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

“This image was linearly registered (9 parameters using cross correlation) to the International Consortium for Brain Mapping (ICBM) average brain space (Evans et al., 1993) using the mritotal automatic stereotaxic registration procedure (Collins et al., 1994).”

“…were registered to the spatially normalized, T1-weighted MR single-subject brain of the Montreal Neurological Institute (MNI; Evans et al., 1993; Collins et al., 1994; Holmes et al., 1998) by using an affine, linear transformation and an 54 H.-J. CHOI ET AL. elastic, nonlinear algorithm…”

“BOLD signal images were spatially smoothed (6-mm Gaussian kernel), corrected for motion, and linearly transformed into standard stereotaxic space (Talairach & Tournoux, 1988) using inhouse software ( Collins, Neelin, Peters, & Evans, 1994 ).”

“…then converted to the MINC file format (http://www.bic.mni.mcgill.ca/ServicesSoftware/HomePage), corrected for RF inhomogeneity non-uniformity (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).”

“Both the head model and the electrode coordinates were registered to the digitized MRI available from the Brain Imaging Centre, Montreal Neurologic Institute (MNI305; Collins, Neelin, Peters, & Evans, 1994; Evans et al., 1993).”

“VBM analyses were performed with software developed at the Montreal Neurological Institute, as previously described (Paus et al., 1999; Pruessner et al., 2001; Watkins et al., 2001; Golestani et al., 2002; Tisserand et al., 2002).”

“, 1998), pairwise (between a brain and each other brain in the dataset) affine registration to create a reference template, and a 12-step nonlinear registration of each brain to that template, which was updated at each step (Collins et al., 1994; Kovacevic et al., 2005).”

“The images were assessed for head motion and realigned to the first frame using AFNI (Cox, 1996).”

“Each matched MRI/PET data set was then linearly resampled into the standardized stereotaxic coordinate system of Talairach and Tournoux (1988) via an automated feature-matching algorithm (Collins et al., 1994).”

“While studies investigating the usefulness of medial temporal lobe atrophy in the diagnosis of AD are ongoing (Coupe et al., 2012; Cuingnet et al., 2011; Jack et al., 2011; Wolz et al., 2011), the assessment of patterns of cortical thinning across the cerebrummay aid to increase the specificity of…”

“Colin27 was selected as the atlas as it is normalized to MNI space and has stable anatomical features so that it can be stably segmented into tissues (Collins et al., 1994).”

“, 1993) and transformed into standardized stereotaxic space (Talairach & Tournoux, 1988) by means of an automated feature-matching algorithm (Collins et al., 1994).”

“, 1993) and transformed into stereotaxic space (Talairach and Tournoux, 1988) by means of an automated feature-matching algorithm (Collins et al., 1994).”

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

“We listed for each brain site the corresponding Brodmann’s areas and MNI coordinates.”

“Here pi(i = 1, K, Ng) are the probabilities of the grid points for belonging to the gray matter and were derived from the average Probabilistic MRI Atlas (PMA) produced by the Montreal Neurological Institute (Collins et al., 1994; Evans et al., 1993, 1994; Mazziotta et al., 1995).”

“This image was linearly registered (nine parameters using cross correlation) to the International Consortium for Brain Mapping (ICBM) average brain space [8] using the mritotal automatic stereotaxic registration procedure [9].”

“In addition to the MRI-to-native transform, a 12-parameter affine transform (M2) from the individual native space to the MNI reference-space defined by the MNI-305 template (Evans et al., 1993; Collins et al., 1994) was calculated for each individual using the ‘Normalise’ function (Friston et al., 1995) in SPM8.”

“Group statistical maps for each frequency band were generated by first normalising the SAM functional volumes to MNI standard space [43] and then combining these volumes across participants for each time window and frequency band.”

