[WIP; ENH] Storage of iEEG electrodes in subject-specific FreeSurfer space by adam2392 · Pull Request #757 · bids-standard/bids-specification

adam2392 · 2021-03-15T15:46:02Z

Closes: #747

~~Currently, this is a draft to demonstrate exactly what would fix issues discussed in #747 .~~

adam2392 · 2021-03-23T17:58:22Z

@sappelhoff not sure what's up w/ the link-checker, i'll take another look today.

Anything holding up this you think?

src/99-appendices/08-coordinate-systems.md

sappelhoff · 2021-03-23T18:41:39Z

So would the workflow for this solution be something like:

README
dataset_description.json
participants.tsv
derivatives/
    freesurfer/
        sub-01/
            T1.mgz <-- based on sub-01_T1w.nii
sub-01/
    anat/
        sub-01_T1w.nii
    ieeg/
        sub-01_space-fsnative_electrodes.tsv
        sub-01_space-fsnative_coordsystem.json <-- IntendedFor contains path to freesurfer T1.mgz in derivatives?

... or am I misunderstanding this?

If I am correct, then we still need to figure out how to appropriately point to a derivatives file, given that they could be stored anywhere and simply using "relative paths from BIDS root" are not guaranteed to work.

cc @effigies

adam2392 · 2021-03-23T18:45:46Z

Yes that is correct!

adam2392 · 2021-03-24T13:45:18Z

Perhaps,

If the derivative data is stored as a subdirectory of `bids_root`, then `IntendedFor` must point to that file relative to `bids_root`. If not, then a DOI should be present that links to that dataset.

?

adam2392 · 2021-04-06T14:16:36Z

If the derivative data is stored as a subdirectory of `bids_root`, then `IntendedFor` must point to that file relative to `bids_root`. If not, then a DOI should be present that links to that dataset.

Is there any update with regards to this? Should I include this part, to specify that fsnative and fsnativetkr are derivative coordinate systems?

sappelhoff · 2021-04-06T14:23:29Z

Thanks for the reminder, and sorry that there is so little progress - it seems like very few people are interested in solving this problem.

If the derivative data is stored as a subdirectory of bids_root, then IntendedFor must point to that file relative to bids_root. If not, then a DOI should be present that links to that dataset.

so am I understanding your proposal correctly?

if derivatives/ is part of a BIDS dir, interpret IntendedFor as a relative path from the BIDS dir root
if derivatives/ is NOT part of a BIDS dir, a DOI "should be present" to point to the derivatives/, and then IntendedFor will be used "as if" derivatives/ were nested in the BIDS dir?

then a DOI should be present that links to that dataset.

where should that DOI be present?

What about datasets that do not have a DOI?

robertoostenveld · 2021-04-06T14:29:47Z

the proposed fsnativetkr coordinate system is specific to a particular anatomical MRI in FS format. E.g. consider that you start with a 1mm T1 scan and another 0.7 mm T1 scan from the patient. The number of slices and hence the alignment of the first (lower-resolution) scan within the 256x256x256 volume are likely to be different than the number of slices and hence the alignment of the higher-resolution scan. If you run freesurfer on the low-res, the output will be shape-wise very similar to that of the high-res, but the data expressed in the fsnativetkr coordinate system will be shifted with respect to each other.

I think that fsnativetkr therefore cannot be specified without the corresponding IntendedFor linking to an MRI that must represent the 256x256x256 volume in the FS file format.

robertoostenveld · 2021-04-06T14:32:34Z

src/99-appendices/08-coordinate-systems.md

+
+-   `fsnativetkr`: The subject-specific FreeSurfer T1w space. The origin of
+    the coordinate system is at the center of isotropic 1 mm 256x256x256
+    volume (that is the voxel center is at slices (128, 128, 128)) in RAS


are these indices 0-offset or 1-offset?

Should the middle of a 256x256x256 volume not be represented as [127.5 127.5 127.5] (when 0-offset) or [128.5 128.5 128.5] (where 1-offset)?

