Error in xy.coords(x, y, xlabel, ylabel, log)

[zqsha]

Hi, experts of ggesgAal. Thanks for developing such an amazing toolbox. After successfully installing the toolbox, I run the example command line: plot(aal), and then it reported the following error:

Error in xy.coords(x, y, xlabel, ylabel, log) :
'x' is a list, but does not have components 'x' and 'y'

Any thoughts on fixing it?

Thanks,
Cain

[zqsha]

Hi again. I also found other issues on the ggsegAal_3d.

1. I try to run the example using
   ggseg3d(atlas = aal_3d) %>%
   remove_axes() %>%
   pan_camera("left medial")
   No matter what terms that I use (i.e. "left medial", "right medial", "left lateral", "right lateral"), it only shows the right hemisphere, it never shows the left hemisphere. I do not know why.

2. When I check the number of cortical regions in this AAL atlas, I found 41 available cortical regions per hemisphere. But, as we know, AAL90 has 45 regions per hemisphere, including 39 cortical regions and 6 subcortical regions. I also did not find the names of regions by running
   aal_3d %>%
   filter(surf == "inflated" & hemi == "right") %>%
   unnest(cols = ggseg_3d)

Thanks.

[zqsha]

I aligned the atlas in the current toolbox with the classical AAL90 atlas, and then get the corresponding names to each of the regions on the atlas.
lh_LH_region_1 Precentral
lh_LH_region_2 Frontal_Sup
lh_LH_region_3 Frontal_Mid
lh_LH_region_4 Frontal_Inf_Oper
lh_LH_region_5 Frontal_Inf_Tri
lh_LH_region_6 Frontal_Inf_Orb
lh_LH_region_7 Rolandic_Oper
lh_LH_region_8 Supp_Motor_Area
lh_LH_region_9 Olfactory
lh_LH_region_10 Frontal_Sup_Medial
lh_LH_region_11 Frontal_Med_Orb
lh_LH_region_12 Rectus
lh_LH_region_13 Frontal_Sup_Orb
lh_LH_region_14 ???
lh_LH_region_15 Frontal_Mid_Orb
lh_LH_region_16 Insula
lh_LH_region_17 Cingulum_Ant
lh_LH_region_18 Cingulum_Mid
lh_LH_region_19 Cingulum_Post
lh_LH_region_20 ParaHippocampal
lh_LH_region_21 ???
lh_LH_region_22 Calcarine
lh_LH_region_23 Cuneus
lh_LH_region_24 Lingual
lh_LH_region_25 Occipital_Sup
lh_LH_region_26 Occipital_Mid
lh_LH_region_27 Occipital_Inf
lh_LH_region_28 Fusiform
lh_LH_region_29 Postcentral
lh_LH_region_30 Parietal_Sup
lh_LH_region_31 Parietal_Inf
lh_LH_region_32 SupraMarginal
lh_LH_region_33 Angular
lh_LH_region_34 Precuneus
lh_LH_region_35 Paracentralobule
lh_LH_region_36 Heschl
lh_LH_region_37 Temporal_Sup
lh_LH_region_38 Temporal_Pole_Sup
lh_LH_region_39 Temporal_Mid
lh_LH_region_40 Temporal_Pole_Mid
lh_LH_region_41 Temporal_Inf

But, I am not sure what do the "lh_LH_region_14" and "lh_LH_region_21" refer to?

Thanks

[drmowinckels]

Thank you for this labelling! I'll get to adding that information to the atlas when I get the time.

@faskowit Could you help us out with the region names for your labels 14 and 21? This atlas was based on your annot file in https://github.com/faskowit/multiAtlasTT

Thanks for any help!

[drmowinckels]

I've made a plot here to highlight each individual parcel in the left hemisphere. I have no experience with this parcellation personally.

library(ggsegAal)
library(ggplot2)
library(ggseg)
#> Warning: package 'ggseg' was built under R version 4.1.1
library(dplyr)
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union

plot(aal)

tmp_data <- tibble(
  region = brain_regions(aal)
)

tmp_data %>% 
  mutate(regionf = region,
         regeionc = region) %>% 
  group_by(regeionc) %>% 
  ggplot() + 
  geom_brain(atlas = aal, hemi = "left",
             aes(fill = regionf), show.legend = FALSE) +
  facet_wrap(~regeionc) +
  theme_brain2()
#> merging atlas and data by 'region'

^{Created on 2021-11-15 by the reprex package (v2.0.0)}

[drmowinckels]

Here are images of just 14 and 21

[zqsha]

Great, thanks, Athanasiamo. Any thoughts on fixing the error that I report about plot(aal)?
Error in xy.coords(x, y, xlabel, ylabel, log) :
'x' is a list, but does not have components 'x' and 'y'

I am still stuck here.

Thanks.

[zqsha]

Also, this is the 3D view of related regions. The numbers on the brain are the labels in the atlas. (Sorry I just can show the right hemisphere, as this 3D atlas (ggestAal_3d) still can not show the left hemisphere.). Thanks again.

[lucasfr]

Thank you for this labelling! I'll get to adding that information to the atlas when I get the time.

@faskowit Could you help us out with the region names for your labels 14 and 21? This atlas was based on your annot file in https://github.com/faskowit/multiAtlasTT

Thanks for any help!

Hi @Athanasiamo and @zqsha

I believe that is AAL2. The one most often used is AAL. Here's the original source: https://www.sciencedirect.com/science/article/pii/S1053811901909784

The original files can be found here:https://www.gin.cnrs.fr/en/tools/aal/

I tried to convert the atlas myself but wasn't very lucky, I'm afraid.

[drmowinckels]

@zqsha hI cannot reproduce the error you are showing, so I dont know whats going on for you. Are you still seeing that error?

library(ggsegAal)
#> Loading required package: ggseg
#> Loading required package: ggplot2
#> Loading required package: ggseg3d

plot(aal)

^{Created on 2022-03-18 by the reprex package (v2.0.1)}

@lucasfr ok, so you think this is actually the AAL2 atlas, not AAL? That should explain the atlas parcellation differences.
I also struggle getting these nifti atlases into a format I can work with for this tool but its on my list!