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/main.nf --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/antsBrainExtraction.sh: 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!