Derivatives output of qsiprep not produce freesurfer directory

Software Support
,
1

Hi,

I am currently running a job using QSIPrep, and I would also like to run FreeSurfer as well. Below is the list of arguments that I am using for the SLURM command:

"--skip_bids_validation",
"--output-resolution 1",
"--omp-nthreads 4",
"--longitudinal",
"--anat-modality T1w",
"--nthreads 8",
"--use-syn-sdc",
"--anatomical-template MNI152NLin2009cAsym",
"--resource-monitor",
"--write-graph",
"-v"

This is the expected QSIPrep output with FreeSurfer:

/qsiprep-outputs/
├── sub-<participant_id>/
│   ├── anat/  
│   ├── dwi/   
│   ├── freesurfer/  
│       ├── mri/     
│       ├── surf/    
│       ├── label/   
│       ├── stats/   
│       ├── scripts/ 
│       └── ...      
└── ...

For some reason, the FreeSurfer output directory is not generated after the job completes. am i missing anything ?

Thank you

2

Hi @trinhdh and welcome to neurostars!

Qsiprep does not do freesurfer or rely on it. On the other hand, Qsirecon can use already made recon-all outputs for certain pipelines.

Best,
Steven

3

Thanks for responding.
Also i have a quick question, i was using docker container from https://hub.docker.com/r/pennbbl/qsiprep/tags with the tag 0.23.0.

here is my build command

singularity build qsiprep.0.23.0.sif docker://pennbbl/qsiprep:0.23.0

However, when i ran the job using the qsiprep.0.23.0.sif , i saw this message in the slurm output file

241002-19:18:31,601 nipype.workflow IMPORTANT:
	 Running QSIPrep version 0.23.1.dev0+g634483f.d20240830

         License NOTICE ##################################################
         QSIPrep 0.23.1.dev0+g634483f.d20240830
         Copyright The PennLINC Developers.

The version display 0.23.1dev …

Not sure if this is a mistake or i am missing anything
Thank you,

4

Hi @trinhdh,

Nothing to worry about, there was an internal issue with how the versioning label appeared but with your build command you got the right container.

Best,
Steven

5

Great. Thanks for responding. Sorry i should have put this topic in different question.