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Hi, We will either make them consistent with the FSLView voxel coordinates or with the FSLView mm coordinates. Probably the former. We are trying to make sure that these are the only two coordinates which people will ever need to deal with. This is the only list for FSL and we make all official announcements here. All the best, Mark On 2 Feb 2009, at 16:05, Marc Lalancette wrote: > Thanks Mark, > > So once it's fixed, are the coordinates supposed to be voxel order > (as they > are stored in the file) times voxel size or real world coordinates as > specified by q/sform but with the origin in the "negative" corner? > Both > seem a bit strange to me. I'd have stuck with either raw voxel > order or > q/sform coordinates. Might be something to consider, perhaps as an > option. > > Also, there isn't another mailing list for official announcements, > like new > patches or releases, is there? > > Cheers, > Marc > > > On Fri, 30 Jan 2009 19:36:56 +0000, Mark Jenkinson <[log in to unmask] > > wrote: > >> Hi, >> >> This does indeed look like a bug that has slipped through the >> net when we were migrating all functionality to work with either >> left or right-handed coordinate systems. We will fix it in the >> next patch. >> >> Thanks for letting us know. >> All the best, >> Mark >> >> >> On 28 Jan 2009, at 21:33, Marc Lalancette wrote: >> >>> Hello, >>> >>> While trying to carefully follow coordinate changes from start to >>> finish, I >>> found out that the .off mesh produced by bet -A has coordinate axes >>> aligned >>> with LAS regardless of the voxel order in the source .nii file. The >>> betsurf >>> documentation however states that the coordinates should be "the >>> integer >>> voxel co-ordinates multiplied by the voxel size values". That's not >>> very >>> clear since it doesn't say which voxel coordinates, but I don't see >>> how it >>> could mean LAS regardless of voxel order. >>> >>> Just to be clear, here is what I did: >>> >>> My dcm files are stored with LPS voxel order. >>> I convert them to NIfTI format using dcm2nii which can produce 2 >>> ouput: the >>> "regular" one has voxel order LAS and the "reoriented" one has voxel >>> order >>> RAS (according to the voxel coordinates shown in fslview and also >>> verified >>> in Matlab). Both of these NIfTI files have correct header info to >>> produce >>> RAS coordinate axes (verified in fslview). >>> Now, if I use bet -A on both of these, the .off mesh files will both >>> have >>> LAS coordinates. (I only looked at inner skull meshes.) >>> >>> So it seems the documentation is misleading or there is a bug. >>> >>> Cheers, >>> Marc >>> >