On 10/30/2023 9:50 PM, Mirsol Choi wrote:
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Hi there,
I am currently going through the dt_recon tutorial on your website and I just have a quick question regarding the recon-all and dt_recon commands on freesurfer.
For me to process dt_recon, my understanding is that I must process recon-all first.
But where my confusion lies is:
- do I perform recon-all on the actual dwi.nii.gz image, then dt_recon
with the same dti files (including the bval and bvec of the same dwi.nii.gz file) OR
- should I have two separate sets of data, one T1 and one DTI, and
perform recon-all on T1 images and take DWI images from the same subject to perform dt_recon?
The 2nd option. You must run recon-all on the T1, then pass the subject name to dt_recon along with the DWI
My understanding was that the second bullet is the right way to go since the dt_recon uses the outputs from T1 recon-all to register properly.
Please let me know which one is correct, and if I am missing something.
Thank you so much for your help, I really appreciate your time. M
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