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ggseg / ggsegChen

https://lcbc-uio.github.io/ggsegChen/
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right hemisphere medial view of superior parietal for CT is labeled wrong? #1

Open mvlombardo opened 4 years ago

mvlombardo commented 4 years ago

Hi,

I was having a look at this Chen atlas, and I noticed that for cortical thickness, the medial view of the right hemisphere shows superior parietal cortex in the same color as dorsolateral prefrontal. I'm not sure how to fix that, so I thought I'd bring it up here in case a quick fix could be made.

Thanks,

Mike

drmowinckels commented 4 years ago

Thanks for pointing this out. We'll get to fixing as soon as we can!

mvlombardo commented 4 years ago

Hi @Athanasiamo,

I revisited this issue today as I was needing to make a plot for a paper I'm writing. As I started looking more into this bug, and I think I see where the issue is.

After loading ggsegChen, I can view the data(chenTh) tibble, and I see that while in the left hemisphere there are rows for superior parietal on the medial and lateral sides, for the right hemisphere, there is only a row for lateral superior parietal, but no row for medial superior parietal.

If I download geobrain_Chencth.Rda from the data-raw directory, I can see that in the id column there are only 3 unique values - 7, 1005, and 2005. I assume there should be 4 though as the medial and lateral views of both hemispheres need to show this region.

If I were to look at the motor-premotor-sma region, I see there are 4 unique id values there, because both LH and RH need to show that region in the medial and lateral views.

So from what I understand, I think the geobrain_Chencth.Rda is missing some data needed for the RH medial superior parietal view. Any idea how I can fill that in? I don't understand what all the other columns are in geobrain_Chencth.Rda like lat, long, order, etc, to somehow fill this in myself.

# load geoBrain_Chencth.Rda
load("/Users/mlombardo/Downloads/ggsegChen/data-raw/geoBrain_Chencth.Rda")

# grab rows for superior parietal region and then find unique id values
sup_par_rows = subset(geobrain_Chencth, geobrain_Chencth$aparc=="superior parietal")
unique(sup_par_rows$id)
[1]    7 1005 2005

# grab rows for motor-premotor-sma region and then find unique id values
mot_premot_sma_rows = subset(geobrain_Chencth, geobrain_Chencth$aparc=="motor-premotor-supplementary motor area")
unique(mot_premot_sma_rows$id)
[1]    4 1004 2002 3005

Thanks,

Mike