scitran-apps Goto Github PK
Type: Organization
scitran-apps's Projects
afni-brain-coreg
Co-Register a functional to an anatomical.
afni-brain-warp
AFNI-based brain warping based on D99 Macaque Atlas warp scripts
afq
Automated Fiber Quantification
afq-browser
Gear to generate files for afq browser
afq-pipeline
Flywheel Gear that runs the AFQ processing pipeline
afq-pipeline-sdk
AFQ Pipeline Gear using Flywheel SDK
apply-canonical-xform
Reorient NIfTI data and metadata fields into RAS space
dcm-convert
SciTran DICOM Conversion Tool
dcm2nii
DICOM/PAR-REC conversion to nifti using Rorden's dcm2nii (v.4AUG14)
dcm2niix
DICOM/PAR-REC conversion to nifti using Rorden's dcm2niix
dicom-mr-classifier
Extract metadata from raw DICOM data from Siemens, Philips, or GE.
dti-error
Calculate the RMSE between a tensor fit from dtiInit and the diffusion weighted imaging data
dtiinit
Vistasoft (mrDiffusion) preprocessing pipeline for diffusion MR data
dwi-norm-flip
Normalize DWI data
dwi-split-shells
Split mutlti-shell dwi data into individual shells
freesurfer-recon-all
Performs all, or any part of, the FreeSurfer cortical reconstruction process.
fsl-bet
FSL's Brain Extraction Tool (BET)
fsl-eddy
Run FSL's Eddy tool
fsl-fast
FMRIB's Automated Segmentation Tool
fslmerge
Uses fslmerge from FSL to merge datasets
gannet
Gannet analysis of edited MRS data
hdft-subsampled-recon
Computes a transformation of multi-shell diffusion weighted data to a set of Spherical Harmonic coefficients and outputs 4D Spherical Harmonic coefficient data. This is a first step in the Schneider Lab HDFT diffusion reconstruction process.
mcr-v901
Matlab Compiler Runtime for v9.0.1 (R2016a)
mrq
Flywheel Gear to execute mrQ from Mezer Lab
mrtrix3preproc
mrtrix3preproc runs the mrTrix3 preprocessing pipeline in the diffussion data. It uses FSLs topup when the optional inverted phase encoding files are found, otherwise uses the eddy tool. It performs some other denoising steps, and it can normalize or align to acpc the data
nifti-montage
Generate montage from NIfTI
parrec-mr-classifier
Classification of par/rec MR data from Philips
prf
PRF analysis with the analyzePRF code
pyafq
Python implementation of AFQ
qa-dtiprep
dtiPrep quality assurance algorithm
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