Tractoflow main.nf fail

#1

Hi Tractoflow team,
I am attempting to run your pipeline on some OASIS DWI data on a CentOS HPC running SLURM.

I have successfully built a tractoflow image, and the HPC team has added singularity 3.6.0 and Nextflow 20.04.1 to the modules.

Upon running, I recieve the following error:

N E X T F L O W ~ version 20.04.1
Pulling nextflow-io/tractoflow …
Remote resource not found: https://api.github.com/repos/nextflow-io/tractoflow/contents/main.nf

I have downloaded the main.nf and nextflow.config from your repo, but to no avail.

Any ideas?

Many Thanks,
Chris

#2

Hi @FL33TW00D,

Did you download the code and the container using manual command or the easy install command ?

1 Like
#3

Hi @Guillaumeth,
Previously I tried building the singularity imaging myself. I have just downloaded and used the easy install method, but still recieve the same error.

The image I am currently using is: tractoflow_2.1.1_650f776_2020-07-15.img

The error is the same as previously.

Any ideas?

Many Thanks,
Chris

#4

Hi @FL33TW00D,

Thanks for the informations. Can you send me what you ran to download TractoFlow. Do you have a folder that looks like tractoflow-2.1.1 ?

Best

Guillaume

1 Like
#5

Hi @FL33TW00D ,

Did you manage to make Tractoflow work ?
If so, can you reply with your fix and finally can you mark this thread as solved ? It helps sort the different issues.

Thank you in advance
Arnaud

#6

Hi @abore,
Unfortunately I did not, but that was not Tractoflows fault.

I moved to QSIPrep due to the acquisition protocol of my data.

Many Thanks,
Chris

#7

Hi @FL33TW00D ,

I’m interested to know what was your acquisition protocol and why tractoflow didn’t suit your needs.

Thank you
Arnaud

#8

Hi @abore ,
The acquistion protocol of my data produced the following b-values:
“0 50 350 600 900 1150 100 400 650 950 150 450 700 1000 1300 200 500 800 1050 1350 300 850 1100 1400”.

Since this is not shelled, FSLs Eddy cannot preprocess it. For this reason we moved to QSIPrep as it supports 3DShore motion correction.

Forgive any mistakes or misunderstandings of the capability of tractoflow, I am a ML researcher not a computational neuroscientist!

Many Thanks,
Chris