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Bug 2441 - anatomy/template: low res and hi res MRIs are stored with left vs right-handed axes system

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
Depends on:
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

Jan-Mathijs Schoffelen - 2014-01-20 22:01:04 +0100

I downloaded the colin27 nifti directly from the mcgill's website (see fieldtrip/anatomy/template for link). and replaced the single_subj_T1_1mm with this one. I replaced the single_subj_T1 with a ft_volumedownsampled version, resulting in both anatomicals having right-handed voxel-axes.