QSIprep Freesurfer Input


I am trying to understand the qsiprep documentation with regards to FreeSurfer.

Does QSIprep (v 0.15) use freesurfer outputs in its preproc pipeline? Or is it used for reconstruction only?

Thanks in advance,

I am specifying the freesurfer directory but have been unsuccessful in integrating the freesurfer output (processed separately through fmriprep) to qsiprep preproc.

Command: singularity run --cleanenv -B /WMH:/WMH /lib/qsiprep-0.15.2.sif /BIDS/ADNI/ /BIDS/ADNI/derivatives/qsiprep participant –participant_label –output-resolution 1.0 –fs_license_file /lib/fs_license.txt –freesurfer_input //BIDS/ADNI/derivatives/sourcedata/freesurfer –skip-bids-validation


It looks from your command that you should also mount your //BIDS/ directory to the singularity container.

Maybe something like that would work better?

singularity run --cleanenv -B //WMH:/WMH,//BIDS:/BIDS  /lib/qsiprep-0.15.2.sif /BIDS/ADNI/ /BIDS/ADNI/derivatives/qsiprep participant –participant_label –output-resolution 1.0 –fs_license_file //lib/fs_license.txt –freesurfer_input 
/BIDS/ADNI/derivatives/sourcedata/freesurfer –skip-bids-validation

Hi Tej,

I believe Freesurfer inputs to qsiprep were introduced in 0.16.0 (which is still in prerelease but should be out soon, you can use the third release candidates on released on dockerhub).

I’ll also in your command you don’t need to bind /WMH as it does not seem to be used in the rest of the command.


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