A small collection of scripts that streamline work with bids-matlab datasets, and designed to work with parsed json configuration files

BIDS related functions

data = crc_bids_query_data(BIDS, images, sub, id)

Retrieves paths to files from BIDS dataset and satisfying query stored in images.query structure (see bids-matlab doc) for subjects cited in sub.

If structure images have number field, it checks if number of retrieved paths is the same as images.number. If it's not the case, an error will be raised.

Function returns the cellarray of found paths, and print out number of retrieved paths prepended by id.

data = crc_bids_retrieve_data(BIDS, selection, subjects)

Same as crc_bids_query_data but retrieves paths from substructures of selection, if these substructures have query field.

Retrieved paths are stored into data structure, with each field corresponds to a field name in selection.

DERIV = crc_bids_gen_dervative(BIDS, outDir, name, selection, subjects)

Generate a derivative dataset based on BIDS in outDir/name, and based on queries stored in selection (see crc_bids_retrieve_data).

If Input dataset and output dataset have same path, do nothing and return a copy of input dataset

crc_bids_merge_suffix(folder_path, varargin)

Scan folder_path for bids-formatted files, and check for multiple suffixes. If such files are found, suffixes are merged.

Optional parameter overwrite set to true (default is false), will overwrite files if they already present.

der_json = crc_bids_create_json(base_json, img_file, varargin)

Creates json structure based on base_json with fields modified by variables contained in varargin.

Variables in varargin must be passed as optional parameters:

crc_bids_create_json(base_json, img_file, `field1`, value1, ...
                     `field2`, value2, ...);

The name of parameter is interpreted as name of field to add to json structure. If field name ends with -add, then corresponding value is added to existing field in json structure (works only with cellarrays and chararrays).

[filename, pth] = crc_create_filename(p, file)

Saved function for managing names of bidsified files. Outdated, better use bids.File class from bids.matlab

codeDir = crc_bids_make_code_dir(ds_path, procStep, conf_files)

Function creating code directory in bidsified dataset: <ds_path>/code/<procStep>, and files in conf_files into it. Usefull to automise saving configuration files for pipeline

General functions

crc_generate_log(log_path, name)

Create a log file wich will contain all output from Matlab terminal. Log file will be written untill command diary off is issued.

crc_compare_batch(ref_batch, test_batch)

Compares two matlab batches structures and prints discrepency If one of the entry is path to file, will compare the basename and original (before bidsification) names, if sidecar json contains field OriginalFile

res = crc_compare_images(ref_img, test_img, diff_path)

Compare two nifti images and print out discrepancies Compares dimentions, orientations, scaling and images themselves, voxel-by-voxel.

If diff_path is defined, the difference image will be saved in given directory

V = crc_read_spm_vol(files)

Function facilitating the reading of multivolumes nii files.

Input parameter files are either a single path to nii, a cellarray of paths to nii, or spm_vol structure.

In all cases function returns a structarray of spm_vol, with each separate element of structure represent a separte volume.