Step 2 : Reconstruction

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Ricardo Morais

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Jan 12, 2023, 8:35:21 AM1/12/23
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Hi Frank,
So I'm tryin to pre-process my .src files. 
I've tried going to corrections and choose TOPUP/EDDY ( i don't have reverse phase encoding) , so it skips that part, but then the correction process seems to be running forever...I've reduced the number os subjects, since I know that it takes time,  but even for 1 subjects the computer is running now for  4 straight days and still haven't finished .

I've also tried going through : Step T2b (2) : specify parameters: check the preprocessing (just in case), and the same thing happens...the process runs forever. 

I did try to use DSI cloud but I just can't get to make it work, can't get the data in Brain Imaging Data Structure (BIDS)  structure, is there is any youtube tutorial about it?.


Anyway, any help would be greatly appreciated.

Thanks

Fang-Cheng Yeh

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Jan 12, 2023, 9:13:29 AM1/12/23
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EDDY preprocessing is very time-consuming, and the only solution I know is to use the GPU version on a desktop with a good NVIDIA GPU card.
Best regards,
Frank



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Ricardo Morais

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Jan 12, 2023, 9:21:56 AM1/12/23
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Is there any difference between checking pre processing in step 2b or going through Correction  and then doing eddy and after motion correction? It's the same ?

I've updated the dsi version , when i go though Correction: and di Eddy and after i do  Motion correction, the process goes quite well.
But if i check in step2b : the pre processing, then it never ends.  

Thanks



Fang-Cheng Yeh

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Jan 12, 2023, 9:27:24 AM1/12/23
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Is there any difference between checking pre processing in step 2b or going through Correction  and then doing eddy and after motion correction? It's the same ?


They should be very similar.

 
I've updated the dsi version , when i go though Correction: and di Eddy and after i do  Motion correction, the process goes quite well.

If you have done eddy, then there is no need for additional motion correction.
 

Best,
Frank
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