Tractoflow: Optional Argument Error (Templates/Paths)

Hello, first of all let me thank you very much for your work on this project, so far everything has been a great and helpful experience.

My problem: I am experimenting with modified T1 templates and tried to implement them using the Optional Local Tracking argument: “–template_t1 PATH (default: /human-data/mni_152_sym_09c/t1)”. To minimize errors with the templates, I sandboxed the tractoflow.sif and extracted the t1 maps from human-data into an extern folder (/home/markz/t1).

Now i am pointing at the original templates, but on my extern folder, running the pipeline with:

sudo nextflow run tractoflow/ --template_t1 /home/markz/t1 --bids /home/markz/Testflow_BIDS/ --dti_shells "0 800" --fodf_shells "0 1600" -with-singularity tractoflow_2.2.1_b9a527_2021-04-13.sif

This gets me a normal start, but the Bet_T1 process fails with:

[5d/7ac12f] NOTE: Process `Bet_T1 (sub-01_ses-01)` terminated with an error exit status (1) -- Execution is retried (1) 

and after a number of tries times this error is ignored.
The command.err file from the work folder reads:

Using antsBrainExtraction with the following arguments:
image dimension = 3
anatomical image = sub-01_ses-01__t1_resampled.nii.gz
extraction template = /home/markz/t1/t1_template.nii.gz
extraction reg. mask =
extraction prior = /home/markz/t1/t1_brain_probability_map.nii.gz
output prefix = bet/
output image suffix = nii.gz

N4 parameters (pre brain extraction):
  convergence             = [50x50x50x50,0.0000001]
  shrink factor           = 4
  B-spline parameters     = [200]

Atropos parameters (extraction):
   convergence            = [3,0.0]
   likelihood             = Gaussian
   initialization         = kmeans[3]
   mrf                    = [0.1,1x1x1]
   use clock random seed  = 0

file /home/markz/t1/t1_template.nii.gz does not exist .
/ants_build/bin/ line 117: 47184 Segmentation fault (core dumped) $cmd

My strong guess goes into the direction of Singularity and options to bind and mount paths (Bind Paths and Mounts — Singularity container 3.0 documentation). But the - -bids argument communicates fine into the “outside world”. Does anybody have an idea how to fix this? Or am I looking at the wrong place?

Best regards and thanks in advance!

Hi @markzsen ,

You definitively end up in a singularity issue here. I would suggest you to add a singularity.conf to manually bind your home directory using this link. Add -c singularity.conf to your command line

Don’t hesitate if you any new issues. This is a little bit off the roadmap for us but if we can help, go !