Documentation of the CApsul PipelineS¶

dMRI¶

Diffusion MRI preprocessings

This pipeline enbables preprocessings of diffusion MRI images:

Distortion correction

Tensor Estimation

dMRI registration

Scalar Map computation

Diffusion MRI model estimation

This set of pipelines enables the estimation of diffusion models:

Tensor model: least square

Tensor model: quartics non negative least square

Diffusion MRI model registration

This set of pipelines enables the registration of diffusion tensor models:

Registration: Non linear anatomical registration

Reorientation: Finite Strain or PPD

fMRI¶

fMRI functional connectivity

This pipeline enbables the functional connectivity analysis of fMRI datasets.

fMRI preclinic pipeline

This pipeline enables the preprossings and statistical analysis of preclinic functional images with SPM and FSL. The different steps involved are:

Reorientation

Slice registration

Slice timing

Realignement

Coregistration

Segmentation/Registration to a template space

Normalization (resampling)

Smoothing

Brain extraction

First level analysis

fMRI preprocessings pipeline

This pipeline enables the preprossings of preclinic functional images with PyPreProcess (SPM). The different steps involved are:

Slice timing

Realignement

Coregistration

Segmentation/Registration to a template space

Normalization (resampling)

Smoothing

Brain extraction

Misc¶

DICOM converter pipeline

This pipeline enbables the NIFTI conversion and the anonymization of DICOM files. Moreover, it is possible to transcode the patient name.

Utility

A set of pipelines that are shared with others.

Quality control pipeline

A set of pipelines to check the quality of a result.

Quality assurance pipeline

A set of pipelines to check the quality of the input images.