The middle of a 2x2x2 volume would be at voxel [0.5 0.5 0.5] if you start counting voxels at [0 0 0], or at [1.5 1.5 1.5] when you start counting at [1 1 1].

I'm pretty sure it is with 0-offset.

That's what I thought initially... but I think there is some offset, so for example, running the following

mri_info --vox2ras-tkr <img> This will generally be the 4x4 matrix for FreeSurfer output.:: [ [-1.0, 0.0, 0.0, 128.0], [0.0, 0.0, 1.0, -128.0], [0.0, -1.0, 0.0, 128.0], [0.0, 0.0, 0.0, 1.0], ]

This essentially centers the coordinates at the "center" of the volume "almost".

Reference: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg69541.html

src/99-appendices/08-coordinate-systems.md

adam2392 · 2021-04-08T01:50:38Z

I think that fsnativetkr therefore cannot be specified without the corresponding IntendedFor linking to an MRI that must represent the 256x256x256 volume in the FS file format.

Then perhaps what is needed to fully define this TKR coordinate system is:

"The IntendedFor also MUST be defined linking to an MRI that MUST represent the 256x256x256 volume in the FreeSurfer file format."?

adam2392 · 2021-04-08T01:51:07Z

https://bids-specification--757.org.readthedocs.build/en/757/99-appendices/08-coordinate-systems.html#ieeg-specific-coordinate-systems

robertoostenveld · 2021-04-08T10:53:54Z

src/99-appendices/08-coordinate-systems.md


+-   `fsnative`: The subject-specific FreeSurfer T1w space. This corresponds to
+    the original scanner image after it is re-sampled and re-scaled
+    to an isotropic 1 mm 256x256x256 volume in RAS orientation. The origin


fsnative is not defined relative to the 1mm 256^3 MRI, but is defined relative to the AC of the individual participant.

I'm not sure I follow. Isn't fsnative just the xyz coordinates in RAS space based on the vox2ras affine transformation?

RAS is only the specification of the direction of the axes, the origin also needs to be defined. That origin is at the anterior commissure, or not?

Ah yes you're right. I just noticed I had two incongruent sentences. Adjusted now to specify AC.

src/99-appendices/08-coordinate-systems.md

adam2392 · 2021-04-13T13:52:30Z

if derivatives/ is part of a BIDS dir, interpret IntendedFor as a relative path from the BIDS dir root

if derivatives/ is NOT part of a BIDS dir, a DOI "should be present" to point to the derivatives/, and then IntendedFor will be used "as if" derivatives/ were nested in the BIDS dir?

then a DOI should be present that links to that dataset.

where should that DOI be present?

What about datasets that do not have a DOI?

@sappelhoff is the best place to handle this within this PR? Perhaps adding a statement:

The `IntendedFor` key must be defined either with: i) a DOI or ii) a relative path from the BIDS directory

?

sappelhoff · 2021-04-13T15:33:14Z

is the best place to handle this within this PR? Perhaps adding a statement:

although it will probably delay the efforts here, I think it's best to first deal with that issue here: #471 (comment)

and then come back to the present one.

sappelhoff · 2022-07-25T13:07:22Z

@adam2392 -- just a note that #918 has been merged and BIDS URIs will be part of the 1.8 release (probably some time in September). Not sure if what you proposed in this PR is still needed and/or salvageable. If not, please close the PR :-)

Else. we can leave it open and keep working on it.

dorahermes

Nice, clarifying surface space would be helpful.

dorahermes · 2022-07-27T08:02:33Z

src/99-appendices/08-coordinate-systems.md

+    volume (that is the voxel center is at slices (128, 128, 128)) in RAS
+    orientation. This corresponds to FreeSurfer's surface RAS coordinates (TKR coordinates).
+    The origin MUST be the Anterior Commissure. The ``IntendedFor`` MUST link to an MRI that represents the 256x256x256 volume in the FreeSurfer file format. The difference between this coordinate system and ``fsnative`` is that TKR coordinates are defined on the surface of the brain based on FreeSurfer.
+


Freesurfer has several surfaces (pial, white, inflated... ), it is unclear which surface is meant

effigies · 2025-06-04T14:15:00Z

Switching to draft to make PRs ready for review more identifiable.

adam2392 added 3 commits March 15, 2021 11:43

Example.

