What do you mean by "ras matlab subscripts"? Those looks like indices,
not RAS. Assuming those are indices, then that looks right.
doug
On 05/18/2012 02:02 PM, Jordan L. Poppenk wrote:
> Dear Doug,
>
> To generalize from this earlier conversion question, to interpret the
> coordinate space of a file loaded by freesufer/matlab/MRIread.m, would one
> use the following transform to move from ras matlab subscripts (e.g.,
> 1:256,1:256,1:256) to mni coords?
>
> mni = talairach.xfm * vox2ras1 * [r a s 1]
>
> The coordinates I get out of this transform do not seem quite right.
>
> Cheers,
> Jordan
>
>
> On May 3, 2012, at 5:40 PM, Jordan Poppenk wrote:
>
>> Dear Douglas,
>>
>> That's exactly the information I was looking for. This worked perfectly.
>> Thank you for your help!
>>
>> Cheers,
>> Jordan
>>
>>
>>> Here's how to convert from surface RAS to mni305
>>>
>>> mni305ras = X*S*inv(K)*ras
>>> X = talairach.xfm
>>> S = scanner vox2ras (mri_info --vox2ras orig.mgz)
>>> K = tkreg vox2ras (mri_info --vox2ras-tkr orig.mgz)
>>> ras = surface ras
>>>
>>> If you want to go from mni305 to approximate talairach, you can use this
>>> transform from Matthew Brett:
>>>
>>>
>>> function outpoints = mni2tal(inpoints)
>>> % Converts coordinates from MNI brain to best guess
>>> % for equivalent Talairach coordinates
>>> % FORMAT outpoints = mni2tal(inpoints)
>>> % Where inpoints is N by 3 or 3 by N matrix of coordinates
>>> % (N being the number of points)
>>> % outpoints is the coordinate matrix with Talairach points
>>> % Matthew Brett 10/8/99
>>>
>>> dimdim = find(size(inpoints) == 3);
>>> if isempty(dimdim)
>>> error('input must be a N by 3 or 3 by N matrix')
>>> end
>>> if dimdim == 2
>>> inpoints = inpoints'; %'
>>> end
>>>
>>> % Transformation matrices, different zooms above/below AC
>>> upT = spm_matrix([0 0 0 0.05 0 0 0.99 0.97 0.92]);
>>> downT = spm_matrix([0 0 0 0.05 0 0 0.99 0.97 0.84]);
>>>
>>> tmp = inpoints(3,:)<0; % 1 if below AC
>>> inpoints = [inpoints; ones(1, size(inpoints, 2))];
>>> inpoints(:, tmp) = downT * inpoints(:, tmp);
>>> inpoints(:, ~tmp) = upT * inpoints(:, ~tmp);
>>> outpoints = inpoints(1:3, :);
>>> if dimdim == 2
>>> outpoints = outpoints'; %'
>>> end
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 05/02/2012 12:54 PM, Jordan Poppenk wrote:
>>> Dear FreeSurfer experts,
>>>
>>>>
>>> How does one properly convert from surfaceRAS coords, as provided by
>>> fs_read_surf.m, to talairach coords? I have tried using
>>> freesurfer_surf2tal.m posted on the web by Darren Weber, supplying it with
>>> transform data from transforms/talairach.xfm, but the values returned often
>>> differ from those in tksurfer by as much as 20mm (and are clearly wrong).
>>> What I would like to do is match the coordinate system in tksurfer (which
>>> is clearly right). How does tksurfer do it?
>>>
>>>>
>>> Cheers,
>>>
>>> Jordan
>>>
>>>>
>>>>
>>> _______________________________________________
>>>
>>> Freesurfer mailing list
>>>
>>>> Freesurfer at nmr.mgh.harvard.edu
>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>>
>>> greve at nmr.mgh.harvard.edu
>>>
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>
>
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
