Automatic 3D Intersubject Registration of MR Volumetric Data in Standardized Talairach Space

“Collins [8] has used a multiresolution approach in which the overall nonlinear transformation is composed of a set of local linear deformations obtained by maximizing the correlation of intensity and gradient features in the images to be registered.”

“For Talairach transformation, the automated registration procedures of the Montreal Neurologic Institute ( Collins et al 1994 ) were used to compute a transformation matrix from the high-resolution 3D sagittal MRI images (free documentation and software are available at ftp://ftp.bic.mni.mcgill.ca/pub/mni_ autoreg/).”

“Unlike the ubiquitous alignment of brains to the atlas of Talairach and Tournoux (1988) or to the collection of 305 normalized brains assembled by the Montreal Neurological Institute (Collins et al., 1994), ROI-AL optimizes regional alignment at the expense of whole-brain alignment to increase the statistical power an…”

“, 1998), spatially registered to stereotaxic space (Collins et al., 1994), and masked to remove extra-cerebral voxels.”

“MRI data were rigidly aligned (three translations and rotations) to PET data in order to get information regarding total glucose metabolism in the hippocampus [32].”

“Finally, average across participants was achieved by first normalizing individual data through linear registration to the Montreal Neurological Institute template (MNI305) using an in-house algorithm (Collins, Neelin, Peters, & Evans, 1994).”

“For the CIVET analysis, images were registered into a standardized stereotaxic space by means of a linear transformation and corrected for intensity non-uniformities [Collins et al., 1994; Sled et al., 1998].”

“Spatial normalization to a stereotaxic space was performed using a nine-parameter linear registration [Collins et al., 1994].”

“PET and MRI data of each subject were individually co-registered (Collins et al., 1994) and the matched PET-MRI data sets were re-sampled in the standardized stereotaxic coordinate system of Talairach and Tournoux (1988).”

“uk/fsl, FMRIB, Oxford) to coregister the b0 image in diffusion MRI space to the T1-weighted structural image and then to the T1 template of ICBM152 in MNI space [73].”

“…which were both registered to the digitized MRI available from the Brain Imaging Centre, Montreal Neurologic Institute [MNI305; Evans et al., 1993; Collins et al., 1994].3 According to the digitized MNI probability atlases, the solution space was restricted to cortical gray matter and…”

“Similar to other related studies (e.g., Golestani et al. 2007), these images were normalized to a standard stereotaxic space using only linear transformations to avoid warping of pertinent brain structures (Collins et al. 1994).”

“Our atlas transformation strategy is similar to that described by Collins and colleagues (Collins et al., 1994).”

“Preprocessing of the data used SPM5 realignment, reslicing with sinc interpolation, normalization to the MNI (Montreal Neurological Institute) coordinate system (Collins et al., 1994), and spatial smoothing with a 6 mm full-width at half maximum isotropic Gaussian kernel.”

“5-T system and transformed these images into standardized stereotaxic space using an automatic feature-matching algorithm (Collins et al. 1994).”

“The source-space is normalized to the Montreal Neurological Institute's probabilistic MRI anatomical template (i.e., MNI305; Evans et al., 1993; Collins et al., 1994), restricted to the cerebral gray matter, hippocampi, and amygdalae on a 7-mm3 isotropic lattice.”

“Most commonly, these tables of coordinates refer to locations in Talairach [19] or MNI standard spaces [20].”

“Preprocessing of the data used SPM5 realignment and unwarping, reslicing with sinc interpolation, normalization to the Montreal Neurological Institute coordinate system (Collins et al. 1994), and spatial smoothing with a 6-mm full width at half maximum isotropic Gaussian kernel.”

“All individual maps were then spatially normalized into CMNITalairach space using a linear transformation (Collins et al., 1994).”

“These consist of data which are transformed into some ''standard brain space'', for example the co-ordinate system specified by Talairach and Tournoux [11].”

“The high-resolution anatomic scan was coregistered to the mean of the realigned (functional) images and then spatially normalized to the T1-weighted Montreal Neurological Institute (MNI single-subject template [Collins et al., 1994; Evans et al., 1992; Holmes et al., 1998] using linear Figure 2.”

“, 2001] with a 9-parameter (9P) transformation (three translations, three rotations, three scales) using the Minctracc algorithm [Collins et al., 1994].”

