceptable values for each IDP, and specify IDPs to be included in the QC Report.

Overview of IDP txt files

non_priority_IDPs.tsv     contains IDPs defined by the user as notable but not important
priority_IDPs.tsv         contains IDPs defined by the user as important
tvb_new_IDPs.tsv          contains TVB-UKBB IDPs generated by `tvb-ukbb/tvb_bb_QC/new_IDP_gen.py`
significant_IDPs.tsv      contains IDPs from all three files above

IDPs in the above files will also appear under corresponding sections of the IDP page in the subject's QC report. Any IDPs not included above can be found in various txt files in the subject's IDP_files_<parcellation name> directory.

Generating new IDPs

TVB-UKBB IDPs are generated by tvb-ukbb/tvb_bb_QC/new_IDP_gen.py. Users may develop new IDPs by defining a new function or contributing to an existing function within new_IDP_gen.py. Note that:

  • write_to_IDP_file() must be called for each new IDP in order for new IDP values to be saved
  • any new function must be called by new_IDP_gen() in order to run.

Defining IDPs of Interest

IDPs of particular interest (whether generated by new_IDP_gen.py, or not) should be listed in tvb-ukbb/bb_IDP/IDPoi.txt under either HIGH_PRIORITY or LOW_PRIORITY. These will appear under "High Priority IDPs" and "Low Priority IDPs" in the QC Report.

Defining acceptable IDP value ranges

Users may define thresholds for multiple IDPs using tvb-ukbb/bb_IDP/thresholds.tsv (one IDP per line). For instance, if the only acceptable values for MCFLIRT_rel_disp_min_rfMRI.ica were between 0.2 and 0.4 or greater than or equal to 0.6, thresholds.tsv would contain a line:

MCFLIRT_rel_disp_min_rfMRI.ica    [0.2,0.4];[0.6,inf]