Hi - I'm confused - if you are using FSLView to find the co-ordinates
in the first place, and then need to use voxel co-ordinates (as
opposed to mm) then you can just read the voxel co-ords in FSLView
directly (just to the left of the mm co-ords).
Cheers.
On 15 Oct 2007, at 02:25, Ping-Hong Yeh wrote:
> Hi Matt and Mark,
>
> Thanks for the reply.
> I only need to know the correpsonding vox for the center of a ROI
> so I can
> use the fslroi to get the tissue imformation after I ran the fast.
> Since the
> MPRAGE (256*256*154) were in the native space and I will not
> transform them
> to the MNI standard space, I don't think the std2imgcoord or
> img2imgcoord
> are what I need.
> I am wondering how fslview get the coordianates in mm of (0,0,0),
> which
> varies between the image even though they were inthe same resolution?
> I can transform the mm to vox once I knew these x y z .
> Regards,
>
> Ping
>
>
>
> On Sun, 14 Oct 2007 22:13:51 +0100, Mark Jenkinson
> <[log in to unmask]> wrote:
>
>> Dear Matt,
>>
>> It has been - under misc flirt utilities linked near the top of
>> the main
>> flirt page (as flirt is the main tool dealing with registration and
>> coordinates).
>> See:
>> http://www.fmrib.ox.ac.uk/fsl/flirt/overview.html#misc
>>
>> All the best,
>> Mark
>>
>>
>>
>> On 14 Oct 2007, at 22:03, Matt Glasser wrote:
>>
>>> Would be nice if that were documented somewhere. :)
>>>
>>> -----Original Message-----
>>> From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On
>>> Behalf
>>> Of Mark Jenkinson
>>> Sent: Sunday, October 14, 2007 4:53 PM
>>> To: [log in to unmask]
>>> Subject: Re: [FSL] mm to vox coordinate
>>>
>>> Dear Ping,
>>>
>>> You can use the command:
>>> std2imgcoord
>>> to convert between coordinates (also img2imgcoord and img2stdcoord).
>>> These are easy to incorporate within scripts.
>>>
>>> All the best,
>>> Mark
>>>
>>>
>>> On 14 Oct 2007, at 21:05, Ping-Hong Yeh wrote:
>>>
>>>> Hi,
>>>>
>>>> I'd like to know the antomate way of converting the coordinates in
>>>> mm to vox
>>>> so I could extract the ROI using fslroi. I knew I can just open the
>>>> fslview
>>>> and get the vox, but would perfer not to do so. I have used the SPM
>>>> scripts
>>>> (i.e. mm = [-22, 50, 50]; % example co-ordinates.
>>>> V = spm_vol(spm_get(1,'*.img'));
>>>> M = inv(V.mat);
>>>> vox = (M(1:3,1:3)*mm' + repmat(M(1:3,4),1,size(mm,1)))', )
>>>>
>>>> but it did not get the right vox coordinate, not knowing why?
>>>>
>>>> Thanks.
>>>>
>>>> Ping
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---
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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