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%
% SPM templates and other images...
% _______________________________________________________________________
%
% /TEMPLATES/ DIRECTORY
% This directory contains images for use as templates for spatially
% normalizing images to the same stereotactic space. The space is
% based upon the Talairach system, but does not make assumptions
% about brain symmetry, and also includes the cerebellum. The
% stereotactic space is based on 152 brains from Montréal
% Neurological Institute, and will eventually be replaced in due
% course by a 450-brain version for the entire ICBM consortium.
%
% Subject details:
% Age: mean=25.0, median=24.0, mode=19.0, stdev=4.9, range=18-44
% Sex: female=66 (43.4%), male=86 (56.6%)
% Handedness: right=129 (90.2%), left=14 (9.8%), unknown=9
%
% In SPM96, we released a single subject brain for use as a
% template. Although the MNI gave us this data, they never
% recommended that this brain should be used as a stereotaxic
% standard. This is something that we at the FIL chose to do.
% The official standard for the ICBM stereotactic space is
% the MNI305 brain - which this was not. This brain has many
% merits for simulation but it suffers from all the single
% brain criticisms that apply to Talairach. In this release, the
% single subject T1 has been replaced by a 152 subject average. We
% (in the SPM group) chose to use the 152 subject T1-weighted
% average rather than the 305 brain average because there are also
% T2-, and PD-weighted images of the same subjects. This should
% allow much more flexibility in the range of different MR
% contrasts that can be spatially normalized to the same
% stereotaxic space (by registering to a linear combination of
% template images).
% _______________________________________________________________________
%
% templates/T1.mnc
% ----------------
% Image derived from icbm_avg_152_t1_tal_lin.mnc, which was
% originally supplied by Alan Evans, MNI, Canada (ICBM, NIH P-20
% project, Principal Investigator John Mazziotta). The image was
% reduced to 2mm isotropic resolution and smoothed with an 8mm FWHM
% Gaussian filter.
% Sequence Details: Spoiled FLASH sequence, TE=10, TR=18, FA=30.
%
% templates/T2.mnc
% ----------------
% Image derived from icbm_avg_152_t2_tal_lin.mnc, which was
% originally supplied by Alan Evans, MNI, Canada (ICBM, NIH P-20
% project, Principal Investigator John Mazziotta). The image was
% reduced to 2mm isotropic resolution and smoothed with an 8mm FWHM
% Gaussian filter.
% Sequence Details: Dual echo spin echo, TE=120ms, TR=3300ms, FA=90.
%
% templates/PD.mnc
% ----------------
% Image derived from icbm_avg_152_pd_tal_lin.mnc, which was
% originally supplied by Alan Evans, MNI, Canada (ICBM, NIH P-20
% project, Principal Investigator John Mazziotta). The image was
% reduced to 2mm isotropic resolution and smoothed with an 8mm FWHM
% Gaussian filter.
% Sequence Details: Dual echo spin echo, TE=35ms, TR=3300ms, FA=90.
%
% templates/EPI.mnc
% -------------
% The image was created from the average of 13 subjects mean fMRI
% images. The grey matter was segmented from the original images
% using the segmentation in SPM. This was spatially normalized by
% matching to the apriori/gray.mnc file using a 12-parameter
% affine registration, followed by a nonlinear registration
% (using the 7x8x7 lowest frequency DCT coefficients, and
% heavy regularization). These estimated parameters were
% then applied to the functional images, which were then averaged
% and smoothed with an 8mm FWHM Gaussian kernel. The EPI images
% were acquired on a Siemens Vision scanner working at 2T. The
% original resolution of the images was an isotropic 3mm (1.8mm
% slice thickness + 1.2mm gap). A gradient echo sequence was
% used with TE@ms and a TR of about 3s. Inter echo spacing is 800
% micro seconds with a sinusoidal gradient waveform and
% nonlinear ADC sampling. Nyquist ghost suppression is achieved
% using a 2 echo reference scan (only 0th and 1st order phase
% correction implemented). Maximum gradient strength is approx.
% 20mT/m.
% Subject numbers: 1285 1286 1287 1291 1314 1379 1381 1399 1479
% 1514 1589 1644 1646.
