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mrtools:talairachcoordinates [2009/10/01 05:32]
justin
mrtools:talairachcoordinates [2010/11/23 23:15] (current)
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 =====Overview===== =====Overview=====
 The way we've implemented the use of registration to the Talairach coordinate system is by keeping track of a single transform. We don't currently support anything other than a single transformation of the whole brain. Once a transform is defined for a given brain, (see below) it can be saved to the base volume for that brain and then it will be inherited by everything aligned to or defined on that base volume. In this way, scans and ROIs from different subjects can be aligned with one another by transforming to Talairach space instead of magnet space. This happens behind the scenes, so that scan2scan and base2base and roi2roi are all computed using the Talairach transform if it's available. The way we've implemented the use of registration to the Talairach coordinate system is by keeping track of a single transform. We don't currently support anything other than a single transformation of the whole brain. Once a transform is defined for a given brain, (see below) it can be saved to the base volume for that brain and then it will be inherited by everything aligned to or defined on that base volume. In this way, scans and ROIs from different subjects can be aligned with one another by transforming to Talairach space instead of magnet space. This happens behind the scenes, so that scan2scan and base2base and roi2roi are all computed using the Talairach transform if it's available.
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 +We keep everything in the base structure, and don't change the NIFTI headers, e.g., we do not re-set sform code to 3, we do not actually rotate the volume, and we do not change s-form to the TalXform. Rather, we leave sform code as 1, leave sform as that which is calculated during alignment,​and save talXform to the base structure to be used for viewing or aligning.
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 +[[talairach|Return to main Talairach page]]
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 =====Defining Talairach Coordinates===== =====Defining Talairach Coordinates=====
-The basic idea is to define the anterior and posterior commissures (AC and PC), and then several points relative to the AC and PC: the anterior and posterior extensions of the AC/PC line (the AAC and PPC), the superior and inferior extensions of the AC perpendicular to the AC/PC line (the SAC and IAC), and the right and left extensions of the AC perpendicular to the AC/PC line (the RAC and LAC). Once these 8 points have been defined, the transform from those coordinates to the standard Talairach coordinates is calculated. The 8 points are saved in the .talInfo field in the base volume on which they were defined, and are used to initialize the Talairach program in case the user decides to refine the choice of points. The (4x4) transform is saved in the .vol2tal field of the base volume on which it was defined.+ 
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 +The basic idea is to define the anterior and posterior commissures (AC and PC; I find [[http://​www.med.harvard.edu/​AANLIB/​cases/​caseNA/​pb9.htm|this website]] useful in identifying them), and then several points relative to the AC and PC: the anterior and posterior extensions of the AC/PC line (the AAC and PPC), the superior and inferior extensions of the AC perpendicular to the AC/PC line (the SAC and IAC), and the right and left extensions of the AC perpendicular to the AC/PC line (the RAC and LAC). Once these 8 points have been defined, the transform from those coordinates to the standard Talairach coordinates is calculated. The 8 points are saved in the .talInfo field in the base volume on which they were defined, and are used to initialize the Talairach program in case the user decides to refine the choice of points. The (4x4) transform is saved in the .vol2tal field of the base volume on which it was defined.
  
 NB These directions and the Talairach setting interface have not been thoroughly debugged. The Talairach transformations have been used successfully for one project, but there are some details particularly with the Talairach setting program in which the interface may still be a bit buggy. Caveat Emptor. NB These directions and the Talairach setting interface have not been thoroughly debugged. The Talairach transformations have been used successfully for one project, but there are some details particularly with the Talairach setting program in which the interface may still be a bit buggy. Caveat Emptor.
  
-You can define the Talairach points on a subject'​s volume, using mrAlign. First startup mrAlign and load the volume you want to define Talairach coordinates on as the destination. Then select the menu item "Set Talairach Transform"​ from the Talairach menu. You should see three views of your anatomy and a control panel.+You can define the Talairach points on a subject'​s volume, using mrAlign ​(Also, note that if you just want an interface for defining Talairach points w/out using them in MLR you can use the program talairach directly). First startup mrAlign and load the volume you want to define Talairach coordinates on as the destination. Then select the menu item "Set Talairach Transform"​ from the Talairach menu. You should see three views of your anatomy and a control panel.
  
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 mrLR saves the base's .vol2tal field in any scan (or roi) that is aligned to the base. The transform can also be exported to sessions that have already been aligned, using mrAlign. Then viewGet uses this information when aligning scans (or rois) using scan2scan (or roi2roi). mrLR saves the base's .vol2tal field in any scan (or roi) that is aligned to the base. The transform can also be exported to sessions that have already been aligned, using mrAlign. Then viewGet uses this information when aligning scans (or rois) using scan2scan (or roi2roi).
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 +[[talairach|Return to main Talairach page]]