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

“These templates were then digitized and non-linearly transformed into MNI space (Collins et al., 1994) using SPM5.”

“A brain template, or an atlas, provides a standard anatomical reference for individual or population based assessment of brain structure and function (Ashburner and Friston, 1999; Collins et al., 1994; Evans et al., 1993; Lancaster et al., 1999; Mazziotta et al., 2001; Toga and Thompson, 2001).”

“Each matched MRI– PET data set was then linearly resampled into a standardized stereotaxic coordinate system based on the Montreal Neurological Institute 305 target, a sample of 305 normal subjects, via an automated feature-matching algorithm (Collins et al., 1994), resulting in a normalized brain space similar to the…”

“To refine this model, all participants’ normalized b 0 images in raw image space were then nonlinearly registered to the linear model in a hierarchical fitting strategy using a step size of 8 mm (27).”

“In addition to published three-dimensional stereotactic coordinates in Talairach (Talairach and Tournoux, 1988) or MNI (Collins et al., 1994; Evans et al., 1993) space that both standardize and summarize the spatial locations of brain activations, BrainMap also archives extensive metadata that furnish formalized descr…”

“A high-resolution MRI (Siemens Sonata 1.5 T; T1-weighted images, 1 mm slice thickness) of each subject's brain was acquired and transformed into standardized stereotaxic space (Talairach and Tournoux, 1988) using automated feature-matching to the MNI template (Collins et al., 1994).”

“82) Age per decade, y, median (range) Overall 50 (18-88) 42 (18-88) 0.”

“The b = 1300 s/mm2 and b = 3000 s/mm2 datasets were acquired in separate sessions and were subsequently registered using semi-automatic techniques (Collins et al., 1994).”

“The resulting registered MRIs were resampled and averaged [71,72].”

“…subject were converted to the MINC file format (http://www.bic.mni.mcgill.ca/ServicesSoftware/MINC), corrected for RF intensity inhomogeneities (Sled et al., 1998) and the second and third T1 and T2 images were rigidly aligned to the first image volume of homologous contrast (Collins et al., 1994).”

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

“Before volumetric measurements, a transformation algorithm was used to align MRIs between time points.(11) First, for each patient the second (and for 2 patients, the third) MRI was aligned to the first MRI in the series using a 6-parameter rigid body transformation.”

“In recent years, the techniques for correction for interindividual differences in overall brain size and shape [8], and fully automated classification of MR images into gray matter, white matter, and CSF space [15] have been developed.”

“MR images were then linearly registered into a standardized stereotaxic space based on the Talairach atlas (Collins et al., 1994; Talairach and Tournoux, 1988).”

“All results were rendered on a structural image of a single subject’s brain in MNI-space ( Collins et al., 1994 ).”

“Preprocessing steps comprised realignment to the first volume of the time series, unwarping by use of a static field map (Andersson et al., 2001), normalization into MNI space (Montreal Neurological Institute, Collins et al., 1994), and spatial smoothing with an isotropic Gaussian filter (10 mm full width at half maxi…”

“…MRI (Siemens Sonata 1.5 T; T1-weighted images, 1 mm slice thickness) of each subject’s brain was acquired and transformed into standardized stereotaxic space (Talairach & Tournoux, 1998) using automated feature-matching to the Montreal Neurological Institute template (Collins et al., 1994).”

“PET frames were summed and co-registered with the MRI, and both images were transformed linearly into standardized stereotaxic space using the Montreal Neurological Institute template (Collins et al., 1994).”

“High-resolution MRI (GE Signa 1.5 T, T1-weighted images, 1 mm slice thickness) of each subject’s brain was acquired and transformed into standardized stereotaxic space (Talairach & Tournoux, 1988) using automated feature-matching to the MNI template (Collins et al., 1994).”

“22 In the present study, we applied this method of normalisation for callosal, hippocampal, and fornix volume measurements.”

“The 66 anatomic scans were normalized in the stereotactic space of the Montreal Neurological Institute template (Collins et al., 1994).”

“…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).”

“All registrations were performed using the mni_autoreg tools (Collins et al., 1994; Collins et al., 1995), which use an elastic registration algorithm (see Table 1 for the exact deformation schedule).”

