Error ~ No subjects found, TractoFlow 2.4.3 on Ubuntu 22.04

1

Hello,

I’m trying to run TractoFlow 2.4.3 on a remote machine with Ubuntu 22.04 with the command NXF_VER=19.04.2 nextflow run tractoflow -r 2.4.3 --input=/home/ubuntu/S1 --run_pft_tracking=false --pft_compress_streamlines=false --local_compress_streamlines=false and I’m getting this error:

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I installed TractoFlow with nextflow pull scilus/tractoflow and my S1 directory contains the following files: T1.nii.gz, bval, bvec, and diff.nii.gz.

I’ve tried several variations for the path of S1, such as ~/S1/ or ./S1/ and it didn’t work. What could be the problem?

Thank you,
Beatriz

2

Hello,

You need an extra folder where you put your subjects, like this:
/home/ubuntu/i_tractoflow/S1 and then use /home/ubuntu/i_tractoflow/ as your input.

Also your subject input should look like this: Input structure — TractoFlow-documentation documentation

Give it a try and if it still doesn’t work I can dig deeper.

Best,
Arnaud

3

It worked! I hadn’t realized that the file names within each subject folder had to be the exact ones from the documentation :sweat_smile:

Thank you so much!
Beatriz