MNI2ACPC command

[m.versteijlen]

Dear Andreas,

First of all thank you for making all features of Lead-DBS publicly available.
But also I wanted to ask if there is a command-like method to warp a list of MNI coordinates to ACPC coordinates?
The manual way works like a charm, but for working from a Matlab script, it would be very nice to transform an entire array at once as a command.
Thanks in advance for your reply.

Kind regards,
Monique

[ningfei]

Dear Monique,

Please check the function ea_reconstruction2acpc (in which ea_native2acpc is called). You just need to set proper options.root, options.patientname and options.sides to make it work.

Best,
Ningfei

[m.versteijlen]

Hi Ningfei,

I’m sorry but I am still not quite clear how this works.
Other than manually setting the options to the desired patientname and rootfolder, I’m not getting further.
Later in the ea_native2acpc file there is another referral to options, which there does not exist, because I set them locally.
So is there a function or script in which the options are defined?

Kind regards,
Monique

[ningfei]

Hi Monique,

You need to manually set options properly for custom script. Which field of options doesn’t exist when you tried?

Best,
Ningfei

[andreashorn]

Hi Monique,

I think what ningfei said may have been helpful but wasn’t exactly what you were looking for.

You can just use this snippet:

uipatdir={'/path/to/my/patientfolder1','/path/to/my/patientfolder2','/path/to/my/patientfolder3'};
cfg.xmm=-4; % x-coordinate
cfg.ymm=-5; % y-coordinate
cfg.zmm=10; % z-coordinate
cfg.acmcpc=2; % relative to midcommissural point, AC would be 1, PC would be 3.
fid=ea_mni2acpc(cfg,uipatdir);

The first line would point to at least one patient normalized with Lead-DBS. Please do read the Horn 2017 NI paper to see why it may make a lot of sense to use a whole cohort to do this conversion. Instead, if you’re interested in the coordinate in ACPC in exactly one specific patient, then just using one patient is ideal.

The transformed coordinate will be fid.WarpedPointACPC;

AC, PC and MSP in native space will also be defined.

Then ea_acpc2mni would do the reverse.

Hope this helps!

Best, Andy

[m.versteijlen]

Ah thank you so much.

This did exactly what I was looking for.

Best,
Monique

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