5c40b3c

Adding the two coordinate systems.

d6044a7

Remove latin.

abe2b41

adam2392 requested review from robertoostenveld and sappelhoff March 21, 2021 20:54

Add should sentence.

35d91e1

adam2392 requested a review from dorahermes March 23, 2021 17:58

sappelhoff reviewed Mar 23, 2021

View reviewed changes

src/99-appendices/08-coordinate-systems.md Outdated Show resolved Hide resolved

sappelhoff added the iEEG label Mar 26, 2021

Fixing comment of mUST/SHOULD.

c9555ef

adam2392 requested a review from sappelhoff April 6, 2021 14:16

robertoostenveld reviewed Apr 6, 2021

View reviewed changes

src/99-appendices/08-coordinate-systems.md Outdated Show resolved Hide resolved

adam2392 added 2 commits April 7, 2021 21:48

Adding Robert's suggestions.

f5aacbd

Merge branch 'master' into fsnative

778e2bd

robertoostenveld reviewed Apr 8, 2021

View reviewed changes

src/99-appendices/08-coordinate-systems.md Outdated Show resolved Hide resolved

adam2392 added 2 commits April 11, 2021 16:39

Adding robert's comments.

4029190

Address Robert's origin issue.

ad3ca38

sappelhoff mentioned this pull request Jun 8, 2021

[ENH] Major update to pointing to files within, outside of, or remote to a current BIDS dataset #820

Closed

sappelhoff mentioned this pull request Nov 8, 2021

[ENH] Add BIDS URIs and deprecate relative paths, RawSources and (possibly unused) BasedOn #918

Merged

dorahermes requested changes Jul 27, 2022

View reviewed changes

effigies marked this pull request as draft June 4, 2025 14:14

Conversation

adam2392 commented Mar 15, 2021 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

adam2392 commented Mar 23, 2021

Uh oh!

Uh oh!

sappelhoff commented Mar 23, 2021 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

adam2392 commented Mar 23, 2021

Uh oh!

adam2392 commented Mar 24, 2021

Uh oh!

adam2392 commented Apr 6, 2021

Uh oh!

sappelhoff commented Apr 6, 2021

Uh oh!

robertoostenveld commented Apr 6, 2021

Uh oh!

robertoostenveld Apr 6, 2021

Choose a reason for hiding this comment

Uh oh!

adam2392 Apr 8, 2021

Choose a reason for hiding this comment

Uh oh!

Uh oh!

adam2392 commented Apr 8, 2021

Uh oh!

adam2392 commented Apr 8, 2021

Uh oh!

robertoostenveld Apr 8, 2021

Choose a reason for hiding this comment

Uh oh!

adam2392 Apr 11, 2021

Choose a reason for hiding this comment

Uh oh!

robertoostenveld Apr 13, 2021

Choose a reason for hiding this comment

Uh oh!

adam2392 Apr 13, 2021

Choose a reason for hiding this comment

Uh oh!

Uh oh!

adam2392 commented Apr 13, 2021

Uh oh!

sappelhoff commented Apr 13, 2021

Uh oh!

sappelhoff commented Jul 25, 2022

Uh oh!

dorahermes left a comment

Choose a reason for hiding this comment

Uh oh!

dorahermes Jul 27, 2022

Choose a reason for hiding this comment

Uh oh!

effigies commented Jun 4, 2025

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

5 participants

adam2392 commented Mar 15, 2021 •

edited

Loading

sappelhoff commented Mar 23, 2021 •

edited

Loading