HYDI is a bit different than HARDI but still many models can be used. It would be great if you could provide
more information about what exactly you want to do.
My current goal is to get a free water corrected tensor map, with which I can get values for specific tracts recreated via probabilistic tractography. Our main goal is to be able to do this for the fornix, as it is a white matter tract most notably affected by CSF, but we would like to implement FW corrections for all of our data going forward.
For some of the models we provide command lines which maybe easier to use than writing your own scripts.
For example have you tried to use the command dipy_fit_dti with your data. I suggest doing that as a learning experience.
Then try to replicate the results with writing your own python script. After you become familiar with this we
can suggest other models such as Mapmri/DSI/GQI which would be great with your type of data.
I had not known this was available! I will explore this as well, as I agree it would be a valuable learning experience for creating my own pipeline.
If you have further suggestions/questions from my explanation of what we are looking to do, I am more than happy to continue to chat. With the information both you and Ariel have provided, I feel much better equipped! Thank you!
Hello DIPY experts,
I am attempting to apply a free water correction to my DWI data in order to look at structures such as the fornix. Normally I process data within FSL, though I do have experience coding with Python. To use the free water correction, do I need to do all of my preprocessing within DIPY, or am I able to use the data I have already preprocessed within FSL? Are there also any tutorials in using my own data for processing, rather than examples? I am able to process examples with no issue, but I am struggling with applying these commands to my own data. I have mainly been confused with where to house my data, and how to proceed when I have a different type of data than the example (I have multi-shelled HYDI data, but many examples are with HARDI). I have not been successful at loading my own data for any of the examples as of yet.
Any advice or resources would be extremely helpful. My lab believes that DIPY will be the way forward, so I am more than willing to learn how to do preprocessing within DIPY, it would just be convenient for my current project to use my already preprocessed data.
Thank you for your help,
Katie
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