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3os.org

Source Code for 3os.org website. The website based on Markdown format, rendered to html and hosted on github-pages

afq

Automated Fiber Quantification

app-acpcart

This app uses the Automatic Registration Toolbox (ART) to perform ACPC alignment of the T1 image. See https://www.nitrc.org/projects/art/ for more information.

app-add-to-t1

This is a test app that will add a value of 1 to each voxel of a t1, and output a new t1

app-afq_figures

This service creates 4 figures of each AFQ tract: axial, left sagittal, right sagittal, coronal. Please choose the t1 image slices you would like displayed. The default slices work well for the HCP t1 images if they have not been re-ACPC aligned. If you have ACPC aligned your t1 images using the ACPC alignment app on Brain Life the following values are a good starting point: coronal = 105, sagittal = 89, axial = 65. The img_min and img_max values refer to the value range displayed for the t1 image. The value range is calulated as follow (mean + img_min * std, mean + img_max * std). The default values are a good starting place, adjust them if your t1 is too dark or too light.

app-afqclean

This service cleans the output from AFQ and WMA using AFQ's AFQ_removeFiberOutliers function. For more information on the inputs of this application, please read the documentation at the top of the function: https://github.com/yeatmanlab/AFQ/blob/master/functions/AFQ_removeFiberOutliers.m

app-analyzeprf

app-apply-projectors

app-benson14-retinotopy

Brainlife.io app for Noah Benson's neuropythy library, retinotopy from T1 anatomy

app-bids-mrtrix3_connectome

BIDS app for Mrtrix3 Connectome DTI processing for BrainLife. Generates subject connectomes from raw image data using tools provided in the *MRtrix3* software package. http://www.mrtrix.org/. Optional preprocessing includes FSL's topup analysis for spatial correction and requires at least 2 input DTI images.

app-classifyber

Linear classification of single streamlines.

app-clean-or

app-combine-2d-to-3d

app-combine-tracts

app-commit

app-compute-average-tractmeasure

app-compute-dsc

Compute the degree of overlap between two bundle masks using the Dice Similarity Coefficient (DSC) score.

app-compute-similarity-parcellations

app-concatenate-tractmeasures

app-convert-eddyqc-to-regressor

app-convert-network-netstats

app-convert-tractmeasures-2-tractprofile

app-cortex-tissue-mapping-stats

app-crop_reorient_t1

This application will crop and reorient the T1 image to standard orientation and FOV using FSL's fslreorient2std and robustfov.

app-cut-tractmeasures-nodes

app-decoding-full-epochs

app-dipy-workflows

Brainlife wrapper app for Dipy workflows.

app-dwinormalise

app-endpointmapgeneration

app-enhanced-ensemble-tracking

Performs ensemble tractography with MRTrix 0.2.12 with user specified values for lmax and curvatures across probabilistic, deterministic, and tensor methods. Additionally, it seeds and tracts extra streamlines through the corpus callosum.