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Center-For-Neurotechnology / Reconstruction-coreg-pipeline

Cash lab code for coregistration of intracranial electrodes
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The RAS coordinates in protocols.io can't work (sEEG electrodes) #1

Open CenXiang opened 1 month ago

CenXiang commented 1 month ago

I chose the RAS coordinates for each contact after aligning the post-op CT with the pre-op T1 in freeview. According to the steps in protocols.io, when load T1 volume, the “Resample to standard RAS space” checkbox was selected, and then only "Heat" color map was selected when loading CT volume (Doesn't this step need to be resampled to RAS standard space like loading T1?). I wrote down RAS coordinates and TkReg(T1) RAS coordinates at the same time, and then I run 'Coregistration_Figures_PreOp_Post_Op/ Protocol_recon_COde.m'. I can obtain a map of the electrode implantation results in the brain when using id_RAS. xlsx, but using id_TkReg.xlsx resulting the bad results, where all contacts or electrodes were located outside the brain. This is inconsistent with what I saw in FreeView that the contacts are located inside the brain. So I am asking for help that if I misled your steps in protocols.io, thanks for help!

djsoper commented 1 month ago

Hello!

To answer your first question, no, the CT does not need to be re-sampled, since you are collecting coordinates in the MRI space.

To answer your second set of questions regarding RAS vs TkReg Ras is more difficult. I believe that you read the RAS coordinates in FreeView with the CT highlighted in the top left. This explains why you got good values for RAS and not TkReg. An example of this is in the Protocol (Step 4.2), which shows where to select. Otherwise, I believe you did everything correctly. Please let me know if you have any other questions, and I will try to answer it as quickly as possible. Thank you!

CenXiang commented 1 month ago

Thank you for your help! I check my coordinates carefully and found that the exchanged R and A in the RAS space. And another question is that the step 8 and step 9 in your protocols.io are too brief and not nearly as clear as the previous steps(https://www.protocols.io/run/modular-reconstruction-and-co-registration-of-imag-cpx8vprw?step=9.3), including the splitting of .mgz files in 3D slicer, running and modifying BIDS code, which is very difficult and time-consuming for a beginner like me to accept. Anyway, thank you for your help!

APaulk commented 1 month ago

Hello, Thank you very much for the feedback. You bring up a great point for that section of the protocol. It was the newest section of the protocol and were unsure if it would be useful to other users. We have also since modified that portion to be more efficient and straightforward. We are happy to share those changes and updates if you think you would like that information? Please let us know. Thank you, Angelique

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Thank you for your help! I check my coordinates carefully and found that the exchanged R and A in the RAS space. And another question is that the step 8 and step 9 in your protocols.io are too brief and not nearly as clear as the previous steps(https://www.protocols.io/run/modular-reconstruction-and-co-registration-of-imag-cpx8vprw?step=9.3), including the splitting of .mgz files in 3D slicer, running and modifying BIDS code, which is very difficult and time-consuming for a beginner like me to accept. Anyway, thank you for your help!

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