ERROR ~ Error executing process > 'Read_BIDS (Read_BIDS)'

1

Hi there,

I’m running tractoflow pipeline to process the DTI and T1 data. And I got the errors as shown below:

tangxc@R940xa:/Data/FreeSurfer20200402/test$ nextflow run tractoflow/main.nf --bids ./ --dti_shells “0 1000” --fodf_shells “0 1000” -with-singularity tractoflow_2.1.1_650f776_2020-07-15.img -resume

N E X T F L O W ~ version 19.04.0

Launching tractoflow/main.nf [nostalgic_pike] - revision: 798dc71854

TractoFlow pipeline

===================

Start time: Thu Jan 14 15:47:48 CST 2021

Input BIDS: ./

executor > local (3)

executor > local (4)

[ad/38aa66] process > README [100%] 1 of 1 :heavy_check_mark:

executor > local (5)

[ad/38aa66] process > README [100%] 1 of 1 :heavy_check_mark:

[0d/784884] process > Read_BIDS [ 75%] 3 of 4, failed: 3

executor > local (5)

[ad/38aa66] process > README [100%] 1 of 1 :heavy_check_mark:

[0d/784884] process > Read_BIDS [100%] 4 of 4, failed: 4 ✘

Pipeline completed at: Thu Jan 14 15:48:00 CST 2021

Execution status: failed

Execution duration: 12.3s

[dc/645ea2] NOTE: Process Read_BIDS (Read_BIDS) terminated with an error exit status (1) – Execution is retried (1)

[06/bdb62c] NOTE: Process Read_BIDS (Read_BIDS) terminated with an error exit status (1) – Execution is retried (2)

[3a/24012b] NOTE: Process Read_BIDS (Read_BIDS) terminated with an error exit status (1) – Execution is retried (3)

ERROR ~ Error executing process > ‘Read_BIDS (Read_BIDS)’

Caused by:

Process Read_BIDS (Read_BIDS) terminated with an error exit status (1)

Command executed:

scil_validate_bids.py test tractoflow_bids_struct.json --readout 0.062

Command exit status:

1

Command output:

(empty)

Command error:

Traceback (most recent call last):

File “/usr/local/bin/scil_validate_bids.py”, line 4, in

import (‘pkg_resources’).run_script(‘scilpy==0.2.dev0’, ‘scil_validate_bids.py’)

File “/usr/local/lib/python3.7/dist-packages/pkg_resources/ init .py”, line 667, in run_script

self.require(requires)[0].run_script(script_name, ns)

File “/usr/local/lib/python3.7/dist-packages/pkg_resources/ init .py”, line 1464, in run_script

exec(code, namespace, namespace)

File “/usr/local/lib/python3.7/dist-packages/scilpy-0.2.dev0-py3.7-linux-x86_64.egg/EGG-INFO/scripts/scil_validate_bids.py”, line 267, in

main()

File “/usr/local/lib/python3.7/dist-packages/scilpy-0.2.dev0-py3.7-linux-x86_64.egg/EGG-INFO/scripts/scil_validate_bids.py”, line 230, in main

layout = BIDSLayout(args.bids_folder, index_metadata=False)

File “/usr/local/lib/python3.7/dist-packages/bids/layout/layout.py”, line 230, in init

self._validate_root()

File “/usr/local/lib/python3.7/dist-packages/bids/layout/layout.py”, line 466, 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.

Work dir:

/Data/FreeSurfer20200402/test/work/0d/784884f9d27b13d78acc420d408cb9

Tip: view the complete command output by changing to the process work dir and entering the command cat .command.out

– Check ‘.nextflow.log’ file for details

My bids inputs folder is like: (Those files and folders are generated directly from dcm2bids without any transformations):

sub-001

  • T1
    sub-001_T1_MPRAGE_T1.json
    sub-001_T1_MPRAGE_T1.nii.gz
  • dti
    sub-001_diff_dti.bval
    sub-001_dif_dti.bvec
    sub-001_dif_dti.json
    sub-001_dif_dti.nii.gz
    sub002
  • T1
    sub-002_T1_MPRAGE_T1.json
    sub-002_T1_MPRAGE_T1.nii.gz
  • dti
    sub-002_diff_dti.bval
    sub-002_dif_dti.bvec
    sub-002_dif_dti.json
    sub-002_dif_dti.nii.gz
    sub003
    …

