Aug 28, 2024

Public workspaceMRI_preprocessing_protocol

DOI
dx.doi.org/10.17504/protocols.io.14egn61byl5d/v1
  • Miguel López-Aguirre1,2,3,
  • José A. Pineda-Pardo1,2,
  • Jose Obeso1,2,3
  • 1HM CINAC;
  • 2Fundación HM Hospitales;
  • 3CIBER
Jose Obeso
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DOI: dx.doi.org/10.17504/protocols.io.14egn61byl5d/v1
Protocol Citation: Miguel López-Aguirre, José A. Pineda-Pardo, Jose Obeso 2024. MRI_preprocessing_protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.14egn61byl5d/v1
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: August 28, 2024
Last Modified: August 28, 2024
Protocol Integer ID: 106575
Abstract
Preprocessing protocol for structural, DWI and T2* MRI acquisitions
Structural T1w (MP-RAGE acquisition)
Structural T1w (MP-RAGE acquisition)
Data transformation from DICOM to NIFTI standard (software: dcm2niix)

Field of view optimization (command: fslreorient2std; software: FSL)
Bias field correction (command: N4BiasFieldCorrection; software: ANTs)
Non-brain tissue removal (command: bet; software: FSL)
Deep-brain nuclei segmentation (command: run_first_all; software: FSL)
CSF, GM and WM tissue segmentation (command: fast; software: FSL)
Diffeomorphic registration to MNI152 2009c sym tempate (command: antsRegistrationSyN.sh; software: ANTs)
T2* (multi-echo gradient echo acquisition)
T2* (multi-echo gradient echo acquisition)
Data transformation from DICOM to NIFTI standard (software: dcm2niix)

Affine registration to structural T1w using the first volume as reference (command: antsRegistration; software ANTs)
Single-shell DWI (single-shot 2D spin-echo, b=1000)
Single-shell DWI (single-shot 2D spin-echo, b=1000)
Data transformation from DICOM to NIFTI standard (software: dcm2niix)
B0 pair isolation (AP and PA)
Image denoising using the overcomplete local PCA appoach (MATLAB)
Geometric distortions and magnetic field inhomogeneities corrections (command: topup; software: FSL)
Eddy current-induced distortion corrections (command: eddy; software: FSL)
Bias field correction (command: N4BiasFieldCorrection; software: ANTs)
Affine registration to structural T1w using the first volume (B0) as reference (command: antsRegistration; software ANTs)