“D cross-correlation approach to match the single MRI volume with the intensity average of 305 MRI brain volumes previously aligned in standardized stereotaxic space [33].”

“Stereotaxic Registration: this is accomplished by the registration of one of the image modalities to a stereotaxic target, using an automated 3D image registration technique [2].”

“D reconstructed, and warped to a common spatial reference system (Evans et al. 1993; Collins et al. 1994; Holmes et al. 1998) using a nonlinear, elastic transformation procedure (Henn et al. 1997; Mohlberg et al. 2002).”

“Afterwards, each matched PET/MRI dataset was linearly resampled into a standardized stereotaxic coordinate system based on theMNI305 target (a sample of 305 normal subjects) via an automated feature-matching algorithm (Collins et al., 1994), resulting in a normalized brain space similar to the Talairach and Tournoux a…”

“This space was defined using the average of 305 normal anatomical MRI scans (MNI 305 template) that were scaled linearly (Collins et al., 1994) to landmarkswithin the Talairach atlas and is more representative of the human population.”

“Higher-level group analysis, where the individual results were registered both to the high-resolution morphological MR images and to the MNI 152 standard image (Collins et al., 1994), was undertaken using FMRIB’s Local Analysis of Mixed Effects (FLAME,www.fmrib.ox.ac.uk/fsl).”

“T 1 images were registered to the ICBM152 nonlinear sixth generation template with a 12-parameter linear transformation (Collins et al., 1994; Grabner et al., 2006), RF inhomogeneity-corrected (Sled et al., 1998) and tissue-classified (Tohka et al., 2004; Zijdenbos et al., 1998).”

“All images were then transformed into Montreal Neurological Institute (MNI) space (Collins et al., 1994) and smoothed using 10-mm FWHM Gaussian smoothing kernel prior to statistical analysis.”

“The intensity-corrected volumes were transformed both linearly (12-parameter affine) and nonlinearly to the MNI space (Collins et al. 1994).”

“All images were translated into the normalized and standardized anatomical framework of Talairach and Tournoux (1988) using the averaged-brain template of the Montreal Neurological Institute (Collins et al., 1994).”

“Each participant’s runs were then averaged and transformed (Collins et al., 1994; Cox, 1996) to conform to the atlas of Talairach and Tournoux (1988) using a nine-parameter transformation matrix with a final voxel size of 2.”

“tracc.(21) Thereafter the performed transformations were applied on the manually defined parcellation, so it matched each subject (Figure 1, E-G).”

“In brief, native structural MR image of each subject was corrected for nonuniformity (Sled et al., 1998), linearly registered into stereotaxic space (Collins et al., 1994) and segmented into gray matter, white matter, cerebrospinal fluid (CSF) and background using a neural net classifier (Zijdenbos…”

“After an initial affine registration of the grey matter DARTEL templates to the tissue probability maps in Montreal Neurological Institute (MNI) space (Collins et al., 1994), non-linear warping was performed to the grey matter images to normalize them onto the MNI space.”

“Next, themean EPIwas computed for each participant and spatially normalized to the MNI single subject template (Collins et al., 1994) using the unified segmentation function of SPM8with a 2 × 2 × 2mm isotropic resolution.”

“The stereotaxic transformation algorithm used applies three linear scaling factors, one for each spatial dimension, to each MRI volume (Collins et al., 1994).”

“Each new brain is endowed with one of these coordinate systems through iconic spatial normalization, namely a deformation matching as far as possible the new brain macroscopic anatomy as revealed by magnetic resonance imaging (MRI) with a template anatomy [21], [30], [27], [39].”

“The MR images were co-registered to a standardized stereotactic atlas, namely the Talairach coordinate system (22) using an automatic algorithm (24), and the MR image of each subject was further co-registered to the PET image using the MINC-TRACC algorithm (24).”

“For the purpose of the group analysis, registration of low-resolution functional images to the corresponding high-resolution structural images was performed, followed by registration to a standard brain (MNI 152 template) (Collins et al., 1994).”

“FreeSurfer was utilized also for obtaining an affine transformation between the each individual brain and the MNI305 (Montreal Neurological Institute) average brain for group-level visualization [Collins et al., 1994].”

