Optic chiasm data as input for COMMIT

[behnam12]

Dear COMMIT group ,

I used COMMIT for whole human brain and the results were great. Now, I am going to use COMMIT framework for ex-vivo optic chiasm data. But, the result does not look reasonable and Intracellular compartment map does match to Mask or DWI as can be seen in the attached image. I adjusted the parallel and perpendicular diffusivity for ex-vivo condition and checked the inputs for COMMIT (fibers, peaks, mask) but I could not find the reason for it.

I appreciate for any idea or suggestion about this problem. Is it possible to send my data for more accurate evaluation ?

Best Behanm

[barakovic]

Hello Behnam, sorry for the late answer. You may want to send me the data so I can check if there are technical problems. I would also like to ask you what are the results that you are hoping to have from the IC map (density in the crossing higher?). Cheers, Muhamed

[behnam12]

Hello Muhamed ,

Thank you for your response. firstly, It would be great if I can find out why IC map does not match with whole DWI data set. I want to have IC map for whole optic chiasm (diffusion data) and then look at how it changes between different regions. I've sent my data to you via E-mail.

Thanks Behnam

[barakovic]

The problem is that tractography and DWI are not aligned. A wrong conversion from ".tck" to ".trk" was done. (image with COMMIT_debugger)

Here a possible solution; a tool that converts properly different formats: https://github.com/MarcCote/tractconverter

Cheers,

Muhamed

[behnam12]

Hi Muhamed ,

Thanks for your response and advice. I'll try it.

Best Behnam

[behnam12]

Hi Muhamed ,

I just want to inform you that tractconvertor works successfully.

Best Behnam