1. Overview - Stereo-Boy/Pipeline_AS GitHub Wiki

The pipeline automates all the steps necessary to extract retinotopic areas from a pRF model, from the conversion of DICOM anatomical files to the drawing of the ROI on flattened cortical patches. It relies on Matlab and mostly on mrVista/vistasoft. The central function (in modules folder) is called pipeline_JAS and it runs a set of modules on demand, most of them optional.

The modules are:

1. nifti conversion of anatomical volume (using dcm2niix from MRIcron)
2. segmentation of anatomical volume (using Freesurfer)
3. correction of gray mesh irregularities (manual step using itkGray)
4. nifti header repair of anatomical image
5. nifti conversion of retinotopy epi/inplane and removal of ''pRF dummy'' frames (using dcm2niix from MRIcron)
6. motion correction of retinotopy epi/inplane (using FSL)
7. MC parameter check and artefact removal (using FSL)
8. retinotopy epi/inplane: nifti header repair
9. initialization of a new mrVista session (using mrVista)
10. registration of inplane and volume in the mrVista session (using spm/mrVista)
11. Installing segmentation in the mrVista session
12. mesh creation and smoothing in the mrVista session
13. Estimation of the pRF model (using mrVista)
14. mesh visualization of pRF values (in mrVista)