Input error with --root options

1

Dear all,

I have Input error with --root options, this is my root input_folder:

image
image1009×581 11 KB

Error: Error ~ No subjects found. Please check the naming convention, your --root path or your BIDS folder.

nextflow run /tractoflow/main.nf --root /home/Documents/test_root_data/input/ --output_dir /home/Documents/test_root_data/output --wm_seeding false --seeding npv --nbr_seeds 24 --fodf_shells “0 3000” --dti_shells “0 500 1000” -with-docker scilus/docker-tractoflow:2.1.1
N E X T F L O W ~ version 19.04.0
Launching /tractoflow/main.nf [sharp_solvay] - revision: d21c9a89e5
TractoFlow pipeline

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

Start time: Tue Sep 20 03:41:18 UTC 2022

null - null [null]

Options

=======

Denoise DWI: true

Run Topup: true

Run Eddy: true
Eddy command: eddy_openmp

Resample DWI: true
Resolution: 1

DTI shells: 0 500 1000

fODF shells: 0 3000

Set FRF: false
FRF value: 15,4,4

Mean FRF: true

FODF basis: descoteaux07
SH order: 8

WM seeding: false

Algo: prob
Seeding type: npv
Number of seeds: 24
Random seed: 0
Step size: 0.5
Theta: 20
Minimum length: 20
Maximum length: 200
FODF basis: descoteaux07
Compress streamlines: true
Compressing threshold: 0.2

Number of processes per tasks

=============================
T1 brain extraction: 4
Denoise DWI: 4
Denoise T1: 4
Eddy: 1
Compute fODF: 4
Registration: 4

Template T1 path

================
Template T1: /human-data/mni_152_sym_09c/t1

Input: /home/Documents/test_root_data/input/
Error ~ No subjects found. Please check the naming convention, your --root path or your BIDS folder.

– Check script ‘main.nf’ at line: 282 or see ‘.nextflow.log’ file for more details
Pipeline completed at: Tue Sep 20 03:41:19 UTC 2022
Execution status: failed
Execution duration: 1.2s

Thanks in advance!

2

Hi @fullcream,

First, if you followed the documentation you should be using the docker 2.2.1.

Plus, there are a couple of things I need to know in order to be able to help you:

  • What is the content of your folders ?
  • Which version of tractoflow are you using ?

Once I get this information I’ll be able to guide you.
Arnaud

3

Thanks for your response! @abore

If I use image “scilus/tractoflow:2.2.1”, it cannot use nexflow. So I use 2.1.1.

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Thank you!

4

Hi @fullcream ,

This is not the way you should be running tractoflow. Please check the documentation: How to launch TractoFlow — TractoFlow-documentation documentation

You should not be trying to run tractoflow within the docker container.

Arnaud

5

Thank you! I will follow the documentation.