在线电子书：
http://www.magnetic-resonance.org/
几个专业名词:
axial diffusivity (AD)
fractional anisotropy (FA)
mean diffusion (MD)
radial diffusivity (RD)
数据查看和格式转换网上资源:
- 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修正网上资源
- 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修正网上资源
- 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的更多资源: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更多资源
- 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
安装
FSL目前只支持PYTHON 2.X .
安装说明:https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FslInstallation/Linux
完整版下载地址:http://neuro.debian.net/install_pkg.html?p=fsl-complete
在linux下的安装非常简单, 只需要打开终端, 输入 sudo python2 fslinstaller.py 即可完成安装.安装后需要重新登录当前用户,或者重启一下系统, 更新系统环境变量.
检查是否安装成功, 就需要在终端输入
echo $FSLDIR
flirt -versionecho $FSLDIR 检查安装路径; flirt -version检查FSL版本.
功能
FSL可以对各种核磁数据进行处理. 核磁数据类型和FSL命令的关系如下:
- 功能核磁共振: FEAT, MELODIC, FABBER, BASIL, VERBENA
- 结构核磁共振: BET, FAST, FIRST, FLIRT & FNIRT, FSLVBM, SIENA & SIENAX, MIST, BIANCA, MSM, fsl_anat
- 弥散核磁共振: FDT, TBSS, eddy, topup
- GLM / 统计: GLM general advice, Randomise, Cluster, FDR, Dual Regression, Mm, FLOBS
- 通用 : FSLeyes, FSLView, Fslutils, Atlases, Atlasquery, SUSAN, FUGUE, MCFLIRT, Miscvis, POSSUM, BayCEST
培训和其它工具
FSL培训: http://fsl.fmrib.ox.ac.uk/fslcourse/oxford2018.html
核磁数据处理以及相关算法的github: https://github.com/bernardng/codeSync
下载: codeSync-master.zip
https://www.youtube.com/watch?v=xxSEx2NTM-w
mitk: 医疗影像工具包: 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博士论文: 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.
数据库
1) IXI数据库, 大脑发育方面, 有如下类型的数据:
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)
网址: http://brain-development.org/ixi-dataset/