“002, FDR corrected), which were color coded and projected on a spatially normalized high-resolution MNI T1 template (Collins et al., 1994).”

“Image preprocessing was performed with either SPM99 or FLIRT (FMRIB Linear Registration Tool, Jenkinson and Smith, 2001) for realignment, reslicing with sinc interpolation and normalisation to MNI coordinate system (Collins et al., 1994).”

“based on the MNI 152 template (Collins et al., 1994) to account”

“Each 3D dataset was subsequently processed using the Brain Imaging Software Toolbox (McGill University (11)).”

“The anatomical image was then spatially normalized to the Montreal Neurological Institute (MNI) single-subject template (Evans et al., 1992; Collins et al., 1994; Holmes et al., 1998) using the “unified segmentation” function in SPM8.”

“Using the Display software (developed at McGill University) and the Montreal Neurological Institute standard brain [8], we measured the volumes for each of these regions of interest (ROI) by defining masks based on anatomical landmarks.”

“A hierarchical multiscale nonlinear fitting algorithm (Collins et al., 1994) was then applied to obtain the 3D deformation vector field that maps the individual T1-weighted images onto the template.”

“The transformation matrix for normalization to Montreal Neurological Institute (MNI) space [Collins et al., 1994] was calculated based on the structural T1-weighted 3-D data set of each subject and subsequently applied to the functional images.”

“FLIRT (FMRIB Centre, Oxford) was used to carry out intermodal registration and spatial normalization to the Montreal Neurological Institute (MNI)-brain (Collins et al, 1994).”

“A fully automated procedure was used to register anatomical reference volumes to the Montreal average volumetric data set aligned with the Talairach stereotaxic coordinate system (Collins et al., 1994).”

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

“INTRODUCTION HE advent of methods dedicated to the automatic analysis of large databases of MRI images of brain anatomy has raised a large interest in the neuroscience community [1], [2], [3], [4], [5], [6], [7], [8], [9], [10], [11], [12].”

“, 1998) and registered to the stereotaxic space (MNI152 template) (Collins et al., 1994) using a linear transformation.”

“Image preprocessing and callosal outlining Images were placed into the Talairach standard space using automated 6-parameter rigid-body transformations (Collins et al., 1994) to correct for differences in head alignment.”

“[6] Collins DL, Neelin P, Peters TM, Evans AC.”

“The registration was performed with MNI's autoreg program (Collins et al., 1994) using mutual information as the cost function.”

“Images underwent automated correction for intensity nonuniformity and intensity standardization and were linearly registered to the MNI152 template.(15,16) A single rater (N.”

“This stereotaxically based method of automated measures has been reported by others to be efficient and accurate for whole brain measures (40).”

“LORETA uses a three-shell spherical head model registered to a standardized stereotactic space available as digitized MRI data from the Brain Imaging Centre (Montreal Neurological Institute, MNI305) [49–51].”

“Before group statistical maps for each contrast of interest were generated, in-house software was used to linearly transform anatomical and functional images from each subject into standard MNI/Talairach stereotaxic coordinate space, using the MNI 305 template (Collins et al., 1994; Talairach & Tournoux, 1988).”

“To allow intersubject analysis, images were normalized to the Montreal Neurological Institute (MNI) standard space ( Collins, Neelin, Peters, & Evans, 1994 ) using the mean of the 468 functional images.”

“Briefly, each scan was first registered using a rigid body (lsq6) transformation to the prior model (Collins et al., 1994).”

“…for magnetic field nonuniformities, normalized for intensity, and linearly registered to ICBM152 standard template in the stereotaxic space [Collins et al., 1994], using a software developed at the McConnel Brain Imaging Centre (Montreal Neurological Institute, McGill University, Montreal,…”

“, 2009), the high-resolution MRI (GE 3 T, T1-weighted images, 1 mm slice thickness) of each subject’s brain was transformed into standardized stereotaxic space (Talairach and Tournoux, 1988) using non-linear automated featurematching to the Montreal Neurological Institute (MNI) template (Collins et al., 1994).”

“Inspection of the video recordings indicated that subjects did not systematically saccade towards the targets on one or the other side (these were located at 25 of eccentricity) and that they were following the instruction to maintain central fixation.”