QSIprep: Preprocessing and analysis of q-space images
Full documentation at https://qsiprep.readthedocs.io
About
qsiprep
configures pipelines for processing diffusion-weighted MRI (dMRI) data.
The main features of this software are
A BIDS-app approach to preprocessing nearly all kinds of modern diffusion MRI data.
Automatically generated preprocessing pipelines that correctly group, distortion correct, motion correct, denoise, coregister and resample your scans, producing visual reports and QC metrics.
A system for running state-of-the-art reconstruction pipelines that include algorithms from Dipy, MRTrix, DSI Studio and others.
A novel motion correction algorithm that works on DSI and random q-space sampling schemes
Preprocessing
The preprocessing pipelines are built based on the available BIDS inputs, ensuring that fieldmaps are handled correctly. The preprocessing workflow performs head motion correction, susceptibility distortion correction, MP-PCA denoising, coregistration to T1w images, spatial normalization using ANTs and tissue segmentation.
Reconstruction
The outputs from the Preprocessing pipelines can be reconstructed in many other
software packages. We provide a curated set of Reconstruction Workflows in qsiprep
that can run ODF/FOD reconstruction, tractography, Fixel estimation and regional
connectivity.
Note
The qsiprep
pipeline uses much of the code from FMRIPREP
. It is critical
to note that the similarities in the code do not imply that the authors of
FMRIPREP in any way endorse or support this code or its pipelines.
Contents
- Installation
- Quick Start
- Usage
- Preprocessing
- Reconstruction
- Using Data Preprocessed by Other Pipelines
- Anatomical Data for Reconstruction Workflows
- Pre-configured recon_workflows
mrtrix_multishell_msmt_ACT-hsvs
mrtrix_multishell_msmt_ACT-fast
mrtrix_multishell_msmt_noACT
mrtrix_singleshell_ss3t_ACT-hsvs
mrtrix_multishell_msmt_ACT-fast
mrtrix_singleshell_ss3t_noACT
pyafq_tractometry
mrtrix_multishell_msmt_pyafq_tractometry
amico_noddi
dsi_studio_gqi
dsi_studio_autotrack
dipy_mapmri
dipy_3dshore
reorient_fslstd
csdsi_3dshore
- Building a custom reconstruction pipeline
- Contributing to qsiprep
- Citing qsiprep
- What’s new
- 0.19.0 (August 10, 2023)
- 0.18.1 (June 26, 2023)
- 0.18.0 (June 9, 2023)
- 0.18.0alpha0 (May 26, 2023)
- 0.16.1 (October 10, 2022)
- 0.16.0RC2 (June 1, 2022)
- 0.16.0RC2 (June 1, 2022)
- 0.16.0RC1 (May 30, 2022)
- 0.15.2 (March 3, 2022) DEPRECATED
- 0.15.1 (February 28, 2022) DEPRECATED
- 0.14.3 (September 16, 2021)
- 0.14.2 (July 11, 2021)
- 0.14.0 (July 2, 2021)
- 0.13.1 (June 14, 2021)
- 0.13.0 (May 5, 2021)
- 0.13.0RC1 (January 19, 2021)
- 0.12.2 (November 7, 2020)
- 0.11.0 (August 12, 2020)
- 0.10.0 (August 4, 2020)
- 0.9.0beta1 (June 17, 2020)
- 0.8.0 (February 12, 2020)
- 0.7.2 (February 4, 2020)
- 0.7.1 (January 29, 2020)
- 0.6.7 (January 9 2020)
- 0.6.5 (Nov 21, 2019)
- 0.6.4, 0.6.4-1 (Nov 11, 2019)
- 0.6.2, 0.6.3RC1, 0.6.3RC2 (October 27, 2019)
- 0.6.0RC1, 0.6.2 (October 13, 2019)
- 0.5.1, 0.5.1a, 0.5.2 (September 10, 2019)
- 0.5.0 (August 11, 2019)
- 0.4.6 (July 23, 2019)
- 0.4.5 (July 22, 2019)
- 0.4.4 (July 19, 2019)
- 0.4.3 (July 18, 2019)
- 0.4.0 (June 7, 2019)
- API
- Comparisons to other pipelines
- Getting help
- License information