Provided template files not loading

[mkkubins]

Provided template files are not load. ImageFileError: Cannot work out file type of ".cache\templateflow\tpl-MNI152NLin2009cAsym\tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii.gz"

Code that I am using: netplotbrain.plot(template='MNI152NLin2009cAsym', templatestyle='surface', nodes=new_nodes, edges=edges, templatealpha=1, nodecolor='blue', templatecolor='gray', view='L') plt.show()

I have tried also to download the file and load this as a template but then the surface is not showing.

[wiheto]

Hi, really sorry for taking 11 days to respond here. I missed the email.

It looks like a bug that can turn up with templateflow (e.g. https://neurostars.org/t/templateflow-error-loading-map/21365)

The advice there is try deleting that file and rerunning. Let me know if it works.

If that does not work, try updating your python api of templateflow.

[mkkubins]

Hi! Thanks so much for the answer. None of the above suggestions worked but I download this manually from TemplateFlow and this is working. However, I have to replace this file each time when I am running code.

[wiheto]

If you download the file manually to a non-templateflow directory. The input to netplotbrain just needs to be:

netplotbrain.plot(tempalte='path/to/local/file.nii.gz')

Which means you do not need to keep downloading manually.

But why templateflow is not working for you is strange and could be some bug there.

[mkkubins]

I tried this one that you suggest. This is my code: netplotbrain.plot(template = './template3D/tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii', templatestyle = 'surface', view = 'S', nodes = nodes, nodecolor ='grey', nodesize = 5, edges = threshold_edges, highlightlevel = 0.1, fig = fig, edgecolor = edge_color, edgewidthscale = 2, showlegend = False, ax = ax, kwargs = {'edgealpha':1}) plt.show()

and this returns the error as below. I have tried to pass this also as a list but then it also returns the error UnboundLocalError: local variable 'img' referenced before assignment.

c:\Users\kubin\Desktop\opto\BCGLAR\Connectivity\plot_brain.py in <module>
      [83](file:///c%3A/Users/kubin/Desktop/opto/BCGLAR/Connectivity/plot_brain.py?line=82) # ax2 = fig.add_subplot(133, projection='3d')
      [84](file:///c%3A/Users/kubin/Desktop/opto/BCGLAR/Connectivity/plot_brain.py?line=83) 
----> [85](file:///c%3A/Users/kubin/Desktop/opto/BCGLAR/Connectivity/plot_brain.py?line=84) netplotbrain.plot(template = './template3D/tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii',
      [86](file:///c%3A/Users/kubin/Desktop/opto/BCGLAR/Connectivity/plot_brain.py?line=85)                   templatestyle = 'surface',
      [87](file:///c%3A/Users/kubin/Desktop/opto/BCGLAR/Connectivity/plot_brain.py?line=86)                   view = 'S',

c:\Users/kubin/Desktop/opto/netplotbrain\netplotbrain\plot.py in plot(nodes, fig, ax, view, frames, edges, template, templatestyle, arrowaxis, arroworigin, edgecolor, nodesize, nodecolor, nodetype, nodecolorby, nodecmap, edgeweights, nodeimg, hemisphere, title, highlightnodes, highlightedges, showlegend, **kwargs)
    197             affine = None
    198             if template is not None:
--> 199                 affine = _plot_template(ax, templatestyle, template,
    200                                         voxsize=profile['templatevoxsize'],
    201                                         azim=azim[fi], elev=elev[fi],

c:\Users/kubin/Desktop/opto/netplotbrain\netplotbrain\plotting\plot_templates.py in _plot_template(ax, style, template, voxsize, azim, elev, hemisphere, **kwargs)
    158             # This may lead to suboptimal performence for some templates
    159             if isinstance(template, list):
--> 160                 template = template[0]
    161         img = nib.load(template)
    162     elif isinstance(template, (nib.Nifti1Image, nib.Nifti2Image)):

IndexError: list index out of range

[wiheto]

Thanks for this. Sorry that you are still getting an error.

I’ll check this out and see if I can replicate the error.

[wiheto]

Should be fixed now if you update from github.

There was a little bug there. Sorry, most testing is done with templateflow as the background.

i.e. netplotbrain.plot(template = './template3D/tpl-MNI152NLin2009cAsym_res-01_desc-brain_T1w.nii', templatestyle = 'surface', view = 'S', nodes = nodes, nodecolor ='grey', nodesize = 5, edges = threshold_edges, highlightlevel = 0.1, fig = fig, edgecolor = edge_color, edgewidthscale = 2, showlegend = False, ax = ax, kwargs = {'edgealpha':1}) plt.show() should work.

Let me know if it does/does not

[mkkubins]

Thanks so much!