Dcm2bids json decode error: expecting delimiter

Software Support
,
1

Hello,

I am new to dcm2bids. I was able to get dcm2bids to run properly with another similar dataset (using the direct download), however in this new bids folder I am receiving the error below when I run the dcm2bids command. I am not sure what the issue is, and any help at all would be appreciated.

INFO    | --- dcm2bids start ---
INFO    | Running the following command: /home/dcm2bidspro/dcm2bids -d /home/BIDS_folder/sourcedata/Data/T1001 -p 001 -c /home/BIDS_folder/code/BIDS_config.json -o /home/BIDS_folder --auto_extract_entities
INFO    | OS version: Linux-5.10.102.1-microsoft-standard-WSL2-x86_64-with-glibc2.35
INFO    | Python version: 3.11.5 (main, Aug 28 2023, 12:41:27) [GCC 9.4.0]
INFO    | dcm2bids version: 3.1.1
INFO    | dcm2niix version: v1.0.20240202
INFO    | Checking for software update
INFO    | Currently using the latest version of dcm2bids.
INFO    | Currently using the latest version of dcm2niix.
INFO    | participant: sub-001
INFO    | config: /home/BIDS_folder/code/BIDS_config.json
INFO    | BIDS directory: /home/BIDS_folder
INFO    | Auto extract entities: True
INFO    | Validate BIDS: False

Traceback (most recent call last):
  File "/tmp/onefile_513_1719354861_355615/dcm2bids.py", line 134, in <module>
  File "/tmp/onefile_513_1719354861_355615/dcm2bids.py", line 125, in main
  File "/tmp/onefile_513_1719354861_355615/dcm2bids/dcm2bids_gen.py", line 53, in __init__
  File "/tmp/onefile_513_1719354861_355615/dcm2bids/utils/io.py", line 18, in load_json
  File "/tmp/onefile_513_1719354861_355615/json/__init__.py", line 293, in load
  File "/tmp/onefile_513_1719354861_355615/json/__init__.py", line 359, in loads
  File "/tmp/onefile_513_1719354861_355615/json/decoder.py", line 337, in decode
  File "/tmp/onefile_513_1719354861_355615/json/decoder.py", line 353, in raw_decode
  File "/tmp/onefile_513_1719354861_355615/json/scanner.py", line 67, in scan_once
  File "/tmp/onefile_513_1719354861_355615/json/scanner.py", line 37, in _scan_once
  File "/tmp/onefile_513_1719354861_355615/json/decoder.py", line 186, in JSONObject
  File "/tmp/onefile_513_1719354861_355615/json/scanner.py", line 40, in _scan_once
  File "/tmp/onefile_513_1719354861_355615/json/decoder.py", line 230, in JSONArray
  File "/tmp/onefile_513_1719354861_355615/json/scanner.py", line 37, in _scan_once
  File "/tmp/onefile_513_1719354861_355615/json/decoder.py", line 186, in JSONObject
  File "/tmp/onefile_513_1719354861_355615/json/scanner.py", line 37, in _scan_once
  File "/tmp/onefile_513_1719354861_355615/json/decoder.py", line 202, in JSONObject
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 9 column 4 (char 174)

Thanks,
marcille

2

Hello @marcille,

You have an error in your config file.
You can validate your JSON file using this link: https://jsonlint.com/

Arnaud

3

This did the trick. Thanks so much!