“…sagittal images with an in-plane resolution of 0.98 mm, extended dynamic range, 2563 256 matrix, 1 nexus, TE5 minimum, Flip Angle 5 20°) were obtained for each subject and were used for transformation of PET data into standard stereotaxic space (Collins et al. 1994; Talairach and Tournoux 1988).”

“…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 and Tournoux, 1988).”

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

“Cortical surfaces were transformed into PET native space using the transformation matrix from a rigid body co-registration between PET and T1 weighted images [20].”

“The tissue-classified white matter and grey matter maps were smoothed using a Gaussian smoothing kernel of 10-mm full width at half-maximum, resulting in three-dimensional maps of white matter and grey matter concentration.”

“…acquisition perpendicular to the long axis of the hippocampus, TR 28 ms, TE 6 ms, FOV 220 mm, 256 · 192 matrix, slice thickness 1.5 mm. MRI scans were rotated and globally scaled to match the ICBM53 average brain imaging template using a 9-parameter linear transformation (Collins et al., 1994).”

“As part of this process, we spatially normalized the CT image of each subject's brain to a CT template brain image in Montreal Neurological Institute spac”

“We have combined preprocessing steps (image intensity non-uniformity correction [24]), linear registration (animal in linear mode [25]) and resampling into stereotaxic space, cortical surface extraction (Multiple surface deformation or msd [26,27]), tissue classification (insect [28]), and non-linear registration (ani…”

“Transformation matrices to align the surface-coil anatomical scans to the head-coil anatomical scans were calculated using an automated script combining correction for intensity gradient (Sled et al. 1998) and intra-subject registration (Collins et al. 1994; Maes et al. 1997).”

“The CT image of each brain was spatially normalized to a CT template brain image in MNI space (Collins et al., 1994).”

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“Handedness was assessed using the Edinburgh handedness inventory (Oldfield, 1971).”

“This average was constructed to create an adult comparison template similar to the ages of the MNI and ICBM templates (Collins et al., 1994; Evans et al., 1993, 1993; Joshi et al., 2004; Mazziotta et al., 2001).”

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

“The MNI/ICBM-152 average brain was used as the standard stereotaxic space template in group analyses [33,34,35].”

“…images were registered to MNI space using the MNI152-2009c template, in two steps: (1) A hierarchical nine-parameter linear registration was computed between native MRI images and the template by maximizing the cross correlation of intensities as the similarity measure (Collins et al., 1994).”

“, 1993) and automatically resampled (Collins et al., 1994) to fit the standardized stereotaxic space of Talairach and Tournoux (1988) as defined by the MNI 305 template.”

“They were normalized to a right/left symmetric template of standard stereotaxic space using only linear transformations to avoid warping of pertinent brain structures (Collins et al., 1994).”

“…of functional images included motion correction, unwarping by use of a static field map, slice time correction to the middle slice, normalization into MNI space (Montreal Neurological Institute, Collins et al., 1994), and spatial smoothing with a Gaussian Filter (10 mm full width half maximum).”

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

“…f e i S f p e a c T i t c w c c a a a W T t B s a i i o F i c r R t t A a s p ( t i t f w n c H 1 i t v e c C a C ( s 2 s T a c b s w s g w t t q d c s t ( w s i t s m ( t tereotaxic coordinate system of Talairach and Tournux (1988) via an automated feature-matching algoithm (Collins et al., 1994).”

“The combined functional runs of each subject were then transformed to MNI305 space (Collins et al., 1994) using a function derived from transforming each individual subjects’ anatomical scan to MNI305 space.”

“brain MRI was co-registered with scaling (nine-parameter transformation) to the ICBM53 average brain template [13].”

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

“normalized to the Montreal Neurological Institute (MNI) single-subject template (Evans et al. 1992; Collins et al. 1994; Holmes et al. 1998) using linear proportions and a nonlinear sampling algorithm (Ashburner and Friston 2003a, 2003c).”

“4 constructed by averaging numerous individual MRI brains (Collins et al., 1994) share the same limitations.”

