Giulia Bertò's repositories
docker-tutorial
Docker tutorial to build an FSL container.
app-classifyber
Code of Classifyber, a robust streamline-based linear classifier for white matter bundle segmentation.
app-compute-dsc
Compute the degree of overlap between two bundle masks using the Dice Similarity Coefficient (DSC) score.
app-ants-mni
ANTs transformation and tractogram registration in MNI space, using as the reference template the MNI152 T1 at 1.25 mm. WARNING: all the given inputs should be in the same anatomical space.
app-multi-lap-anat
White matter bundle segmentation as Anatomically-Informed multiple Linear Assignment Problems (multi-LAP-anat).
3dbraingen
Official Pytorch Implementation of "Generation of 3D Brain MRI Using Auto-Encoding Generative Adversarial Network" (accepted by MICCAI 2019)
abcd-spec
Application for Big Computational Data Specification (v1.1). This specification provide information on how to write an Application that can run on the open platform
app-ants-CFA-registration
CFA-based non linear ANTs registration of the tensor to the FMRIB58_FA_1mm.nii.gz template or the IITmean_FA template.
app-ants-FA-registration
FA-based non linear ANTs registration of the tensor to the FMRIB58_FA_1mm.nii.gz template or the IITmean_FA template.
app-compute-cfa
App to compute the colored FA
dl_with_pytorch
Preliminary experiments with DL and Pytorch on anatomical images
giulia-berto.github.io
Portfolio of main projects.
app-extract-peaks
App to extract the peaks of a spherical harmonic function at each voxel using the MRtrix command sh2peaks.
app-freesurfer
Freesurfer segments the t1w anatomical data into functionally different parts of the brain. Segmentation/parcellation can then be fed to many other subsequent analysis.
app-mrtrix3-preproc
Run the recommended preprocessing procedure provided by mrtrix3. The options available mostly reflect the optimal DESIGNER pipeline that was recently proposed. This App runs for >15 on topup if both PA and AP dwi files are provided. It detects bvecs flipping (dwigradcheck) and update the gradient table accordingly.
app-multi-lap
White matter bundle segmentation as multiple Linear Assignment Problems (multi-LAP).
app-rsHRF
Hemodynamic Response Function Retrieval and Deconvolution (RS-HRF)
app-subj2reference
This app warps your input set of ROIS to a reference space. As it is currently set up, the master branch of this app warps to MNI space.
app-template-python
This is a template for a python-based brainlife.io/app
app-test-matlab
Test to run matlab compiled code on HCP systems
app-tractanalysisprofiles
Create plots of diffusion metrics (i.e. FA, MD, RD, AD) for each of the segmented tracts from AFQ, known as Tract Profiles. Obtains streamline positions from segmented tracts and plots the metrics of interest along "nodes" of the tract, allowing for comparison of individual subject tracts. Requires the dt6 output from dtiinit and a white matter classification output from AFQ or WMA
dipy
DIPY is the paragon 3D/4D+ imaging library in Python. Contains generic methods for spatial normalization, signal processing, machine learning, statistical analysis and visualization of medical images. Additionally, it contains specialized methods for computational anatomy including diffusion, perfusion and structural imaging.
docker-mne
brainlife MNE container
master
A machine learning course using Python, Jupyter Notebooks, and OpenML
PyNets
A Reproducible Workflow for Structural and Functional Connectome Ensemble Learning
tutorials
PyTorch tutorials.
warehouse
Service that allows data warehousing and workfow orchestration