indi_bidsification

Scripts related to the process of converting INDI datasets into BIDS format.

Study Folders:

ABIDE, ABIDE2, CORR, ADHD200, ACPI, Rockland

Subfolders:

• participants_tsvs -> Phenotypic files in tsv format broken out by subject, and session where suitable
• phenotypic_files -> All phenotypic data in csv format
• scan_jsons -> MRI Acquisition parameters in json formatsessions option for parse pheno 3 months ago

Validation Folder

• Two scripts, one to download subsets of datasets on S3 and run the bids validator, and one to download and fix tsv files with NaNs instead of NAs

GenScript Folder

• checkperm.py -> script to check permissions of s3 bucket objects versions
• counts.py -> basic count script for bucket
• niftiheadcheck.py -> script for looking at the dim_info field in nii headers, using bit-shifting
• parsenii.py - > script for interacting with and changing nii headers
• parsepheno.py -> turns one big spreadsheet into participant and session tsvs for BIDs
• parsescanparams.py -> Turns a site level mri acq params spreadsheet into scan jsons for each modality listed
• regex_orgchange.py -> reformats file structures based on regular expressions, locally and on S3
• s3etag.sh -> Figures out file md5sum based on AWS etag
• s3md5sumcheck.py -> Can compare md5sums of s3 objects and local ones to figure out inconsistencies
• s3tar.py -> downloads data from s3, tars and reuploads
• slice_timing_calc.py -> generates slice times for each slice in fMRI data based on TR, number of slices, slice acquisition method and manufacturer

dicomfieldnames

Matches DICOM standard fields to BIDS definitions, as well as proposing BIDS compatible field names for those not yet defined

s3changes.csv

Lists changes made to datasets hosted on S3 as well as future necessary changes.