Peaks file

[HamidZarandi]

Hi ,

I want to apply COMMIT framework on a diffusion MRI data set. I need help for generation of peak file. Could you give me information about this file and how I can create it.

Best Zarandi

[barakovic]

Hello Hamid, each volume corresponds to the x, y & z component of each peak direction vector in turn. If you have your own code you should create a NIfTI file volume with x, y & z component for each peak. For example, if you want to use 3 peaks you should have a Nifti with 9 volumes, 5 peaks 15 volumes, ecc.. To generate this file we usually use the function of mrtrix sh2peaks ( http://mrtrix.readthedocs.io/en/latest/reference/commands/sh2peaks.html ) or we use dipy code ( http://nipy.org/dipy/ ).

Hope this can help,

Muhamed

[behnam12]

Hi Muhamed ,

I am going to create a peak map the same as example dataset (peaks.nii.gz). In order to do that, I've created a map containing principal eigenvectors in x, y and z components (V1 map in FSL). Now, Can I use this map as an input of sh2peaks function to creak peak file?

Thank you Behnam

[barakovic]

Hello Behnam, the V1 map in FSL is in the format required by COMMIT, so no need to convert. However, if you use peaks from DTI you will find problems in the crossing. If you use spherical harmonics functions you can convert the spherical harmonics coefficients to the peaks with sh2peaks from MrTrix.

Best, Muhamed

[behnam12]

Hello Muhamed ,

Thank you for your explanation. I am new in COMMIT and need to understand it very well. If I understood correctly, I can directly use V1 map in FSL instead of peaks.nii.gz file in COMMIT tutorial or I should extract the peaks from V1 map and then use the peaks file in COMMIT framework.

Best, Behnam

[barakovic]

Hello Behnam, you can directly use the V1 map (principal diffusion direction). Hence, replace the peaks.nii.gz with your V1 map output.

Cheers, Muhamed