MRIQC dataset_description.json

1

Hi there,

I’m getting an error where mriqc cannot locate my dataset_description.json. My command and error look like:

sudo docker run -it --rm -v /bids:/data:ro -v fmriprep:/out poldracklab/mriqc:latest /data /out participant -->participant_label 001

2019-10-29 20:52:50,935 mriqc:IMPORTANT
Running MRIQC version 0.15.2rc1:
* BIDS dataset path: /data.
* Output folder: /out.
* Analysis levels: participant.

Process Process-2:
Traceback (most recent call last):
File “/usr/local/miniconda/lib/python3.7/multiprocessing/process.py”, line 297, in _bootstrap
self.run()
File “/usr/local/miniconda/lib/python3.7/multiprocessing/process.py”, line 99, in run
self._target(self._args, **self._kwargs)
File “/usr/local/miniconda/lib/python3.7/site-packages/mriqc/bin/mriqc_run.py”, line 400, in init_mriqc
ignore=[‘derivatives’, ‘sourcedata’, r’^…’])
File “/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py”, line 185, in init
self._validate_root()
File “/usr/local/miniconda/lib/python3.7/site-packages/bids/layout/layout.py”, line 324, in _validate_root
“‘dataset_description.json’ is missing from project root.”
ValueError: ‘dataset_description.json’ is missing from project root. Every valid BIDS dataset must have this file.

Any help would be appreciated.

Best,
Caleb

2

Definitely exists at /bids

48%20PM
Screen Shot 2019-10-29 at 5.01.48 PM.png1447×35 12.4 KB

3

Hi @Caleb_Haynes - when you are in the bids folder, type pwd in terminal to get the full path. You’ll have to put that path, as well as the full path to your output folder, into your docker command:

sudo docker run -it --rm -v fullpath:/data:ro -v fullpath:/out poldracklab/mriqc:latest /data /out participant --participant_label 001
1 Like
4

amazing! thanks so much

5

it also helps me to solve the problem. thank you :slight_smile: