Welcome to the linescanning repository
This repository contains all of the tools used during the acquisition and postprocessing of line scanning data at the Spinoza Centre for Neuroimaging in Amsterdam. The main goal of the package is to create the most accurate segmentations (both volumetric and surface) by combining various software packages such as Nighres, fMRIprep, FreeSurfer, CAT12, and SPM, and analyze line-scanning data (mainly including GLMs and deconvolutions with Nideconv). Also has the capability to read in any type of input file (npy, gii, nii, nii.gz, np.ndarray), and return a dataframe index on subject, run, and voxels so it’s compatible with Nideconv.
Contents
Getting started
Example gallery
Reference
- Bash modules
- 00: spinoza_lineplanning
- 02: spinoza_scanner2bids
- 03: spinoza_linerecon
- 04: spinoza_qmrimaps
- 05a/05b: spinoza_registration
- 06: spinoza_averagesanatomies
- 07: spinoza_sinusfrommni
- 08: spinoza_biassanlm
- 09: spinoza_brainextraction
- 10: spinoza_nordic
- 11: spinoza_dura
- 12: spinoza_sagittalsinus
- 13: spinoza_masking
- 14: spinoza_freesurfer
- 15: spinoza_fmriprep
- 16: spinoza_denoising
- 17: spinoza_fitprfs
- 18: spinoza_bestvertex
- 19: spinoza_segmentfast
- 20: spinoza_mgdm
- 21: spinoza_extractregions
- 22: spinoza_cortexrecon
- 23: spinoza_layering
- 24: spinoza_subcortex
- 25: spinoza_line2surface
- 26: spinoza_profiling
- Python functions