Seeking Guidance on Cortical and Subcortical Visualization

[2307532042]

Hello, congratulations on your successful completion of a very important paper!

Currently, I am attempting to create visualizations of ​single ROI values (not functional connectivity) within ​cortical (Schaefer-400) and subcortical atlases(Tian-32) (MNI_152 space) for my research. I noticed that the visualization methodology in your study closely aligns with my objectives. I carefully reviewed your code, and the three functions surf_schaef2(lda_vec1(1:400), limits), surf_cbm(lda_vec1(455:482), limits), and subcort_plot(lda_vec1); appear to be used for visualizing cortical, cerebellar, and subcortical activations, respectively. However, I could not locate the implementation code for these functions. I am unsure if this is an issue and would appreciate your guidance!

Any response would be extremely helpful to me!

Thank you！

[macshine]

Hi Songke Thanks for reaching out. Josh – can you please add these (+ any dependencies) to a separate github repo when you get a chance? Mac From: Songke Fang ***@***.***> Date: Wednesday, 26 March 2025 at 7:19 pm To: ShineLabUSYD/WM_Manipulation ***@***.***> Cc: Subscribed ***@***.***> Subject: [ShineLabUSYD/WM_Manipulation] Seeking Guidance on Cortical and Subcortical Visualization (Issue #1) Hello, congratulations on your successful completion of a very important paper! Currently, I am attempting to create visualizations of ​single ROI values (not functional connectivity) within ​cortical (Schaefer-400) and subcortical atlases(Tian-32) (MNI_152 space) for my research. I noticed that the visualization methodology in your study closely aligns with my objectives. I carefully reviewed your code, and the three functions surf_schaef2(lda_vec1(1:400), limits), surf_cbm(lda_vec1(455:482), limits), and subcort_plot(lda_vec1); appear to be used for visualizing cortical, cerebellar, and subcortical activations, respectively. However, I could not locate the implementation code for these functions. I am unsure if this is an issue and would appreciate your guidance! Any response would be extremely helpful to me! Thank you！ — Reply to this email directly, view it on GitHub<#1>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACJHXWZLO346GACCYMMP5AT2WJPGZAVCNFSM6AAAAABZZTU5VSVHI2DSMVQWIX3LMV43ASLTON2WKOZSHE2DQNZUGU3TIMY>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> [Image removed by sender. 2307532042]2307532042 created an issue (ShineLabUSYD/WM_Manipulation#1)<#1> Hello, congratulations on your successful completion of a very important paper! Currently, I am attempting to create visualizations of ​single ROI values (not functional connectivity) within ​cortical (Schaefer-400) and subcortical atlases(Tian-32) (MNI_152 space) for my research. I noticed that the visualization methodology in your study closely aligns with my objectives. I carefully reviewed your code, and the three functions surf_schaef2(lda_vec1(1:400), limits), surf_cbm(lda_vec1(455:482), limits), and subcort_plot(lda_vec1); appear to be used for visualizing cortical, cerebellar, and subcortical activations, respectively. However, I could not locate the implementation code for these functions. I am unsure if this is an issue and would appreciate your guidance! Any response would be extremely helpful to me! Thank you！ — Reply to this email directly, view it on GitHub<#1>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACJHXWZLO346GACCYMMP5AT2WJPGZAVCNFSM6AAAAABZZTU5VSVHI2DSMVQWIX3LMV43ASLTON2WKOZSHE2DQNZUGU3TIMY>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[JoshuaBTan]

Hi Songke,

Thanks a lot for the interest! I've added a folder "Visualisation" with the brain visualisation code. I've also included some instructions for setting up any dependencies required.

[2307532042]

Hi，Joshua. Thank you very much for your help. It is of great help to me!

[2307532042]

Hi，Joshua. I'm sorry to bother you again. The code you provided was very helpful, and I have successfully plotted the subcortical visualization. However, I have a concern: my subcortical data consists of values from 32 ROIs based on the MNI_152 space atlas, while ENIGMA seems to use the fsaverage5 space. Therefore, I'm unsure whether it is correct to directly input the sorted subcortical data (32 ROIs) into plot_subcortical. Do I need to convert subcortical regions to fsaverage5? Looking forward to your response！
Thank you！

[JoshuaBTan]

Hi Songke,

So for all the visualisations (cortical, subcortical, cerebellum), the data gets mapped from parcellations back into the freesurfer space. For the cerebral and cerebellar visualisations it is a bit easier in that we can use labels that map from the parcellations to freesurfer.

For the ENIGMA plots, it is a bit more coarse. As you saw, the ENIGMA toolbox has the "plot_subcortical.m" function for making the subcortical plots (using freesurfer space), however it only accepts 14 data points/labels (excluding ventricles) that then get mapped back onto fsaverage5 space. The exact structures that each data point corresponds to is mentioned in the script (plot_subcortical.m) but these are "large" structures in that there can be 1 data point for the whole left thalamus. In our case, we had 54 subcortical regions which we had to manually map (using atlas labels) into the 14 labels (e.g. averaging across multiple thalamus parcels to make 1 left thalamus value). For your case, I would expect similar in that you need to map your 32 ROIs to the 14 labels of the ENIGMA toolbox. You don't need to convert your data to fsaverage5 space as their labels are so coarse that you're more plotting whole structures vs individual parcels.

Hope that makes sense, I can try clarify anything confusing.

Thanks,
Josh

[2307532042]

Hi，Joshua.

Once again, thank you very much for your help! This has cleared up all my doubts!

Songke Fang