核磁數處理和資料分析的資源彙總-不斷更新

##線上電子書：

http://www.magnetic-resonance.org/

##幾個專業名詞:

axial diffusivity (AD)

fractional anisotropy (FA)

mean diffusion (MD)

radial diffusivity (RD)

資料檢視和格式轉換網上資源:

• A wiki that provides more information on converting diffusion images from the DICOM format
• Video on how to use the graphical user interface of dcm2nii
• Additional information from dcm2nii on data repositories and alternatives tools
• Website dedicated to medical imaging formats
• Other dicom converters: mri_convert by freeserver, dimon by afni, dicom2nifti for SPM
• Other data viewers: 3D Slicer: Image Visualization Software, MedINRIA: DTI Analysis and Visualization Software.

Eddy修正網上資源

• You can also use the FSL Diffusion Toolbox, which has a graphical user interface
• If you acquired two diffusion scans with opposing polarity, you can use FSL’s eddy instead
• Distortion correction and preprocessing tutorial from Stanford

EPI修正網上資源

• Distortion correction tutorial for TOPUP from UCDavis
• Distortion correction tutorial by Andy’s Brain Blog, with video’s
• EPI distortion correction using ExploreDTI

• Distortion correction tutorial by MNI

  附5: Camino的更多資源:Additional online resources:

• More info from this blog on tensor fitting
• Camino has a comprehensive list of tutorials for their tools here
• Camino can also run higher order models like Q-ball/HARDI

Sanity check更多資源

• General tutorial on “Diffusion Tensor Imaging Analysis using FSL”
• Overview of other software packages on this blog
• Article on the do’s and don’ts of diffusion imaging
• Article that is the hitchhikers guide to diffusion imaging
• Preprocessing tutorial by the Enigma group

FSL

安裝

FSL目前隻支援PYTHON 2.X .

安裝說明:https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux

完整版下載下傳位址:http://neuro.debian.net/install_pkg.html?p=fsl-complete

在linux下的安裝非常簡單, 隻需要打開終端, 輸入 sudo python2 fslinstaller.py 即可完成安裝.安裝後需要重新登入目前使用者,或者重新開機一下系統, 更新系統環境變量.

檢查是否安裝成功, 就需要在終端輸入

echo $FSLDIR
flirt -version
           

echo $FSLDIR 檢查安裝路徑; flirt -version檢查FSL版本.

功能

FSL可以對各種核磁資料進行處理. 核磁資料類型和FSL指令的關系如下:

• 功能核磁共振: FEAT, MELODIC, FABBER, BASIL, VERBENA
• 結構核磁共振: BET, FAST, FIRST, FLIRT & FNIRT, FSLVBM, SIENA & SIENAX, MIST, BIANCA, MSM, fsl_anat
• 彌散核磁共振: FDT, TBSS, eddy, topup
• GLM / 統計: GLM general advice, Randomise, Cluster, FDR, Dual Regression, Mm, FLOBS
• 通用 : FSLeyes, FSLView, Fslutils, Atlases, Atlasquery, SUSAN, FUGUE, MCFLIRT, Miscvis, POSSUM, BayCEST

教育訓練和其它工具

FSL教育訓練: http://fsl.fmrib.ox.ac.uk/fslcourse/oxford2018.html

核磁資料處理以及相關算法的github: https://github.com/bernardng/codeSync

下載下傳: codeSync-master.zip

https://www.youtube.com/watch?v=xxSEx2NTM-w

mitk: 醫療影像工具包: http://mitk.org/wiki/Projects

PANDA: A pipeline tool for diffusion MRI

https://www.nitrc.org/forum/message.php?msg_id=22917

BrainSuite: http://brainsuite.org/

VBM大神John Ashburner博士論文: http://www.fil.ion.ucl.ac.uk/spm/doc/theses/john/

neurosynth.org: http://neurosynth.org

Neurosynth is a platform for large-scale, automated synthesis of functional magnetic resonance imaging (fMRI) data.

資料庫

1. IXI資料庫, 大腦發育方面, 有如下類型的資料:

   T1 images (all images)

   T2 images (all images)

   PD images (all images)

   MRA images (all images)

   DTI images (all images, bvecs.txt, bvals.txt)

   Demographic information (spreadsheet)

   網址: http://brain-development.org/ixi-dataset/

2. openmri: 開源的研究資料

   https://openneuro.org/datasets