%
% templates/filT1.mnc
% -------------------
% Average of images from 12 subjects spatially normalized to a
% linear combination of T1.mnc, T2.mnc and PD.mnc using a 12-
% parameter affine transformation, followed by a nonlinear
% registration (using the 7x8x7 lowest frequency DCT coefficients,
% and medium regularization). Images acquired on a 2 Tesla Siemens
% Magnetom Vision scanner at the FIL, using a T1 weighted MPRAGE
% sequence (TRel=9.7, TEch=4, TInv=600, Fang=12, SThi=1.5). Same
% subjects were also used for templates/PET.mnc and
% templates/Transm.mnc. This image is included as it has the
% same contrast as the T1 weighted images from the FIL (so we can
% use it for spatial normalization).
% Subject numbers: 617 622 627 630 639 662 817 824 825 826 827 828.
%
% templates/PET.mnc
% -----------------
% Average of images from 12 subjects spatially normalized to ICBM.
% Images were first registered to the T1-weighted MR images, and
% spatially transformed using the same transformation. Images were
% acquired on a Siemens ECAT HR+ at the FIL, using Oxygen-15
% labeled water. Averaged images smoothed using 8mm FWHM Gaussian.
% Subject numbers: 617 622 627 630 639 662 817 824 825 826 827 828.
%
% templates/Transm.mnc
% --------------------
% Average transmission image of 11 subjects. Template generated in
% similar way to PET.mnc.
% Subject numbers: 617 622 627 630 639 662 817 824 825 827 828.
%
% templates/SPECT.mnc
% -------------------
% The SPECT template was created by Leighton Barnden et al, and is
% the mean of 75 normal subjects consisting of 39 Females (18-74Y)
% and 36 Males(20-81Y). Mean (SD) ages were Females 45.2 (15.4)
% and Males 44.6 (16.9). The numbers of subjects in sequential 5
% year age intervals starting at 16-20 were:
% Female: 3,4,3,0,1,7,6,3,6,3,2,1,0,0
% Male: 2,4,4,2,2,5,4,4,4,1,1,0,2,1
%
% All 75 subjects were acquired after injection of 500 MBq Tc-99m
% HMPAO on a triple head Philips Irix camera with high resolution
% parallel hole collimators. The photopeak window was 20% wide
% centered on 140 keV. The lower scatter window was half the
% photopeak width (111-125 keV). The scatter projections were
% smoothed with a Butterworth filter (cutoff 0.3 cycles/pixel,
% order 3.0). Pixel size was 3.47 mm. The smoothed scatter images
% were multiplied by 1.3 before subtraction from the photopeak
% projections. The resulting projections were smoothed with a
% Butterworth filter (cutoff 0.5*cycles/pixel, order 5.0) before
% filtered backprojection reconstruction. Uniform attenuation
% correction was performed with an attenuation coefficient of
% 0.12/cm (0.10/cm without scatter subtraction) within elliptical
% edges manually fitted to sections 2 pixels thick. Scatter has
% been subtracted from the images.
%
% The 'raw' transaxial sections were first edited to remove hot
% facial activity and yield e* files. Two passes of Spatial
% Normalisation were performed. The first was affine spatial
% normalisation to the SPM99 SPECT template after a 10 mm fwhm
% Gaussian smooth to yield nse*. The resulting parameters were also
% applied to the edited 'raw' sections to yield ne*. The mean of
% ne*, the normalised edited 'raw' sections, yielded the first
% estimate of the template. The spatial normalisation was then
% repeated to this first estimate template with nse* for parameter
% estimation using the non-linear method with 3x4x3 basis functions
% and masking with -/spm99/apriori/brainmask. The result was nnse*
% and nne*. The mean of nne* produced the final template.
%
% _______________________________________________________________________
% _______________________________________________________________________
% /APRIORI/ DIRECTORY
% Images in this directory represent the a priori probabilities of the
% voxels in a spatially normalized (9-parameter affine) brain image
% belonging to a particular tissue type.
