[FieldTrip] questions on Fieldtrip anatomical workflow

Arjen Stolk a.stolk8 at gmail.com
Wed Jul 10 06:38:43 CEST 2019

Hi Luca,

Let me CC the mailing list on this email given that others might be running
into similar issues now or in the future. The short answer is that based on
this information I can only guess as to why the electrodes are outside the
brain (issue #1), and why they appear in the other hemisphere (issue #2).

Regarding #1, can you confirm that the apparent mislocalization only
pertains to the surface mesh and not the MR volume? You can verify this by
reading in the freesurfer-polished MRI (/freesurfer/mri/T1.mgz) and
visualize this scan along with the previously localized electrodes using
*ft_electrodeplacement*. For a background, FreeSurfer uses different
coordinate systems for volumetric images and for surface meshes extracted
from those images. The call to *mri_convert* at step 6
<http://www.fieldtriptoolbox.org/tutorial/human_ecog/>works around this
default feature by forcing the two to have the same coordinate system,
meaning you won't need to convert electrode locations when plotting them
with either modality. It's possible something did not well during this step
for you, though that would not explain the left-right flip.

As for #2, it seems likely indeed there's a left-right flip in the CT scan.
You might want to thoroughly check whether you correctly identified the
left-right axis, i.e. it could be any of the x, y, or z-axes depending on
the native coordinate system in which the scan came. And then, as you said,
check whether that axis runs from left to right or right to left, as
demonstrated in the movie
corresponding to step 3 (and Box 3 of the original protocol
<https://www.nature.com/articles/s41596-018-0009-6>). Fusion step 14
produces a plot of the CT and MR overlaid, providing a final checkpoint of
your preprocessing. That is, the CT and MR need to show a snug fit here. A
left-right flip, by the way, could affect the precision of the final
electrode locations given that the fusion step would not produce an optimal
match between CT and MR unless the participant's brain/head were perfectly

As a side note, make sure to specify the *cfg.spmmethod = 'new'* option
when calling *ft_volumenormalize*, as in the online tutorial (step 26). Our
experience is that the new algorithm works better than the previous one for
projecting electrodes to MNI space.


On Thu, Jul 4, 2019 at 9:13 AM Luca Iemi <luca.iemi at gmail.com> wrote:

> Hi Arjen,
> I hope my email finds you well.
> I finished the anatomical workflow for the first patient (see attached).
> This is the first time that I completed the whole pipeline and I have some
> very basic questions (I read the article as well as the online tutorial but
> couldn't find the answers). No one in my group has any experience with this
> so I am asking you. I apologize if my questions sound very basic.
> 1) I plotted the cortical hulls for left and right hemispheres and
> overlayed the depth electrodes as localized in ft_electrodeplacement (red)
> and the same electrodes transformed in MNI space (black).
> The problem is that some of these electrodes lie outside the cortical
> hulls. This problem didn't appear at the ft_electrodeplacement stage. I
> wonder if you could perhaps point me to the part of the anatomical workflow
> I may be doing incorrectly.
> 2) Also another quick question: both the CT and the MRI have a
> left-to-right orientation (the axis increases to the right according to
> ft_determine_coordsys). The implant was on the left hemisphere, but my
> reconstruction shows it on the right hemisphere. Should I flip the scans?
> How can I do that and at what stage should I become aware of this problem?
> Thanks for your help
> Best wishes,
> --
> Luca
> --
> Dr. Luca Iemi
> Post-Doc, Department of Neurological Surgery, Columbia University College
> of Physicians and Surgeons, New York, NY 10032
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