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fcx-3 data-how to get the MNI coordinates for each electrode

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fcx-3 data-how to get the MNI coordinates for each electrode

Posted by Jin Li at October 06. 2020

Dear expert, 

I have downloaded the fcx-3 dataset, and read the position of all electrodes from the s<<subject number>>_MNI_grid file. However, the position seems to be described in head coordinates. We are wondering where we can get the MNI coordinates of each electrode, or if there is any way to convert the provided head coordinates into the MNI coordinates.

Thank you so much!

Jin Li

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Re: fcx-3 data-how to get the MNI coordinates for each electrode

Posted by Elizabeth Johnson at October 08. 2020
 

The electrode localization procedure is described in the associated publication: https://doi.org/10.1371/journal.pbio.2004274. See also https://doi.org/10.1038/s41596-018-0009-6

Re: fcx-3 data-how to get the MNI coordinates for each electrode

Posted by Jin Li at October 10. 2020

Previously Elizabeth Johnson wrote:

 

The electrode localization procedure is described in the associated publication: https://doi.org/10.1371/journal.pbio.2004274. See also https://doi.org/10.1038/s41596-018-0009-6

 

Dear Elizabeth,

Many thanks for your prompt reply and the useful information. We have carefully read the two papers, and still have the following questions

Background: We need the MNI coordinates to look up the labels of each electrode in anatomical atlases.

1.     We checked the value following "#Position" of each electrode from the s<<subject number>>_MNI_grid.csv, but this position was not MNI coordinate. Because we tried taking these values as MNI coordinates, and found that the corresponding electrodes are all outside of the brains (shown in the attached picture).

2.     The elecpos seems to be generated by the BioImage Suite. As described (https://www.fieldtriptoolbox.org/getting_started/bioimage/), the original brain image is also needed to get the MNI coordinates. Therefore, it seems that we cannot generate the MNI coordinates from the released csv file without brain image file (e.g., NIfTI, .nii). In your Plos Biology paper (https://doi.org/10.1371/journal.pbio.2004274), you mentioned that "Electrodes were localized for each subject based on individual anatomy and then separately transformed into standard MNI space". Therefore, we are wondering where we can find these MNI coordinates from the released file, which seems generated after step 29 and/or step 32 by using fieldtrip (https://www.fieldtriptoolbox.org/tutorial/human_ecog/#anatomical-workflow). Or if these MNI coordinates for each electrodes could be kindly released.

All the best!

Jin

 

 

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Re: fcx-3 data-how to get the MNI coordinates for each electrode

Posted by Elizabeth Johnson at October 14. 2020
Dear Jin, 
 
Since the original publications, our group has done the work of getting the coordinates into MATLAB format using the pipeline described in Stolk et al., 2018. You can find these data attached here. Note that there are two repeats between datasets: (1) fcx-2 s5 = fcx-3 s5; (2) fcx-2 s8 = fcx-3 s7. Total n = 15. 
 
best, 
Dr. Johnson
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Re: fcx-3 data-how to get the MNI coordinates for each electrode

Posted by Jin Li at October 18. 2020

Dear Dr. Johnson,

Many thanks for kindly sharing these data. We found two subjects with null MNI coordinate data (fcx-2 s4, fcx-2 s9). The two subjects were not the repeats between datasets, and were included in your Plos Biology paper (https://doi.org/10.1371/journal.pbio.2004274). Therefore, we are wondering if there is any reason for excluding the two subjects’ MNI coordinates, or if it is possible to send us the data on these two subjects as well.

Thank you again and All the best!

Jin

Re: fcx-3 data-how to get the MNI coordinates for each electrode

Posted by Elizabeth Johnson at October 20. 2020

Please find the corrected files attached.

Attachments

Re: fcx-3 data-how to get the MNI coordinates for each electrode

Posted by Jin Li at October 27. 2020

Dear Dr. Johnson,

Many thanks for the updating. It works for us.

All the best!

Jin

Re: fcx-3 data-how to get the MNI coordinates for each electrode

Posted by Jin Li at November 26. 2020

Dear Dr. Johnson,

Many thanks for sharing us the data. We like your paper on Plos Biology, and hope to calculate the distribution of raw higher-frequency amplitudes across 18 theta phase (after PAC calculation), as you did in the paper (as attached). However, we could not find the corresponding script for this step in your shared scripts. Therefore, could you give us some hint about where we can find the script? Or could the corresponding script be kindly released?

All the best!

Jin

Attachments

Re: fcx-3 data-how to get the MNI coordinates for each electrode

Posted by Elizabeth Johnson at November 30. 2020
Hi Jin,
 
You are welcome to perform any analyses you'd like on these data provided you cite the corresponding paper(s). Doing so is your responsibility. Various procedures for indexing data points and plotting are described on the MATLAB help website, and are not specific to the reported results.
 
best,
Dr. Johnson

Re: fcx-3 data-how to get the MNI coordinates for each electrode

Posted by Jin Li at November 30. 2020

Dear Dr. Johnson,

Thank you for your quick reply, last time we are wondering how to calculate the amplitude at different pahse bins after calculating the PAC. Thank you for your reminder, I will search the corresponding website to find a solution. Thank you again for your shared information.

Best,

Jin

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