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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