Tractoflow with Docker

1

Hi. I’m new with neuroimaging and programming and I’m trying to run Tractoflow with Docker using Mac OS (32GB RAM). I’m following the instructions from the Tractoflow Documentation:

  • Installation:
    docker pull scilus/docker-tractoflow:2.1.1

  • Launching Tractoflow:
    nextflow run tractoflow/main.nf --root Neuroimages --dti_shells “0 1000” --fodf_shells “0 1000” -with-docker scilus/docker-tractoflow:2.1.1 -resume

I’m getting the following error:
N E X T F L O W ~ version 20.10.0
Pulling nextflow-io/tractoflow …
Remote resource not found: https://api.github.com/repos/nextflow-io/tractoflow/contents/main.nf

Please, if appreciate it if anyone could help me.

2

Hi @dubergonzoni,

Did you downloaded TractoFlow ? You can do it using this command:

wget https://github.com/scilus/tractoflow/releases/download/2.1.1/tractoflow-2.1.1.zip && unzip tractoflow-2.1.1.zip

After that, you can launch the pipeline with the same command that you used but replacing the path of the tractoflow code. You command line will looks like:

nextflow run PATH_TO_TRACTOFLOW/main.nf --root Neuroimages --dti_shells “0 1000” --fodf_shells “0 1000” -with-docker scilus/docker-tractoflow:2.1.1 -resume

Best

Guillaume Theaud

3

Hi @Guillaumeth,

I forgot to mention that the installation is being a problem, sorry.
I’m getting the error “Failed to connect to github.com port 443: Operation timed out”

I can’t fix this error. I don’t know if it is about the network security of the Hospital or something else. Please, could you help me to think about a possible solution?

Thank you.

4

Hi @dubergonzoni,

I think it is a security issue on your side. Github is widely used by the community and the command to install tractoflow is often used on our side too. So, my guess is that the hospital filter websites for security purposes.

Thanks

5

You can try to download the code here: https://github.com/scilus/tractoflow/releases/tag/2.1.1

Download the zip file: tractoflow-2.1.1.zip

Best

6

It worked for me. At least the code is running right now.

Thank you so much!

Best

7

Hi @Guillaumeth,

My code is running since yesterday, with just one participant, e.g:
Tractoflow_test (main folder)
S3 (subfolder)

  • dwi.nii.gz
  • t1.nii.gz
  • bvec
  • bval

It’s not progressing (0%):

Below is my code and wat the terminal is showing:

(base) iMac-de-Neurovascular:Processamento_DTI_Tractoflow brainsmclab$ nextflow run tractoflow-2.1.1/main.nf --root Tractoflow_test/ --dti_shells “0 1000” --fodf_shells “0 1000” -with-docker scilus/docker-tractoflow:2.1.1 -resume
N E X T F L O W ~ version 20.10.0
Launching tractoflow-2.1.1/main.nf [scruffy_archimedes] - revision: d21c9a89e5
TractoFlow pipeline

Start time: 2020-12-01T12:56:43.503970-03:00

[Git Info]
null - null [null]

Options

[Denoise DWI]
Denoise DWI: true

[Topup]
Run Topup: true

[Eddy]
Run Eddy: true
Eddy command: eddy_openmp

[Resample DWI]
Resample DWI: true
Resolution: 1

[DTI shells]
DTI shells: “0

[fODF shells]
fODF shells: “0

[Compute fiber response function (FRF)]
Set FRF: false
FRF value: 15,4,4

[Mean FRF]
Mean FRF: true

[FODF Metrics]
FODF basis: descoteaux07
SH order: 8

[Seeding mask]
WM seeding: true

[PFT tracking]
Algo: prob
Seeding type: npv
Number of seeds: 10
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: Tractoflow_test/
executor > local (3)
[d1/b44565] process > README (README) [ 0%] 0 of 1
[a3/34f642] process > Bet_Prelim_DWI (S3) [ 0%] 0 of 1
[e5/bcc9e4] process > Denoise_DWI (S3) [ 0%] 0 of 1
[- ] process > Topup -
[- ] process > Eddy -
[- ] process > Eddy_Topup -
[- ] process > Extract_B0 -
[- ] process > Bet_DWI -
[- ] process > N4_DWI -
[- ] process > Crop_DWI -
[- ] process > Denoise_T1 [ 0%] 0 of 1
[- ] process > N4_T1 -
[- ] process > Resample_T1 -
[- ] process > Bet_T1 -
[- ] process > Crop_T1 -
[- ] process > Normalize_DWI -
[- ] process > Resample_DWI -
[- ] process > Resample_B0 -
[- ] process > Extract_DTI_Shell -
[- ] process > DTI_Metrics -
[- ] process > Extract_FODF_Shell -
[- ] process > Register_T1 -
[- ] process > Segment_Tissues -
[- ] process > Compute_FRF -
[- ] process > Mean_FRF -
[- ] process > FODF_Metrics -
[- ] process > PFT_Maps -
[- ] process > Seeding_Mask -
[- ] process > Tracking -

Best Regards

8

Dear @dubergonzoni,

Sorry for the delay, do you still have the same issue? If so, can you send us a link to the nextflow log please?

Thank you.
Arnaud

9

Dear @abore,

I’m so sorry for the late response.
My DICOM image was corrupted. Probably that was the cause of the problem.
Now I’m getting trouble pulling the singularity image. But I will open a new question related with the topic.

Thank you.
Eduardo

10

Hi @dubergonzoni ,

Can you tag this thread as solved? Even if this issue came from your data, it helps us sorting everything related to tractoflow.

Thank you in advance
Arnaud