Hello !

First thanks for this very nice plotting tool ! I just have an error popping out when trying to use ggseg.plot_dk() with ggseg version 0.1, on Ubuntu 22.04.1 LTS, matplotlib version 3.5.2 and numpy 1.22.3.

I am initializing a dictionary with all DK labels, assigning mostly zeros and a few ones here and there. And then calling the ggseg.plot_dk() function, I get an error saying:

File ~/Software/anaconda3/envs/code_testing/lib/python3.9/site-packages/ggseg/__init__.py:168, in plot_dk(data, cmap, background, edgecolor, ylabel, figsize, bordercolor, vminmax, title, fontsize)
    166 NA = set(dkt_regions).difference(data_regions).difference(whole_reg)
    167 files = [open(op.join(wd, e)).read() for e in NA]
--> 168 _render_regions_(files, ax, 'gray', edgecolor)
    170 # A colorbar is added
    171 _add_colorbar_(ax, cmap, norm, edgecolor, fontsize*0.75, ylabel)

File ~/Software/anaconda3/envs/code_testing/lib/python3.9/site-packages/ggseg/__init__.py:92, in _render_regions_(files, ax, facecolor, edgecolor)
     89 from matplotlib.path import Path
     90 import matplotlib.patches as patches
---> 92 codes, verts = _svg_parse_(' '.join(files))
     93 path = Path(verts, codes)
     95 ax.add_patch(patches.PathPatch(path, facecolor=facecolor,
     96                                edgecolor=edgecolor, lw=1))

File ~/Software/anaconda3/envs/code_testing/lib/python3.9/site-packages/ggseg/__init__.py:32, in _svg_parse_(path)
     30         codes.append(commands[cmd.upper()])
     31     vertices.append(points)
---> 32 return np.array(codes), np.concatenate(vertices)

File <__array_function__ internals>:180, in concatenate(*args, **kwargs)

ValueError: need at least one array to concatenate

If I remove one entry of the dictionary (eg superiorparietal_left), then the code runs, but the displayed figure lacks some unrelated regions, as the rostralanteriorcingulate, cuneus, or inferior parietal for example. I tried removing different regions from the dictionary but the plot is always lacking the same regions... I also tried assigning a random value to all entries instead of zeros and ones, but the error pops out again. Is anybody having the same issue ? Would you know how to fix it ?

import ggseg
ggseg_dict={'NA_left': 0.0,
'NA_right': 0.0,
'bankssts_left': 0.0,
'bankssts_right': 0.0,
'caudalanteriorcingulate_left': 1.0,
'caudalanteriorcingulate_right': 1.0,
'caudalmiddlefrontal_left': 0.0,
'caudalmiddlefrontal_right': 0.0,
'corpuscallosum_left': 0.0,
'corpuscallosum_right': 0.0,
'cuneus_left': 0.0,
'cuneus_right': 0.0,
'entorhinal_left': 0.0,
'entorhinal_right': 0.0,
'fusiform_left': 0.0,
'fusiform_right': 0.0,
'inferiorparietal_left': 0.0,
'inferiorparietal_right': 0.0,
'inferiortemporal_left': 0.0,
'inferiortemporal_right': 0.0,
'insula_left': 0.0,
'insula_right': 0.0,
'isthmuscingulate_left': 0.0,
'isthmuscingulate_right': 0.0,
'lateral_left': 0.0,
'lateral_right': 0.0,
'lateraloccipital_left': 0.0,
'lateraloccipital_right': 0.0,
'lateralorbitofrontal_left': 0.0,
'lateralorbitofrontal_right': 0.0,
'lingual_left': 0.0,
'lingual_right': 0.0,
'medial_left': 0.0,
'medial_right': 0.0,
'medialorbitofrontal_left': 0.0,
'medialorbitofrontal_right': 0.0,
'middletemporal_left': 0.0,
'middletemporal_right': 0.0,
'paracentral_left': 0.0,
'paracentral_right': 0.0,
'parahippocampal_left': 1.0,
'parahippocampal_right': 1.0,
'parsopercularis_left': 0.0,
'parsopercularis_right': 0.0,
'parsorbitalis_left': 0.0,
'parsorbitalis_right': 0.0,
'parstriangularis_left': 0.0,
'parstriangularis_right': 0.0,
'pericalcarine_left': 0.0,
'pericalcarine_right': 0.0,
'postcentral_left': 0.0,
'postcentral_right': 0.0,
'posteriorcingulate_left': 0.0,
'posteriorcingulate_right': 0.0,
'precentral_left': 0.0,
'precentral_right': 0.0,
'precuneus_left': 0.0,
'precuneus_right': 0.0,
'rostralanteriorcingulate_left': 0.0,
'rostralanteriorcingulate_right': 0.0,
'rostralmiddlefrontal_left': 0.0,
'rostralmiddlefrontal_right': 0.0,
'superiorfrontal_left': 1.0,
'superiorfrontal_right': 1.0,
'superiorparietal_left': 0.0,
'superiorparietal_right': 0.0,
'superiortemporal_left': 0.0,
'superiortemporal_right': 0.0,
'supramarginal_left': 0.0,
'supramarginal_right': 0.0,
'transversetemporal_left': 0.0,
'transversetemporal_right':0.0}
ggseg.plot_dk(ggseg_dict,cmap='Spectral', figsize=(15,15),
              background='k', edgecolor='w', bordercolor='gray',
              ylabel='Cortical thickness (mm)', title='Title of the figure')

