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Dear FreeSurfer Devs,

I'm following the fswiki ( https://secure-web.cisco.com/1W5RqZmGDk4DqrkitgyXA6TeSK5f9Nimf0vTibPbawbImAx...) to map sEEG contacts to the template *cvs_avg35_inMNI152*.

*I've got MNI305 coordinates for each contact, and I want to plot them on cvs_avg35_inMNI152.*

According to the wiki, once I have MNI305 coordinates, I have two choices to calculate the transform from MNI305 to the scanner RAS for this template (instruction 2 and 8b, see below for comparisons).

Normally I use instruction 2 since it seems to be more general and can be applied to any template. For MNI152-based templates, instruction 8b seems to be more straightforward. According to your Wiki, these two instructions would yield the identical mapping.

*However, a recent case suggested a result of ~5mm difference between these two methods.*

My questions are:

* Is this error range expected/acceptable in the eyes of FreeSurfer? * Which image defines MNI305 RAS. (For example, MNI152 RAS usually aligns with the scanner RAS of one of ICBM 152 Nonlinear atlases version 2009) * If I need more accurate scanner->MNI305 mapping (instead of using talairach.xfm), what's your recommendations on FreeSurfer templates that are not sitting in MNI152a/b/c space?

*Here's my case study:*

Here is a screenshot of the native subject's brain. The two contacts (in red) are at the level of thalamus. [image: image.png]

Choice 1: Following the instruction 2,

I have an RAS point on the surface (tkrR tkrA tkrS) ("Vertex RAS" from tksurfer)

and want to compute the MNI305 RAS that corresponds to this point:

MNI305RAS = TalXFM*Norig*inv(Torig)*[tkrR tkrA tkrS 1]'

This is the method that I usually use. I can calculate MNI305 RAS from scanner RAS via talairach.xfm (in mri/transforms/). This transform is 1.0540 0.0028 -0.0071 -0.0761 -0.0105 1.0914 0.0090 1.7791 0.0201 -0.0599 1.1014 *-5.4613*

Result: the contacts are at the level of brainstem [image: image.png]

Choice 2: instruction 8b

However, since the template already aligns with MNI152, as an alternative, I can follow the instruction 8b,

I have an RAS from a voxel in MNI152 space which I want to convert to

MNI305 space (fsaverage space). Create a vector of the MNI152 space point like v = [R A S 1]'. Multiply this vector by the matrix below (ie, M*v)

1.0022 0.0071 -0.0177 0.0528 -0.0146 0.9990 0.0027 -1.5519 0.0129 0.0094 1.0027 *-1.2012*

*Notice the translation on Z axis is -1.2mm instead of -5.5mm* Result: This mapping seems better

[image: image.png]

Best, - Dipterix