# how to use viz.plot\_alignment() on SEEG data?

**URL:** <https://mne.discourse.group/t/how-to-use-viz-plot-alignment-on-seeg-data/1407>\
**Category:** Mailing List Archive (read-only)\
**Tags:** list-archive\
**Created:** [January 26, 2018, 11:05pm UTC](https://mne.discourse.group/t/how-to-use-viz-plot-alignment-on-seeg-data/1407 "2018-01-26T23:05:47Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [January 26, 2018, 11:05pm UTC](https://mne.discourse.group/t/how-to-use-viz-plot-alignment-on-seeg-data/1407/1 "2018-01-26T23:05:47Z")

</div>

To clarify, I have been using the data from the ECOG demo ([https://martinos.org/mne/stable/auto\_examples/visualization/plot\_3d\_to\_2d.html#sphx-glr-auto-examples-visualization-plot-3d-to-2d-py](https://martinos.org/mne/stable/auto_examples/visualization/plot_3d_to_2d.html#sphx-glr-auto-examples-visualization-plot-3d-to-2d-py)) in my demo notebooks since other MNE users have easy access to that data.

To facilitate my attempts to use the Brainstorm demo, I have run the pre-implantation MRI from the Brainstorm demo ([http://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity](http://neuroimage.usc.edu/brainstorm/Tutorials/Epileptogenicity)) through freesurfer as that seemed the path of least resistance to using the data in MNE. I'm not using that scan in these demos because it is not mine to share and I don't think anyone else wants to run it through freesurfer just to try my demo.

I think my issue is that I have electrode coordinates in the MRI coordinate system as suggested by the observation that they make sense when plotted using pysurfer. However MNE seems to use a different default coordinate system ('head'?) and I haven't figured out how to convert or make MNE recognize that the coordinates are not in the default system. I have created yet another demo notebook using the MRI from the ECOG demo ('sample') with some electrode coordinates in the MRI coordinate system. As shown, they can be plotted with pysurfer but viz.plot\_alignment doesn't work.

[https://gist.github.com/lneisenman/38ca9cf2e4075776f8476cebb114d2a1](https://gist.github.com/lneisenman/38ca9cf2e4075776f8476cebb114d2a1)

How do I find/create the transform to convert the coordinates to the default system? The coordinates included in the ECOG demo clearly are not in the MRI coordinate system.

Larry

---

<div class="post-metadata">

**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [January 27, 2018, 5:12pm UTC](https://mne.discourse.group/t/how-to-use-viz-plot-alignment-on-seeg-data/1407/2 "2018-01-27T17:12:36Z")

</div>

hi Larry,

indeed sEEG were ignored in plot\_alignment.

This PR should fix it: [https://github.com/mne-tools/mne-python/pull/4903](https://github.com/mne-tools/mne-python/pull/4903)

let us know directly on github if it does the job for you.

thanks for reporting the issue.

Best,  
Alex

---

<div class="post-metadata">

**Author:** ![system](https://global.discourse-cdn.com/free1/uploads/mne/original/1X/85cc6bd2b69cb698a166dc6d880fb550510d0144.jpeg) [@system](https://mne.discourse.group/u/system)\
**Post date:** [January 28, 2018, 9:10pm UTC](https://mne.discourse.group/t/how-to-use-viz-plot-alignment-on-seeg-data/1407/3 "2018-01-28T21:10:37Z")

</div>

hi,

the PR is merged.

Here a tiny script I wrote that should get you started with these data:

[https://gist.github.com/agramfort/3690a41529ffa9534701e6a330460f07](https://gist.github.com/agramfort/3690a41529ffa9534701e6a330460f07)

Note that I use neo to read the TRC file. We should have this reader  
via neo in the next release.

HTH  
Alex