Cortex Tissue Mapping (Native & Template Space)

doi  10.25663/brainlife.app.379
   Registered  6/17/2020    25  Users    45456  Requests    0 - 3.5 hour

This app will map volumated measure files (i.e. tensor, NODDI) to the cortical surface following Fukutomi et al (2018; 10.1016/j.neuroimage.2018.02.017) using Connectome Workbench.

postprocessing

54.5% Success Rate


This App uses the following input/output datatypes

Input
dwi
Validator
dwi

The path to the DWI datatype

Diffusion-weighted magnetic resonance data (dMRI), saved in NIfTI-1 format.

dwi: dwi.nii.gz • bvecs: dwi.bvecs • bvals: dwi.bvals • sbref: sbref.nii.gz • sbref_json: sbref.json
freesurfer
Validator
freesurfer

The path to the top directory containing the output from Freesurfer

Folder structure generated by FreeSurfer recon-all process.

freesurfer: output/
noddi
noddi
optional

The path to the NODDI datatype files (optional)

NODDI: Neurite Orientation Dispersion and Density Imaging. 4D image with ICVF, OD, ISOVF; where ICVF is the intracellular volume fraction (also known as NDI), OD is the orientation dispersion (the variance of the Bingham; also known as ODI) and ISOVF is the isotropic component volume fraction (also known as IVF).

dir: dir.nii.gz • ndi: ndi.nii.gz • isovf: isovf.nii.gz • odi: odi.nii.gz
tensor
tensor

The path to the tensor datatype files

Diffusion Tensor Image Scalars

fa: fa.nii.gz • md: md.nii.gz • rd: rd.nii.gz • ad: ad.nii.gz • cl: cl.nii.gz • cp: cp.nii.gz • cs: cs.nii.gz • tensors: tensors.nii.gz • kurtosis: kurtosis.nii.gz • ga: ga.nii.gz • mk: mk.nii.gz • ak: ak.nii.gz • rk: rk.nii.gz • rgb: rgb.nii.gz
warp
transform/nifti
not linear

These files are needed to generate surfaces in template space (usually MNI). If you need to generate these files, please look at brainlife app FSL Anat. A version of this app not requiring this input is being generated

Linear & Non-Linear Image Warping in FSL format (warp.nii.gz / inverse-warp.nii.gz)

warp: warp.nii.gz • inverse_warp: inverse-warp.nii.gz • affine: affine.txt
brainmask
Validator
mask
optional

The path to the dwi brainmask. optional. will be computed internally if not provided

Volume Mask

brainmask: mask.nii.gz
cortexmap
cortexmap
optional

Cortext Mapping

cortexmap: cortexmap/
Output
cortexmap
cortexmap

The cortexmap output, containing the surfaces and mapped data

Cortext Mapping

cortexmap: cortexmap/
raw
raw
cortexmap_derivatives

A directory containing all of the derivatives generated. Useful for QA and debugging

Unstructured data not meant to be used as input to any other Apps. You can use this datatype for development purposes. Please register a new datatype once your App is ready to be used by other users.

output: ./

Configuration
fsurfparc: enum = aparc.a2009s
  • aparc Desikan-Killiany
  • aparc.a2009s Destrieux Atlas Default
  • aparc.DKTatlas DKT Atlas

Parcellation from freesurfer wanted to for future stats

snr: boolean = true

controls whether bad vertices are masked out based on temporal SNR of dwi. if true, will mask. default == true

Maintainers

List of users who currently maintains this App.

Brad Caron


Contributors

List of code contributors.(brainlife/app-cortex-tissue-mapping).

Brad Caron

Franco Pestilli