micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
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Updated
Apr 16, 2024 - Shell
micapipe from the Multimodal imaging and connectome analysis lab (http://mica-mni.github.io) at the Montreal Neurological Institute. Read The Docs documentation below
Scripts for MRI preprocessing
Peak width of Skeletonized Mean Diffusivity (PSMD)
Run the recommended preprocessing procedure provided by mrtrix3. The options available mostly reflect the optimal DESIGNER pipeline that was recently proposed. This App runs for >15 on topup if both PA and AP dwi files are provided. It detects bvecs flipping (dwigradcheck) and update the gradient table accordingly.
Brainlife wrapper app for dipy_fit_dki workflows. Fit a Diffusion Kurtosis Imaging model to multishell Diffusion-weighted data
This app will fit the diffusion tensor model (DTI) to a diffusion MRI image using FSL's dtifit commmand.
Tract Segmentation from input tractography using ROIs
Brainlife wrapper app for dipy_track_pft workflows.
Brainlife wrapper app for dipy_track workflows.
Brainlife wrapper app for dipy_fit_csa workflows
Brainlife wrapper app for dipy_reslice workflows.
Brainlife wrapper app for dipy_denoise_lpca workflows.
Brainlife wrapper app for dipy_denoise_mppca workflows.
Brainlife wrapper app for dipy_gibbs_ringing workflows.
Brainlife wrapper app for dipy_denoise_nlmeans workflows.
Brainlife wrapper app for dipy_recobundles workflows.
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