“Images were registered into a standardized stereotaxic space using a linear transformation (Collins et al., 1994).”

“…et al., 1999; Thiran and several parts of the brain to be removed on the image, Butz, 2000), and normalized cross-correlation (e.g. Bajcsy creating black holes, and thus sudden discontinuities at and Kovacic, 1989; Collins et al., 1994; Rexilius et al., some locations in the image sequence.”

“Group statistical maps were generated by first normalizing the SAM functional volumes to standard MNI space (Collins et al., 1994) and then combining these volumes across subjects for each time window and frequency band.”

“Studies were included only if they investigated unmedicated healthy children or adults, used PET and fMRI scanning, reported the coordinates of activations in the space of the MNI template (Collins et al., 1994) or the atlas of Talairach and Tournoux (1988).”

“, 2001) with a 9-parameter (9P) transformation (3 translations, 3 rotations, 3 scales) using the Minctracc algorithm (Collins et al., 1994).”

“The template brain also contained information concerning anatomical boundaries, which were “projected” onto each subject's brain in native space using the corresponding deformation field, whichwas then fine-tuned by combining it with the tissue classification map (Collins et al., 1994, 1995, 1999).”

“Images were then linearly registered into a standardized stereotaxic space based on the Talairachatlas (Collins et al.,1994; TalairachandTournoux,1988).”

“Data from each run were transformed ( Collins, Neelin, Peters, & Evans, 1994 ) to a standard coordinate system (Talairach & Tournoux, 1988) with a final resolution of 2.5 mm3, and the seven runs were concatenated into a”

“aMontreal Neurological Institute (MNI) standard space (Collins et al., 1994). bAccording to Atlas of Schmahmann (Schmahmann et al., 2000).”

“Most of the efforts define a preferred origin modeling deformations delasticallyT based on small deformation vector maps on the dense volumes; vector mappings restricted to the cortical manifold are being computed as well (Cachier et al., 2001; Christensen, 1999; Christensen et al., 1996a,b; Collins et al., 1994; Dava…”

“Non-linear registration of 3D geometric atlases onto individual datasets has been used to support automated brain structure labeling for hippocampal morphometry [91], analysis of subcortical structure volumes in schizophrenia [92], estimation of structural variation in normal and diseased populations [38,39,93,94], an…”

“In order to measure the cortical thickness, the native MR images were first registered into stereotaxic space (Talairach and Tournoux, 1988) using a 9-parameter linear transformation (Collins et al., 1994).”

“Subsequently, all images were transformed into standard proportional stereotaxic space (Talairach and Tournoux, 1988) using in-house dedicated software (Collins et al., 1994).”

“The ICBM152 was generated from 152 T1-weighted brain volumes. A hierarchical fitting strategy with a minimum step size of 2 mm was used for this registration procedure.”

“This procedure uses an automatic, multi-scale feature-matching algorithm (Collins et al., 1994) that performs a 9-parameter linear transformation to match each brain to a template brain.”

“original) MR images to standardized MNI-Talairach space based on the ICBM152 data set (Talairach and Tournoux 1988; Collins et al. 1994; Mazziotta et al. 1995).”

“The latter images were nonlinearly coregistered (19) to the ICBM-452 T1 5th Order Polynomial Warps Atlas (20).”

“Going further, most of the functional studies involving fMRI have a prerequisite deformable registration (6) towards a common reference (often the Talairach space).”

“The CBF images were reconstructed with a 14mm Hanning filter, normalized for differences in global CBF, coregistered with the individual MRIs and transformed into stereotactic space(12) by means of an automated featurematching algorithm.(13) Data were analyzed to generate t statistic subtraction maps of significant ch…”

“To correct for differences in head size and to enable the automation of the tissue classification process, images were normalized to MNI-Talairach space, using the Collins et al. (1994) methods and resampled to 1.0 mm isotropic voxels.”

“MR scans were linearly transformed into stereotaxic space (Talairach and Tournoux, 1988), using an automatized feature-matching algorithm (Collins et al., 1994) and viewed using an interactive threedimensional imaging software package that allowed simultaneous inspection in the coronal, horizontal,…”

“Briefly, the regions defined using the AAL template (Tzourio-Mazoyer et al., 2002) were warped from MNI space to the diffusion MRI native space using the FLIRT tool from the FSL toolbox (www.fmrib.ox.ac.uk/fsl, FMRIB, Oxford) (Collins et al., 1994).”