“Structural and functional images were spatially normalized into a standardized anatomical framework (Montreal Neurological Institute [MNI]-space; Collins et al. 1994) using the T1 template provided by the Medical Research Council--Cognition and Brain Sciences Unit in Cambridge, UK…”

“…EEG epochs were analyzed with LORETA, which used a three-shell spherical head model [Ary et al., 1981] registered to the MNI-305 brain atlas [Collins et al., 1994; Evans et al., 1993] from the Brain Imaging Centre of the Montreal Neurologic Institute (referred to here as MNI coordinate…”

“single MRI volume with the intensity average of 305 MRI brain volumes previously aligned into the standardized stereotaxic space (Collins et al., 1994). This resampling results in a volume of 160 axial slices with an in-plane matrix of 256 3 256 pixels. The thickness of the interpolated sagittal, axial and coronal sli…”

“Each participant’s daily anatomical and functional images were transformed into common Talairach and Tournoux stereotaxic space with an affine transformation to the ICBM 152 template (Collins et al., 1994).”

“BOLD signal images were smoothed using a 12 mm Gaussian kernel, corrected for motion and transformed into standard stereotaxic space using in-house software (Collins et al., 1994).”

“In-house software (Collins et al. 1994) was used in the preprocessing of the BOLD images.”

“The contrasts from the two runs for each subject were combined in a weighted average, transformed to a standardized space (MNI coordinates) using in-house software (Collins et al., 1994), and then entered into group maps (fixed effect).”

“…and transformed into the covariance (Sokal and Rohlf 1981), with subjects as a main effectstandardized stereotaxic space with an automatic feature-detection and the number of pulse-trains administered during the scan as aalgorithm (Collins et al. 1994); the MRIs (160 contiguous 1-mmcovariate.”

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

“Preprocessing comprised realignment, unwarping [41], slice time correction, and normalization into MNI space (Montreal Neurological Institute [42], resampled voxel size: 3 3 3 3 3 mm3).”

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

“(Collins et al. 1994), a conversion to Talairach space was carried out using the BrainMap software developed by the Research Imaging Institute, University of Texas Health Science Center San Antonio (Eickhoff et al.”

“In particular, use of spatial smoothing and/or averaging subjects in a common (linear) stereotaxic space (Collins et al., 1994; Talairach and Tournoux, 1988) will decrease the effective spatial resolution and thereby sacrifice the increased sensitivity and specificity.”

“Conversely, highdimensional warping algorithms (Christensen et al., 1993, 1996; Collins et al., 1994a; Rabbitt et al., 1995; Thirion, 1995; Davatzikos, 1996; Thompson and Toga, 1996a, Bro- Nielsen and Gramkow, 1996) can also be used to transfer all the information in a 3-”

“Next, each dataset was stereotaxically transformed using an affine transformation into the Talairach-like MNI coordinate system (Collins et al., 1994) and resampled onto a 1 mm isotropic grid using a tri-linear kernel.”

“The motion-corrected functional scans were registered to the Montreal Neurological Institute (MNI152) atlas (Collins et al., 1994) using FSL (FMRIB Software Library, www.”

“While volume-averaging techniques are simple and reliable [Collins et al., 1994], they suffer from a key limita-* tion.”

“The resulting effects and SD images were then linearly transformed into the standard proportional stereotaxic space of the MNI template (ICBM152) using the parameters of the anatomical MRI to template transformation, which were computed using a feature-matching algorithm (Collins et al., 1994).”

“Given the fact that subdural electrodes are positioned on the cortical surface, this method of group analysis should prove more accurate when compared to the standard volumetric-based analyses (Collins et al., 1994; Miller et al., 2007; Ritzl et al., 2007; Talairach and Tournoux, 1988).”

“…between ages 10 and 19 according to the definition of the World Health Organization), used fMRI scanning, involved non-emotional stimuli or tasks, and reported the coordinates of activations in the space of the MNI template [Collins et al., 1994] or the atlas of Talairach and Tournoux (1988).”

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