215 Works

Brain reconstruction

Soichi Hayashi & Serge Koudoro
Reconstruction of the diffusion signal with the Tensor model (dipy / reconst_dti)

Freesurfer Deface

Soichi Hayashi
Runs freesurfer/mri_deface with talairach_mixed_with_skull.gca and face.gca

ANTs transformation

Giulia Berto
Compute ANTs transformation between two subjects based on T1 and FA volumes.


Soichi Hayashi, Franco Pestilli & Brad Caron
This app will fit the diffusion tensor model (DTI) to a diffusion MRI image using FSL's dtifit commmand.

Diffusion Predictor Grid Search (AppA)

Soichi Hayashi, Franco Pestilli & Cesar F. Caiafa
Runs FitFullModelSampleAllTracts with 665 parameter set and find the optimal parameters and fit model with the optimal parameters

Ensemble Tracking (dwi)

Soichi Hayashi, Lindsey Kitchell, Brent McPherson & Brad Caron
This service uses MRtrix 0.2.12 to do ensemble tracking using tensor and constrained spherical deconvolution (csd) algorithms. It generates a large set of candidate streamlines using a tensor-based deterministic model, csd-based deterministic model, and csd-based probabilistic model. The csd-based models can be computed at lmax values of 2, 4, 6, 8, 10, and 12. All candidate streamlines are combined into a single track.mat file. If you know the max lmax value for your data input...

fMRI Preprocessing

Lollopasquini@Gmail.Com & Soichi Hayashi
fMRI preprocessing via CONN

LiFE and AFQ Quality Check

Lindsey Kitchell & Daniel Bullock
Generates multiple graphs that can be used as a quality check for the outputs of AFQ and LiFE. This application will only work if the zero weighted fibers are removed AFTER AFQ.

Generate Equivolumetric Surfaces

David Hunt
Computes n equally spaced offset surfaces between the white and pial surfaces with equal ratios between areas of successive surfaces, which samples the same layers in gyri and sulci.

ANTs transformation and wmc registration with T1

Giulia Berto
Compute ANTs transformation between two subjects based on T1 or FA volumes and apply the transformation to the AFQ segmentation provided.

Quantitative Statistics of Classified Fiber Tracts

Soichi Hayashi, Lindsey Kitchell & Daniel Bullock
This will give you the fiber count, mean length, standard deviation of length, total length, and volume of each fiber tract classified by AFQ or WMA.

HRSC: High Resolution Structural Connectome Processing

Kate Alpert
App for running high resolution structural connectome processing from Pierre Besson

Shape Signature

Soichi Hayashi
This App takes tract masks and convert them to series of numerical values that chracaterizes each masks. The numerical values are generated from the flattened output of 3D convolutional layers of the model trained to classify tract names. Output values could be used as a "shape signature" and compared against other similar shaped tracts.

Diffusion Predictor Grid Search (AppA) (old)

Soichi Hayashi
This is an old version that used dwi instead of dtiinit

Registration Year

  • 2018
  • 2019

Resource Types

  • Software