Hello authors, I want to use python-ggseg to draw the result graph of my paper, but the atlas I use is not one of the three atlases you provided, could you kindly tell me how to make other atlases documents, such as DK-308, HCP-360. Thank you so much!

Hi! I already saw one closed issue about adding new atlases, but I just wanted to ask, if you could elaborate on how you generated these svg files for all DK ROIs? For example, Do you still have the script for creating this and could share this?

Hi again !

I think I found a bug in the labeling of 'superiorparietal_left' and 'superiorfrontal_left' ROIs in Desikan-Killiany atlas.

I have a dictionary {'superiorparietal_left': 1}, and running ggseg.plot_dk() also labels the medial superiorfrontal_left cortex:

Similarly, when setting 'superiorfrontal_left' to 1.0, only the lateral part gets labelled (the largest medial part is not labelled):

Labelling of right ROIs works fine.

Here is the code I am running in case you want to have a look:

import ggseg
ggseg.plot_dk({'superiorparietal_left': 1.0},cmap='Spectral', figsize=(15,15),
              background='k', edgecolor='w', bordercolor='gray',
              ylabel='Cortical thickness (mm)', title='Title of the figure')
ggseg.plot_dk({'superiorfrontal_left': 1.0},cmap='Spectral', figsize=(15,15),
              background='k', edgecolor='w', bordercolor='gray',
              ylabel='Cortical thickness (mm)', title='Title of the figure')

Thank you so much for that great module!
I wondered if it is possible to set colorbar limits as well? As I would like to make several plots with the same colorbar range.

Thank you very much in advance!

Good evening,

Thanks again for the great plotting tool ! I think I also found some bugs in ggseg.plot_aseg().

Shouldn't the brain stem, cerebellum white matter and cerebellum gray matter appear in light gray when not specified in the dictionary ? In the example plot for instance, the 3 structures appear in some very dark gray. Might be related to the fact that they are also labeled with this same dark color when specifying a value for them in the dictionary ? Here is the plot I get when I set them to 1, 2, and 3 respectively:

Otherwise, labelling the Left-Caudate creates a figure with the Right-Caudate:

and labelling the Right-Caudate creates a figure with the Left-Caudate:

It's a small detail, but you probably want the input regions to map to the correct structures in the plot ;)

Cheers !
David

PS: here's some code in case you want to replicate the plots:

import ggseg
ggseg.plot_aseg({'Brain-Stem': 1, 'Cerebellum-Cortex': 2, 'Cerebellum-White-Matter': 3.0}, cmap='Spectral', background='k', edgecolor='w', bordercolor='gray', ylabel='Volume (mm3)', title='Title of the figure')
ggseg.plot_aseg({'Left-Caudate': 1.0}, cmap='Spectral', background='k', edgecolor='w', bordercolor='gray', ylabel='Volume (mm3)', title='Title of the figure')
ggseg.plot_aseg({'Right-Caudate': 1.0}, cmap='Spectral', background='k', edgecolor='w', bordercolor='gray', ylabel='Volume (mm3)', title='Title of the figure')

Thanks a lot for ggseg, it's really easy to use and the output figures look really good!
Just wanted to mention that temporal pole and frontal pole are missing from ggseg/data/dk. https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation

Thanks!