% _______________________________________________________________________
%
% apriori/gray.mnc, apriori/white.mnc & apriori/csf.mnc
% ---------------- ----------------- ---------------
% Images supplied by Alan Evans, MNI, Canada (ICBM, NIH P-20
% project, Principal Investigator John Mazziotta). Original 1mm
% resolution images were icbm_avg_151_gm.mnc, icbm_avg_151_wm.mnc
% and icbm_avg_151_csf.mnc. Images were masked using
% average_305_mask_1mm.mnc, reduced to 2mm resolution and smoothed
% using an 8mm FWHM Gaussian. These images represent the
% probabilities of finding gray matter, white matter or cerebro-
% spinal fluid at any point. These volumes are used largely for
% image segmentation, although they can be used as templates for
% spatial normalization. 151 subjects were used to create each
% volume.
%
% apriori/brainmask
% -----------------
% Image derived from average_305_mask_1mm.mnc, which was originally
% supplied by Alan Evans, MNI, Canada (ICBM, NIH P-20 project,
% Principal Investigator John Mazziotta). The original image
% contained ones and zeros, where ones represented voxels that were
% part of the brain. It was subsequently smoothed using an 8mm
% FWHM Gaussian. This volume can be used to weight the spatial
% normalization so that the final solution is not influenced by
% voxels outside the brain.
%
% _______________________________________________________________________
% _______________________________________________________________________
% /CANONICAL/ DIRECTORY
% Images in this directory are intended for superimposing results
% on to.
% _______________________________________________________________________
%
% canonical/avg305T1.mnc
% ----------------------
% Image derived from norm_avg_305_mri_1mm.mnc, which was originally
% supplied by Alan Evans, MNI, Canada (ICBM, NIH P-20 project,
% Principal Investigator John Mazziotta). The image which defines
% the 305 space, and is intended for superimposing blobs on to.
% See: AC Evans, DL Collins, SR Mills, ED Brown, RL Kelly & TM
% Peters (1993) "3D statistical neuroanatomical models from 305 MRI
% volumes" Proc. IEEE-Nuclear Science Symposium and Medical Imaging
% Conference pages 1813-1817
%
% canonical/avg152T1.mnc, avg152T2.mnc & avg152PD.mnc
% ---------------------- ------------ ------------
% These images were derived from icbm_avg_152_t1_tal_lin.mnc,
% icbm_avg_152_t2_tal_lin.mnc and icbm_avg_152_pd_tal_lin.mnc res-
% pectively, which were originally supplied by Alan Evans, MNI,
% Canada (ICBM, NIH P-20 project, Principal Investigator John
% Mazziotta). See templates/T1.mnc, T2.mnc and PD.mnc.
%
% canonical/single_subj_T1.mnc
% ----------------------------
% A T1 weighted MRI of a representative male individual. This
% image was used for the T1 template supplied with SPM96. It
% should be noted that the MNI never recommended this brain as a
% stereotactic standard. This is something that we at the FIL
% chose to do. The official standard for the ICBM stereotactic
% space is the MNI305 brain - which this is not. This brain has
% many merits for simulation but it suffers from all the single
% brain criticisms that apply to Talairach.
% The same dataset was used for the brain simulation project at
% Montreal, details of which can be found at
% http://www.bic.mni.mcgill.ca/brainweb The simulator is described
% in: RK-S Kwan, AC Evans, GB Pike (1996) "An Extensible MRI
% Simulator for Post-Processing Evaluation" Visualization in
% Biomedical Computing (VBC'96). Lecture Notes in Computer
% Science, vol. 1131. Springer-Verlag. 135-140. and: DL Collins,
% AP Zijdenbos, V Kollokian, JG Sled, NJ Kabani, CJ Holmes, AC
% Evans (June 1998) "Design and Construction of a Realistic Digital
% Brain Phantom" IEEE Transactions on Medical Imaging, vol.17,
% No.3, p.463-468.
%
% =======================================================================
% Note that the images are in neurological orientation, whereby the
% left side of the image refers to the left side of the brain.
% This is contrary to the orientation that Analyze expects images
% to be in.
%
% To generate your own templates which fill the same volume, use a
% bounding box of -90:90 -126:90 -72:108, and voxel sizes of 2x2x2
% mm.
%
% =======================================================================
% The images were converted from the .img format of SPM99 to resolve
% confusion about left- versus right-handedness of co-ordinate systems.
% _______________________________________________________________________
% @(#)spm_templates.man 2.11 John Ashburner 03/05/09