Hi,

Indeed. Images I_2 and I_3 are different, and I know their qform and sform matrices are too. However, I_2 is actually acquired for motion correction purposes, as there is no way to do it based on I_3 due to its inherent nature.

I do not understand the issue though... The transformation matrix should be, theoretically, just a bunch of translations and rotations in millimeters; shouldn't they be applied from the image origin independently from its FOV and voxel size?

Thank you very much!
--
Angel Torrado-Carvajal
Postdoctoral Research Fellow
Pain Neuroimaging Laboratory
MGH/HST Athinoula A. Martinos Center for Biomedical Imaging
Building 149, Room 1101, 13th Street, Charlestown, MA 02129 USA
[log in to unmask] | www.nmr.mgh.harvard.edu | @MGHMartinos

________________________________________
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Fidel Alfaro Almagro <[log in to unmask]>
Sent: Wednesday, February 28, 2018 7:38:43 AM
To: [log in to unmask]
Subject: Re: [FSL] Issue with Transformation Matrix

Hi,

Even if images I_2 and I_3 were acquired sequentially, their acquisition parameters are different. The FoV is different and therefore, the sform and qform matrices are probably very different. Applying T_21 to I_3 will not work. It would be better if you could run flirt on I_3 to generate a T_31 matrix.

Cheers

2018-02-27 17:55 GMT-05:00 Torrado Carvajal, Angel <[log in to unmask]<mailto:[log in to unmask]>>:

Hi,


I have a problem with a transformation matrix, maybe because I do not understand a step or something in the header of the images...


Let's say I have MRI images I_1, I_2 and I_3, where images I_2 and I_3 where acquired sequentially, but they have different field of views and voxel sizes. If I register I_2 to I_1 with FLIRT I obtain matrix T_21. Then, if I apply this matrix to I_2, the registration to I_1 looks great, but if I apply the same matrix to I_3 the registration does not look good at all. What could be the reason?


Thank you very much!

--
Angel Torrado-Carvajal
Postdoctoral Research Fellow
Pain Neuroimaging Laboratory
MGH/HST Athinoula A. Martinos Center for Biomedical Imaging
Building 149, Room 1101, 13th Street, Charlestown, MA 02129 USA
[log in to unmask]<[log in to unmask]" target="_blank">http:[log in to unmask]> | www.nmr.mgh.harvard.edu<http://www.nmr.mgh.harvard.edu> | @MGHMartinos

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