Great. That does make a lot of sense.
Thanks for taking the time to help.
Cheers,
Marc
On Mon, 2 Feb 2009 16:23:33 +0000, Mark Jenkinson <[log in to unmask]> wrote:
>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
>>>>
>>
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