However, after I moved the T1 and DTI files into every subjects’ folders and ran by --input instead of --bids, it was working:

tangxc@R940xa:/Data/FreeSurfer20200402/test$ nextflow run tractoflow/main.nf --input …/test-data/ --dti_shells “0 1000” --fodf_shells “0 1000” -with-singularity tractoflow_2.1.1_650f776_2020-07-15.img -resume
N E X T F L O W ~ version 19.04.0
Launching tractoflow/main.nf [scruffy_hilbert] - revision: 798dc71854
TractoFlow pipeline

Start time: Thu Jan 14 17:13:19 CST 2021

Input: …/test-data/
executor > local (23)
[ee/e4ad03] process > Denoise_DWI [100%] 3 of 3 :heavy_check_mark:
[1b/da7765] process > Bet_Prelim_DWI [100%] 3 of 3, cached: 2 :heavy_check_mark:
[58/4104ea] process > README [100%] 1 of 1 :heavy_check_mark:
[63/bedc8d] process > Denoise_T1 [100%] 3 of 3 :heavy_check_mark:
[2a/e1b353] process > Eddy [ 0%] 0 of 3
[8c/37c5fb] process > N4_T1 [100%] 3 of 3 :heavy_check_mark:
[96/803d96] process > Resample_T1 [100%] 3 of 3 :heavy_check_mark:
[83/2d09b2] process > Bet_T1 [100%] 3 of 3 :heavy_check_mark:
[ac/b683a6] process > Crop_T1 [100%] 3 of 3 :heavy_check_mark:

My --input folder is like:

sub-001
bval
bvec
dwi.nii.gz
t1.nii.gz
sub002
bval
bvec
dwi.nii.gz
t1.nii.gz
sub003
…

Anyone knows how to fix the --bids to make it work? Thank you!

2

Dear @Shirley_Su,

From what I see, your bids inputs folder is not bids compatible.
You can use bids-standard.github.io/bids-validator/ to validate your bids structure.

Have a good day
Arnaud

3

Hi @Shirley_Su,

Did you find a way to fix your issue? If so, can you tag this thread as solved ? It helps us sort all @tractoflow threads.

Thank you in advance
Arnaud

5

Hi Shirley,
It sounds like I have the same issue. Did you find a proper way to resolve it? My folder seems bids compatible (I checked with the online validator) but tractoflow cannot read my bids file.

6

Hi @Ophelie_Martinie

Could you create an empty dataset_description.json in your bids directory. I think this file is mandatory in the bids structure and is required by TractoFlow.

Best

Guillaume

7

Hi @Guillaumeth
I already have created a json file (not really sure if its format is correct though). It contains the following information :

{
“Name”: “MotorPlanning”,
“BIDSVersion”: “1.0.2”
}

My project folder contains a DICOM folder and another one with Bids structure. Within the bids folder, I have created one folder by participant (sub-001) which contain 2 subfolders:

  • anat
  • dwi
    With their corresponding data within, renamed according to the Bids guidelines.

Thanks for your help!

8

Could you send me the output of tree command of your input data given to TractoFlow using --bids.

Thanks

9

Do you mean the command to run tractoflow? I use :

nextflow run tractoflow/main.nf/ --bids ProjectFolder/BidsFolder/ --dti_shells “0 2000” --fodf_shells “0 2000” --with-singularity tractoflow_2.1.1_650f776_2020-07-15.img -resume

10

Hi @Ophelie_Martinie ,

@Guillaumeth was talking about the output of this command
tree ProjectFolder/BidsFolder/

Thanks

11

Oh my bad!
@Guillaumeth The output is the following :

MotorPlanning/Niftii/
├── dataset_description.json
└── sub-001
├── anat
│ ├── sub-001_T1w.json
│ └── sub-001_T1w.nii.gz
└── dwi
├── sub-001_acq-64_dwi.bval
├── sub-001_acq-64_dwi.bvec
├── sub-001_acq-64_dwi.json
└── sub-001_acq-64_dwi.nii.gz

3 directories, 7 files

12

Thanks @Ophelie_Martinie

So your bids folder looks good.

Can you confirm to me your command looks like this:
nextflow run tractoflow/main.nf/ --bids MotorPlanning/Niftii …

If it was already this command that you ran, could you, if possible, send me your data for testing ?

Guillaume