Templates - MRC CBU Imaging Wiki

Upload page content

You can upload content for the page named below. If you change the page name, you can also upload content for another page. If the page name is empty, we derive the page name from the file name.

File to load page content from
Page name
Comment
Type the missing letters from: Lodon is th capial of nglnd

location: Templates

SPM templates and other images...

This page is a copy of the templates help file in the SPM99 help system. It is copied here with the kind permission of John Ashburner.

/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.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 In this release, the single subject T1 has been replaced by a 152 subject average.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.img

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.

templates/T2.img

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.

templates/PD.img

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.

templates/EPI.img

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.img 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.img

Average of images from 12 subjects spatially normalized to a linear combination of T1.img, T2.img and PD.img 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.img and templates/Transm.img. 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.img

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.img

Average transmission image of 11 subjects. Template generated in similar way to PET.img.Subject numbers: 617 622 627 630 639 662 817 824 825 827 828.

templates/SPECT.img

The SPECT template was created by Leighton Barnden et al from the Department of Nuclear Medicine at the Queen Elizabeth Hospital in Adelaide and was used in their SPECT to MR coregistration validation. It is the mean of 22 normal female subjects. Each was scanned after injection of Tc-99m HMPAO on a triple head camera with ultra-high resolution fanbeam collimators using a 126-154keV (20%) photopeak and a 111-125 keV scatter window. After lower window scatter subtraction (1.5xscatter images after 2D Butterworth smooth with cutoff 0.25 cycles/cm, order 3.0) the photopeak projections were rebinned, pre-filtered (2D Butterworth smooth with cutoff 0.7 cycles/cm,order 6.0) and reconstructed using Filtered BackProjection. The SPECT tomograms were then coregistered to the subject's 3D T1 MR using AMIR. Parameters from SPM99b MR to MR Spatial Normalisation (affine + non-linear) were used to transform the SPECT images to SPM's standard anatomical space. The mean yielded the SPECT 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.img, apriori/white.img & apriori/csf.img

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.img

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.img, avg152T2.img & avg152PD.img

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.img, T2.img and PD.img.

canonical/single_subj_T1.img

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 -90:91 -126:91 -72:109, and voxel sizes of 2x2x2 mm.


From spm_templates.man - v2.6 John Ashburner 99/10/12n\