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problem about mcx and different atlas


YiShu Li
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im having two problems using atlasviewer these days about different atlas and mcx. i looked up the forum and internet but didnt find the solution, so i start this topic to seek for some help.

 

1. im asked to use ICBM 152 atlas (2009a nonlinear symmetric) to fit the result of NIRSite, i downloaded the atlas in NIFTI form from their website http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009 , and got these files

d6f1524efb033272b9eb0fbcabd2ca3

i used 'import mri anatomy' and selected 't1' for head, 'csf' for cerebral spinal, 't1_mask' for brain and 'wm' for white matter. after that i got the anatomy of the icbm atlas like the picture below:

image

then the refs were selected and the mc input was successfully generated. however, when i finally clicked the generate sensitivity profile, nothing was plot on the image like this:

B$~[P0R~23H%ZF7 3@N@ G2

im wondering whether the problem is caused by the anatomy files because last time i used a mri anatomy from a specific subject and the process worked just fine. i suppose the problem may be the brain file but idk how to fix it. do anyone have such experience in changing atlas?

 

 

2. The second question is about mcx. i downloaded atlasviewer 2.16 and found that there is a run mcxlab button but the button is disabled and i cannot find how to use mcx in atlasviewer on the internet... how can i used the mcx instead of tmcimg in atlasviewer?

 

 

im not an english speaker so i apologize if my language seems strange or rude. thx alot for viewing or even replying my post!

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David Boas
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I can answer the MCX question. I leave the first question to others.

You need to install MCXlab on your computer. Go here to register and download it and install it.

Then in matlab, you change to the AtlasViewer directory and run

setpaths

. Then you change to the mcxlab directory and add that path with (I believe)

path(path,cd)

Then you go to your directory where you want to run AtlasViewer and run it. When AtlasViewer launches, it finds mcxlab in the path and enables that menu item.

 

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YiShu Li
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@dboas Thanks so much for you replying and it's really helpful!

 

I found that there's big difference between the tMCimg result and the MCXlab result. May i ask why there's such difference and which one is more reliable?

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David Boas
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show us a plot exhibiting the difference. I suspect any difference you observe is likely from different placement of the optodes, optical properties, or scaling of the fluence profiles. Long ago, tMCimg and MCXlan agreed with each other, and I suspect they still do when everything is set up the same.

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YiShu Li
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David Boas
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what is 10-6, 10-7, 10-8?

I guess you are showing the accumulated sensitivity to the brain in these plots. If yes, then did you set the scale to be the same for the two plots? What is that scale? Did you confirm you used the same optical properties for both monte carlo runs?

I suspect I know all the answers to the above: yes it is brain sensitivity, you use a scale of [-2 0]. You did use the same optical properties. This would mean that the scaling for MCXlab and tMCimg is different. Another possibility is of slight optode position differences, but I suspect more a scaling issue. This will impact the magnitude of the image, but not the statistics or spatial location.

This deserves a deeper dive into how the MCXlab scaling is done versus that in tMCimg. I do recall looking at this 2 years ago when I added MCXlab to AtlasViewer and it checked out. But I also kind of recall that MCXlab might have changed after that and I continue to use an older version. I hope someone can find time to dig deeper into this.

 

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David Boas
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How did you calculate the tMCimg? Did you use the precalculated profiles? If you didn't download the premium Homer profiles, then the precalculated is only calculated every 5 or 10 mm and not at the exact optode locations. The premium Homer profiles are calculated every millimeter. That could give rise to this difference.

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