scitran-apps

Pinned Repositories

afq-pipeline
Flywheel Gear that runs the AFQ processing pipeline
Language:MATLAB29
dcm2niix
DICOM/PAR-REC conversion to nifti using Rorden's dcm2niix
Language:Shell4 3 174
dicom-mr-classifier
Extract metadata from raw DICOM data from Siemens, Philips, or GE.
Language:Python5 6 216
dti-error
Calculate the RMSE between a tensor fit from dtiInit and the diffusion weighted imaging data
Language:MATLAB2 4 30
freesurfer-recon-all
Performs all, or any part of, the FreeSurfer cortical reconstruction process.
Language:Shell14
fsl-bet
FSL's Brain Extraction Tool (BET)
Language:Shell1 3 12
fsl-fast
FMRIB's Automated Segmentation Tool
Language:Shell2 3 02
qa-dtiprep
dtiPrep quality assurance algorithm
Language:Python1 3 00
retinotopy-templates
Applies the retinotopy templates from Benson et al. (2014) PLOS Comput Biol to a FreeSurfer subject output.
Language:Shell2 3 70
spm8-mcr-v713
SPM8 with MATLAB MCR 2010a
1 4 02

scitran-apps's Repositories

scitran-apps/dicom-mr-classifier
Extract metadata from raw DICOM data from Siemens, Philips, or GE.
Language:Python5 6 216
scitran-apps/dcm2niix
DICOM/PAR-REC conversion to nifti using Rorden's dcm2niix
Language:Shell4 3 174
scitran-apps/afq-pipeline
Flywheel Gear that runs the AFQ processing pipeline
Language:MATLAB29
scitran-apps/dti-error
Calculate the RMSE between a tensor fit from dtiInit and the diffusion weighted imaging data
Language:MATLAB2 4 30
scitran-apps/fsl-fast
FMRIB's Automated Segmentation Tool
Language:Shell2 3 02
scitran-apps/retinotopy-templates
Applies the retinotopy templates from Benson et al. (2014) PLOS Comput Biol to a FreeSurfer subject output.
Language:Shell2 3 70
scitran-apps/apply-canonical-xform
Reorient NIfTI data and metadata fields into RAS space
Language:Shell1 3 00
scitran-apps/freesurfer-recon-all
Performs all, or any part of, the FreeSurfer cortical reconstruction process.
Language:Shell14
scitran-apps/fsl-bet
FSL's Brain Extraction Tool (BET)
Language:Shell1 3 12
scitran-apps/qa-dtiprep
dtiPrep quality assurance algorithm
Language:Python1 3 00
scitran-apps/spm8-mcr-v713
SPM8 with MATLAB MCR 2010a
1 4 02
scitran-apps/afni-brain-coreg
Co-Register a functional to an anatomical.
Language:Python4 0
scitran-apps/afni-brain-warp
AFNI-based brain warping based on D99 Macaque Atlas warp scripts
Language:Shell
scitran-apps/afq-browser
Gear to generate files for afq browser
Language:Python4 0
scitran-apps/afq-pipeline-sdk
AFQ Pipeline Gear using Flywheel SDK
Language:Python3 0
scitran-apps/dcm-convert
SciTran DICOM Conversion Tool
Language:Python3 62
scitran-apps/dcm2nii
DICOM/PAR-REC conversion to nifti using Rorden's dcm2nii (v.4AUG14)
Language:Shell3 1
scitran-apps/dtiinit
Vistasoft (mrDiffusion) preprocessing pipeline for diffusion MR data
Language:Python3 92
scitran-apps/dwi-norm-flip
Normalize DWI data
4 0
scitran-apps/dwi-split-shells
Split mutlti-shell dwi data into individual shells
Language:MATLAB4 0
scitran-apps/fsl-eddy
Run FSL's Eddy tool
scitran-apps/fslmerge
Uses fslmerge from FSL to merge datasets
Language:Shell
scitran-apps/gannet
Gannet analysis of edited MRS data
Language:Shell3 23
scitran-apps/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.
Language:Python3 0
scitran-apps/mrq
Flywheel Gear to execute mrQ from Mezer Lab
Language:MATLAB7 1
scitran-apps/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
Language:Shell4 07
scitran-apps/nifti-montage
Generate montage from NIfTI
Language:Python3 21
scitran-apps/parrec-mr-classifier
Classification of par/rec MR data from Philips
Language:Python
scitran-apps/PRF
PRF analysis with the analyzePRF code
Language:MATLAB4 0
scitran-apps/pyafq
Python implementation of AFQ
3 01