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

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

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

 

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

Please find the corrected files attached.

Dear Dr. Johnson,

Many thanks for the updating. It works for us.

All the best!

Jin

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

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