diff --git a/doc/whats_new.rst b/doc/whats_new.rst index 80b7bdd70..fa0ddc6ff 100644 --- a/doc/whats_new.rst +++ b/doc/whats_new.rst @@ -47,6 +47,8 @@ Enhancements - Add support for iEEG data in the coordinate frame ``Pixels``; although MNE-Python does not recognize this coordinate frame and so it will be set to ``unknown`` in the montage, MNE-Python can still be used to analyze this kind of data, by `Alex Rockhill`_ (:gh:`976`) +- Add an explanation in :ref:`ieeg-example` of why it is better to have intracranial data in individual rather than template coordinates, by `Alex Rockhill`_ (:gh:`975`) + API and behavior changes ^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/examples/convert_ieeg_to_bids.py b/examples/convert_ieeg_to_bids.py index 60bfe6c1c..936220982 100644 --- a/examples/convert_ieeg_to_bids.py +++ b/examples/convert_ieeg_to_bids.py @@ -1,4 +1,6 @@ """ +.. _ieeg-example: + .. currentmodule:: mne_bids ==================================== @@ -195,7 +197,7 @@ # # `acpc_aligned=True` affirms that our MRI is aligned to ACPC # if this is not true, convert to `fsaverage` (see below)! -write_raw_bids(raw, bids_path, anonymize=dict(daysback=30000), +write_raw_bids(raw, bids_path, anonymize=dict(daysback=40000), montage=montage, acpc_aligned=True, overwrite=True) # check our output @@ -270,8 +272,15 @@ # Here we'll use the MNI Talairach transform to get to ``fsaverage`` space # from "mri" aka surface RAS space. # ``fsaverage`` is very useful for group analysis as shown in -# `Working with SEEG -# `_. +# :ref:`tut-working-with-seeg`. Note, this is only a linear transform and so +# one loses quite a bit of accuracy relative to the needs of intracranial +# researchers so it is quite suboptimal. A better option is to use a +# symmetric diffeomorphic transform to create a one-to-one mapping of brain +# voxels from the individual's brain to the template as shown in +# :ref:`tut-ieeg-localize`. Even so, it's better to provide the coordinates +# in the individual's brain space, as was done above, so that the researcher +# who uses the coordinates has the ability to tranform them to a template +# of their choice. # ensure the output path doesn't contain any leftover files from previous # tests and example runs @@ -293,7 +302,7 @@ montage.apply_trans(mri_mni_t) # write to BIDS, this time with a template coordinate system -write_raw_bids(raw, bids_path, anonymize=dict(daysback=30000), +write_raw_bids(raw, bids_path, anonymize=dict(daysback=40000), montage=montage, overwrite=True) # read in the BIDS dataset