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presurfer

Scripts to prepare MP2RAGE for Freesurfer

https://github.com/srikash/presurfer

Science Score: 54.0%

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    Low similarity (6.5%) to scientific vocabulary
Last synced: 6 months ago · JSON representation ·

Repository

Scripts to prepare MP2RAGE for Freesurfer

Basic Info
  • Host: GitHub
  • Owner: srikash
  • Language: MATLAB
  • Default Branch: main
  • Size: 58.6 KB
Statistics
  • Stars: 26
  • Watchers: 2
  • Forks: 9
  • Open Issues: 2
  • Releases: 1
Created over 5 years ago · Last pushed over 2 years ago
Metadata Files
Readme Citation

README.md

presurfer DOI

Example

Step-0 : MPRAGEise UNI

Run presurf_MPRAGEise

MPRAGEising is better than background removal ('denoising')

Optional: \ Strip dielectric pads if used now (see PadsOff, needs ANTs)

Step-1 : Get a stripMask from INV2

Run presurf_INV2

Step-2 : Get a brainMask from UNI

Run presurf_UNI

Step-3 : Freesurfer

Use the INV2 stripMask to clean up the non-brain parts of the MPRAGEised UNI image.

e.g. fslmaths MPRAGEised.nii -mul stripMask.nii MPRAGEised_stripped.nii

Run recon-all using the MPRAGEised_stripped image

Here is an example of a fully automated segmentation using presurfer + Freesurfer and laminar surfaces:


Misc. note

Run presurf_biascorrect to do just do SPM bias-correction.

Every step produces a sub-directory in the working directory containing all relevant segmentations and masks.

e.g. running presurf_INV2 creates a presurf_INV2 sub-directory

Owner

  • Name: Sriranga Kashyap
  • Login: srikash
  • Kind: user
  • Location: Toronto, Canada
  • Company: University Health Network

Neuroimaging researcher with a background in biotech engineering and pre-clinical research. Curious about everything.

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
  - family-names: Kashyap
    given-names: Sriranga
    orcid: https://orcid.org/0000-0003-0307-9773
title: srikash/presurfer: ondu
version: 1.0
date-released: 2021-03-22

GitHub Events

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