Dear Sir or Madam,
In our institution we try to implement an automatic routine for the co-registration of MRI images and 3 dimensional MR spectroscopic metabolic maps acquired on SIEMENS MR Scanner. We try to realize it by using the Dicom reading function as implemented in MATLAB. To evaluate the transformation matrix extracted from the DICOM header tag “ImageOrientationPatient” we compared it with the matrix extracted by tool “tkregister2”contained in the freesurfer package. Because of some observed obscurities we would like to ask you following questions:
1) How does tkregister2 rebuild the transformation matrix of the corresponding Nifti-file (inversion?) which is used in the freesurfer-tool “flirt” for the coregistration (the matrix in the file with the extension .fsl)?
2) Is the order of rotations performed by the data acquisition relevant for the several steps of matrix construction? If so is there a general way how ‘tkregister2’ extract this order and consider for the further calculations?
3) By the reading and plotting the 3D DICOM image data sets with MATLAB we figured out, that directions of several spaces axes are changing (negativepositive; positivenegative) depending on the image orientation using during the acquisition (sagital, coronar, transversal). We guessed that we should at first correct our data by flipping some axes (e.g. in sagital case LR-axis) and then apply the matrix extracted from DICOM-header to the corrected data set. If it is correct how ‘tkregister2’ tool perform this correction for several orientation cases?
With best regards,
Alexander Gussew
Medical Physics Group Instut for Diagnostic and Interventional Radiology Hospital of Friedrich-Schiller-University Jena, Germany
Dipl.-Ing. Alexander Gussew Institut für Diagnostische und Interventionelle Radiologie AG Medizinische Physik Klinikum der Friedrich-Schiller-Universitaet Jena Philosophenweg 3 D-07743 Jena Germany Tel. +49 (0)3641 935361 Fax +49 (0)3641 936767 e-mail: alexander.gussew@med.uni-jena.de
____________________ Universitätsklinikum Jena Körperschaft des öffentlichen Rechts und Teilkörperschaft der Friedrich-Schiller-Universität Jena Bachstraße 18, 07743 Jena Verwaltungsratsvorsitzender: Prof. Dr. Walter Bauer-Wabnegg; Medizinischer Vorstand: Prof. Dr. Klaus Höffken; Wissenschaftlicher Vorstand: Prof. Dr. Klaus Benndorf; Kaufmännischer Vorstand und Sprecher des Klinikumsvorstandes Rudolf Kruse Bankverbindung: Sparkasse Jena; BLZ: 830 530 30; Kto.: 221; Gerichtsstand Jena Steuernummer: 161/144/02978; USt.-IdNr. : DE 150545777