autotrack- what does CNII refer to

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Linying Guo

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Nov 28, 2023, 8:48:08 AM11/28/23
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Hi Frank,

Thanks for developing and maintaining DSIStudio. I ran AutoTrack on some of my DSI data, I selected CNII and noticed that what I obtain seems to contain both the optic nerve and the optic tract but I am not sure. Can you tell me Which tract CNII refer to? only the optic nerve or both the optic nerve and the optic tract? 

Best,
Lin

Frank Yeh

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Nov 28, 2023, 8:56:13 AM11/28/23
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CNII should be optic nerve only.

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Linying

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Nov 28, 2023, 9:36:54 PM11/28/23
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Thank you very much for your reply! But I still have some confusions. In  Masanori Yoshino 's work,   the optic nerve is located before the optic chiasm while the optic tract is behind the optic chiasm as shown in the first figure below. But the tract I obtained using autotrack CNII seems to obtain the whole optic tract and part of the optic nerve, as shown in the second firgure below. Is there something wrong with my data or processing ?
Visualization of Cranial Nerves Using High-Definition Fiber Tractography.png
Yoshino M, Abhinav K, Yeh FC, Panesar S, Fernandes D, Pathak S, Gardner PA, Fernandez-Miranda JC. Visualization of Cranial Nerves Using High-Definition Fiber Tractography. Neurosurgery. 2016 Jul;79(1):146-65. doi: 10.1227/NEU.0000000000001241. PMID: 27070917.

CNII.png

Frank Yeh

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Nov 28, 2023, 9:39:10 PM11/28/23
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Yes, CNII includes the optic tract and optic nerve here.

Linying

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Nov 29, 2023, 9:29:20 AM11/29/23
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Thank you for your kindly reply! I hope to get a tract containing the full and the only optic tracts, and a tract containing the full and the only optic nerve, can I use AutoTrack CNII to achieve them?

Sorry that I can receive your message several hours later after you reply.

Best wishes!

Frank Yeh

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Nov 29, 2023, 9:35:07 AM11/29/23
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Unlikely, because they are the same continuous pathway. 

Linying

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Nov 29, 2023, 10:26:19 PM11/29/23
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Thank you for your reply!
 
Best regards,
Linying

Linying

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Nov 30, 2023, 8:59:42 PM11/30/23
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Dear Frank,
Thanks for your last reply reminding me that the optic tract and the optic nerve can not be separated by autotracking. I am now trying to track the optic tract by ROI. Since the starting point of the optic tract is the optic chiasm and the ending point the lateral geniculate body, I hope to use them as "ROI". Now I have three questions hoping to get your help:
1. Is it doable to select the "optic chiasm" and "lateral geniculate body" from the atlas for my tracking by ROI?
2. If it is, should I select the type as "ROI" for both the optic chiasm and the lateral geniculate body, as the figure below shows?
3. I remember in one of your previous version of DSI studio, there is "left lateral geniculate body"  and "right lateral geniculate body" in one of the atlas template, but I can not find it now, would you please send me the template?
Great thanks


Best regards,
Linying

Linying

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Nov 30, 2023, 9:02:55 PM11/30/23
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Sorry not providing the figure, It is as follows:
微信截图_20231201100133.png

在2023年11月30日星期四 UTC+8 11:26:19<Linying> 写道:

Frank Yeh

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Nov 30, 2023, 9:03:19 PM11/30/23
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On Thu, Nov 30, 2023 at 8:59 PM Linying <guolin...@gmail.com> wrote:
Dear Frank,
Thanks for your last reply reminding me that the optic tract and the optic nerve can not be separated by autotracking. I am now trying to track the optic tract by ROI. Since the starting point of the optic tract is the optic chiasm and the ending point the lateral geniculate body, I hope to use them as "ROI". Now I have three questions hoping to get your help:
1. Is it doable to select the "optic chiasm" and "lateral geniculate body" from the atlas for my tracking by ROI?

There is no atlas for optic chiasm.
 
2. If it is, should I select the type as "ROI" for both the optic chiasm and the lateral geniculate body, as the figure below shows?

Yes
 
3. I remember in one of your previous version of DSI studio, there is "left lateral geniculate body"  and "right lateral geniculate body" in one of the atlas template, but I can not find it now, would you please send me the template?
Great thanks

 
Search for LGN and you may find it.

Best regards,
Frank
 

Linying

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Dec 2, 2023, 4:13:38 PM12/2/23
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Dear Frank,
I appreciate your kindly reply very much!
Following your advice, I search for "LGN" instead of "lateral geniculate body" and am pleased to get it finally.  
I also try "optic chaism" and find optic chaism from two template as the figure below shows. Can these optic chaism template be used for my optic tract tracking by ROI?
Thank you for your time!

Best regards,
Linying  chiasm.png 

Frank Yeh

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Dec 2, 2023, 4:18:21 PM12/2/23
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I also try "optic chaism" and find optic chaism from two template as the figure below shows. Can these optic chaism template be used for my optic tract tracking by ROI?

It should work.
Sorry I did not know it is included.
Frank
 

Linying

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Dec 4, 2023, 1:41:48 AM12/4/23
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Thank you for your help, I really appreciate it!

Best regards,
Linying
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