“Table 5 provides the average coordinates (n = 20 volunteers) of the identified hypothalamic areas, nuclei and white matter fascicles in anatomical MNI space.”

“Third, a linear (nine parameter) transformation estimated with the mritotal tool from the MINC mni_autoreg software package (Collins et al., 1994) was applied to achieve intersubject spatial alignment to the Talairach-like ICBM152 stereotaxic space.”

“Scans were first registered to the ICBM 152 template and corrected for radiofrequency intensity nonuniformities (Collins et al., 1994; Sled et al., 1998).”

“This procedure includes the removal of all extracranial tissue and the cerebellum and has been validated before (Collins et al., 1994).”

“The functional images were low pass filtered (6-mm FWHM Gaussian kernel) and transformed into stereotaxic space (Collins et al., 1994).”

“…of the data used SPM2 realignment, reslicing with sinc interpolation, normalization to the Montreal Neurological Institute coordinate system (Collins et al., 1994) used throughout this study, and spatial smoothing with a 8 mm full width at half maximum isotropic Gaussian kernel and global…”

“All images were resampled into stereotaxic space (Collins et al., 1994).”

“2) Linear registration of the native MRI into a Talairach like stereotaxic space based on the ICBM152 template (Collins et al., 1994; Mazziotta et al., 2001, 1995; Talairach et al., 1988).”

“Next, these maps were smoothed (FWHM 8 mm) and normalised into standard CMNI space (Collins et al. 1994)”

“, 2002) to co-register the b0 image in diffusion MRI space to the T1-weighted structural image and then to the T1 template of ICBM152 in MNI space (Collins et al., 1994).”

“Because FreeSurfer uses the automated MNI Talairach transformation (Collins et al., 1994), we transformed these coordinates to standard Talairach space with Matthew Brett's method (http://imaging.mrc-cbu.cam.ac.uk/imaging/MniTalairach ).”

“For the group analysis, all volumes were registered to the Montreal average volumetric data set aligned on the Talairach stereotactic coordinate system (Collins et al., 1994).”

“5 T, T1-weighted images, 1-mm slice thickness) of every subject’s brain was acquired and transformed into standardized stereotaxic space using the algorithm of Collins et al.(25) The coordinates selected for right DLPFC (x 5 40, y 5 32, and z 5 30) were similar to those used in our previous studies.”

“…individuals, all scans were linearly registered to the stereotactic space defined by the International Consortium for Brain Mapping (ICBM-53) (Mazziotta et al., 2001) with a 9-parameter (9P) transformation (3 translations, 3 rotations, 3 scales) using the Minctracc algorithm (Collins et al., 1994).”

“Initial processing included computation of the Talairach transformation matrix using tools developed at the Montreal Neurological Institute [Collins et al., 1994; Talairach and Tournoux, 1988] and intensity normalization to correct for variability in the signal due to magnetic field inhomogeneities and artifacts [Dale…”

“Therefore, prior to sampling the images the different image modalities are aligned to a common stereotaxic space so as to achieve this spatial correlation between brain volumes (Collins et al., 1994).”

“The resulting registered MRIs were resampled and averaged (Collins et al., 1994; Kovacevic et al., 2004).”

“The MRIs were spatially normalized into the Montreal Neurological Institute (MNI) stereotaxic space using a global affine transform [11], which gives the 3-D alignment of brain.”

“First, we transformed the subject’s MRI into standardized space (Talairach and Tournoux, 1988; Collins et al., 1994).”

“Images were automatically registered into stereotaxic space to adjust for differences in total brain volume and brain orientation.(11) Each image underwent automated correction for intensity non-uniformity and intensity standardization.”

“Postprocessing of functional images including3-Dmotioncorrection, slice timecorrection, normalization into MNI (Montreal Neurological Institute) space (Collins et al., 1994), and spatial smoothing (10 mm FWHM) relied on SPM99 (Welcome Department of Cognitive Neurology, London, UK; http//: www.”

“Hierarchical nine-parameter linear registration based on intensity cross-correlation as a similarity measure is performed between each native T1-weighted (T1w) volume (Ni) and the ICBM152 template (P) (Collins et al., 1994).”

“Anatomical normalization to the Montreal Neurological Institute (MNI) standard template [42] was performed using 12-parameter affine transformation.”