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Bug 2441 - anatomy/template: low res and hi res MRIs are stored with left vs right-handed axes system
| Status | CLOSED FIXED |
| Reported | 2014-01-18 12:19:00 +0100 |
| Modified | 2014-03-06 15:37:58 +0100 |
| Product: | FieldTrip |
| Component: | core |
| Version: | unspecified |
| Hardware: | PC |
| Operating System: | Mac OS |
| Importance: | P5 normal |
| Assigned to: | Jan-Mathijs Schoffelen |
| URL: | |
| Tags: | |
| Depends on: | |
| Blocks: | |
| See also: |
Jan-Mathijs Schoffelen - 2014-01-18 12:19:25 +0100
the 1mm res and 2mm res anatomical template MRIs (both Colin 27, but downloaded from different locations) have their axes represented inconsistently. One is left-handed, the other right-handed. I suggest to make this consistent (and document this).
Robert Oostenveld - 2014-01-19 10:01:39 +0100
I guess that the axes (x/y/z) are correct, but that the voxel orientation is inconsistent? I.e. that in one of them there is a -1 or -2 along the diagonal of the mri.transform.
Jan-Mathijs Schoffelen - 2014-01-19 14:12:14 +0100
good guess indeed
Jan-Mathijs Schoffelen - 2014-01-19 14:15:01 +0100
That is, both mris seem internally consistent (although I haven't checked whether Colin has a crooked nose). What we could do is just downsample the 1 mm version to 2 mm, and replace the current 2 mm version. Makes them both consistent relative to one another, and we can still specify the 1 mm resolution image as the source.
Robert Oostenveld - 2014-01-19 16:29:11 +0100
(In reply to Jan-Mathijs Schoffelen from comment #3) I suggest to keep the original 2mm. I suspect it originates from spam. Keeping it (after flipping one axis) makes it easier to explain where it came from.
Jan-Mathijs Schoffelen - 2014-01-19 17:51:44 +0100
the 2 mm comes from the surfrend toolbox (an spm add-on) the 1 mm comes from cambridge
Robert Oostenveld - 2014-01-19 18:31:48 +0100
Why don't we (re)use the SPM canonical template? That was a 2mm, might now be in 1mm form.
Jan-Mathijs Schoffelen - 2014-01-19 19:33:40 +0100
isn't spm's canonical template a smoothed volume?
Jan-Mathijs Schoffelen - 2014-01-19 19:48:27 +0100
We could also consider to upload the 152MNI template (as e.g. used in FSL) from http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009