Introduction to Diffusion Tensor Imaging (DTI)
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- เผยแพร่เมื่อ 3 ส.ค. 2024
- Overview of DTI, and how to fit tensors to a single subject. Future tutorials will use dataset #3 from the following link: fsl.fmrib.ox.ac.uk/fslcourse/ (Navigate to Data Files and select File 3)
- วิทยาศาสตร์และเทคโนโลยี
Thanks Prof.Andrew!!you are the one
Thanks a lot Andrew, really good job!
Hi, excellent videos on FSL. How can I calculate ROI values for the white matter tracts? Your help will be appreciated. Thank you very much!
YOU ARE THE BEST!!!
Thank you. This tutorial is really helpful!
No problem! I'm glad you find it useful.
-Andy
Hi Andrew! Thank you for video. I have one question. I am using FSL 6.0.1 and for Eddy current & motion correction/Outlier detection I need also Index file and Acquisition parameter file in .txt format. I have no idea where I can find these files. From Siemens Biograph mMR I get only one additional folder PhoenixZipReport with .sr files.
Thank you! It's a great work! could you show a demo of DTI analysis for probabilistic tracking if FSL, thanks
thank you very much!
Can I register the structural and functional image to a standard space (using MNI template) in the FDT diffusion GUI with registration?
Hi Andrew! Great videos, they are very helpful. I was wondering if you know where I can get the bvec/bval files for a 2dseq file that I converted to nifti using Jim(xinapse). Is there a similar program like dcm2nii for bruker files? I have the acqp text file but I don't think this is the same format. Thank you!
Hi Elizabeth,
I don't know how to get those particular files; I haven't used Bruker files before. If you find out, please reply here and let us know how you solved the problem.
Best,
-Andy
For anyone still wanting to download the tutorial dataset, the link now has been changed. You need to download file#3 - diffusion MRI
Thanks for letting me know; the video description now points to the right file.
-Andy
Dear Jahn
Do you have some courses about the FMRIB Diffusion Toolbox.Such as DTI model fit,BEDPOSTX modelling crossing fibres,PROBTRACKX propagating uncertainty in tractography
Hi Kaixin, not yet! I am starting to sketch out some modules on diffusion analysis with MRtrix and TRACULA, but those may take a while.
Best,
-Andy
Great video! I do just as the video do but my output is hdr/img, not nii. I wonder if there is some setting? Thanks:)
Hi Ninngrong,
You can convert to NIFTI using FSL's fslchfiletype; e.g., if your file is myfile.hdr:
fslchfiletype NIFTI myfile
Hope this helps!
-Andy
thank you!
Do you have an email? I'd like to ask a few questions about DTI if you don't mind.
would you mind give me the link please... I can´t see the url
Follow the link in the information box, and then download File 3.
Dear Andrew,
Is it possible you learn Mrtrix and Cammino ? Because these software use another algorithm for tractography.
Hi Mohammed,
I might get to those packages sometime in the future! Camino in particular looks like a good program to use. I'll let you know when I start on those.
Best,
-Andy
Andrew Jahn
Hi Andrew,
Mrtrix is very powerful software for Probability CSD tractography.
Thank you so much :)
+Andrew Jahn Hi Andrew,
Did you ever get around to making the videos using Mrtix?
한글자막 달아주실 분 없나요ㅠㅠ
Great video! I was wondering which is the video that teaches us how to get the brain mask? Thanks :)
Hi Heidi,
You can do this through FSL's BET. Click on the Advanced Options dropdown menu, and select "Output binary brain mask image." Use the anatomical as an input image. That should be a good place to start.
-Andy
Hi Andrew Jahn, thanks for your advice. I'll give it a try!
Hi Andrew, Apologies. I was wondering if I should run the brain mask first or eddy current correction. I am not sure what the brain mask does actually. Thanks!
Hey Heidi,
Eddy uses a mask as one of its options, so create the mask first and then run eddy.
-Andy
Great, thanks Andrew for the clarification!
How did you get the brain mask?
In this case, I believe the brain mask came with the downloaded files; you can create your own mask by using BET on the DTI data. Make sure to click on the dropdown menu on Advanced Options in the BET GUI and select "Output binary brain mask image".
-Andy
is there any way to create only the mask of the brain running BET? or another program? Thanks
@@carolinajimenezgomez2498 I am trying to create a brain mask for creating FA files. Should I run a bet on each subject's DWI data?
Fsl, human data, early steps (convert, setup)
If you're looking for some open access DTI data to play around with, you might want to check out the 'Lite' NKI-Rockland sample or the CoRR dataset:
fcon_1000.projects.nitrc.org/indi/enhanced/download.html
fcon_1000.projects.nitrc.org/indi/CoRR/html/index.html
John Pellman Thanks for the links, John! Those would definitely be useful in showing how to apply DTI techniques to datasets other than the pre-cooked ones on the FSL website; I'll see if I can get to those eventually.
-Andy
lo necesito en español :(((((
Thank you! It's a great work! could you show a demo of DTI analysis for probabilistic tracking if FSL, thanks
It's on the agenda, but it may be a while before I get to it; in the meantime, I've made some videos on MRtrix which might be of interest. Check them out and let me know if they help!
-Andy