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Liu Mengxing edited this page Nov 27, 2022 · 8 revisions

How to use RTP-preproc

Inputs

input folder should contain the following folders:

  • DIFF

    • Name: DIFF
    • Type: nifti
    • Description: Diffusion NIfTI image.
    • Notes:{}

  • BVAL

    • Name: BVAL
    • Type: bval
    • Description: BVAL file.
    • Notes:{}

  • BVEC

    • Name: BVEC
    • Type: bvec
    • Description: BVEC file.
    • Notes:{}

------ optional ----------------

  • ANAT

    • Name: ANAT
    • Type: nifti
    • Description: Optional anatomical T1w NIfTI image. Required only if anatalign=true
    • Optional:true
    • Notes:{}

  • FSMASK

    • Name: FSMASK
    • Type: nifti
    • Description: Optional freesurfer mask, if not passed FSL will calculate it internally.
    • Optional:true
    • Notes:{}

  • RDIF

    • Name: RDIF
    • Type: nifti
    • Description: Optional reverse phase encoded (rpe) diffusion NIfTI image.
    • Optional:true
    • Notes:{}

  • RBVL

    • Name: RBVL
    • Type: bval
    • Description: Optional reverse phase encoded (rpe) BVAL file.
    • Optional:true
    • Notes:{}

  • RBVC

    • Name: RBVC
    • Type: bvec
    • Description: Optional reverse phase encoded (rpe) BVEC file.
    • Optional:true
    • Notes:{}

Running

With the input organized in the correct way, running the preprocessing pipeline on Docker:

docker run --rm -ti \
    -v </path/to/input/>:/flywheel/v0/input/ \
    -v </path/for/output/>:/flywheel/v0/output \
    -v </path/for/example_config.json>:/flywheel/v0/config.json
    garikoitz/rtppreproc:<version-tag>

or Singularity:

singularity run -e --no-home \
    --bind /scratch:/scratch \
    --bind </path/to/input/>:/flywheel/v0/input/:ro \
    --bind </path/for/output/>:/flywheel/v0/output \
    --bind </path/for/example_config.json>:/flywheel/v0/config.json \
    rtppreproc_<version>.sif
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