___ ____ __ __ / __)( _ \( \/ ) Statistical Parametric Mapping \__ \ )___/ ) ( The Wellcome Department of Cognitive Neurology (___/(__) (_/\/\_) SPM99: Example data sets Example SPM99 spatial manipulations of MoAEpilot example epoch (block) fMRI dataset ________________________________________________________________________ OVERVIEW These whole brain BOLD/EPI images were acquired on a modified 2T Siemens MAGNETOM Vision system. Each acquisition consisted of 64 contiguous slices (64x64x64 3mm x 3mm x 3mm voxels). Acquisition took 6.05s, with the scan to scan repeat time (RT) set arbitrarily to 7s. 96 acquisitions were made (RT=7s), in blocks of 6, giving 16 42s blocks. The condition for successive blocks alternated between rest and auditory stimulation, starting with rest. Auditory stimulation was bi-syllabic words presented binaurally at a rate of 60 per minute. The functional data starts at acquisiton 4, image fM00223_004. Due to T1 effects it is advisable to discard the first few scans (there were no "dummy" lead-in scans). A structural image was also acquired: sM00223_002 ---------------- This experiment was conducted by Geriant Rees under the direction of Karl Friston and the FIL methods group. The purpose was to explore new equipment and techniques. As such it has not been formally written up, and is freely available for personal education and evaluation purposes. Those wishing to use these data for other purposes, including published evaluation of methods, should contact the methods group at the Wellcome Department of Cognitive Neurology. Thu May 13 10:18:03 BST 1999 ________________________________________________________________________ THIS EXAMPLE This file explains in a step by step manner a basic spatial preprocessing stream. (1) Realignment (2) Spatial normalisation (3) Spatial smoothing (*) ...plus some additional spatial processing techniques on the structural image ( To run the example analyses here you need analyze images ) ( fM00223_[004-099].{hdr,img} ) ( These are available from http://www.fil.ion.ucl.ac.uk/spm/data ) ________________________________________________________________________ THE DATA & SPM'99 SPATIAL PRE-PROCESSING fM00223_[004-099].{img,hdr} Analyze format functional images 64x64x64 3mmx3mmx3mm voxels, TR = 7 seconds Epochs of rest alternating with auditory stimulation (60 words/min) Epochs are 42 seconds long (6TR), sequence begins with a rest epoch ---------------- rfM00223_004.{img,hdr} & meanfM00223_004.{img,hdr} Realigned functional images All 96 images were realigned to the first (rfM00223_004) To REALIGN with SPM99: Press in the upper left SPM window 'Number of subjects' - 1 'Num Sessions for subject 1' - 1 Select all fM00223_004.{img} and press 'Done' Pull down menu - select 'Coregister and Reslice' Pull down menu - select 'Sinc Interpolation' Pull down menu - select 'Create All Images + Mean image' 'Adjust sampling errors' - no Output: r* files - realigned images fM00223_[005-099].mat - affine transformation matrices mapping for each image, mapping from voxel co-ordinates to the mm co-ordinates, such that in mm co-ordinates, each image is in alignment with the first - (these are written alongside the input images) spm99.ps - printout of realignment parameters meanr* image - mean realigned image ---------------- nrfM00223_004.{img,hdr} & meanfM00223_004_sn3d.mat Normalised realigned functional images Parameters were generated from the mean realigned functional image, normalised to the EPI template. To NORMALISE with SPM99: Press Pull down menu - 'Determine Parameters and Write Normalised' Number of subjects - 1 'Image to determine parameters' - meanrM00223_004.img 'Images to write Normalised' - meanfM00223_004.img AND all rfM00223.{img} 'Template image' - EPI.img Pull down menu - 'Bilinear interpolation' Output: nr* files - the spatially normalized images *_sn3d.mat - the estimated parameters describing the spatial transformation spm99.ps - printout of spatial normalisation parameters ---------------- snrfM00223_004.{img,hdr} Smoothed normalised realigned images Smoothed with an isotropic Gaussian kernel with FWHM = 6mm These images are suitable for voxel-by-voxel statistical analysis ---------------- sM00223/nsM00223 Contains the normalized structural image normalized using meanfM00223_004_sn3d.mat with the default bounding box, 1mm isotropic resolution and trilinear interpolation. Results can be superimposed on this image via "Slices" and "Sections". Operations: Press Pull down menu - 'Spatial Normalization' Pull down menu - 'Defaults for Writing Normalized' Pull down menu - '-78:78 -112:76 -50:85 (Default)' Pull down menu - '1 1 1' Press Pull down menu - 'Write Normalized Only' '# Subjects' - '1' 'subj 1 - Normalisation parameter set' - meanfM00223_004_sn3d.mat 'subj 1 - Images to write normalised' - sM00223_002.img Pull down menu - 'Bilinear Interpolation' Press Pull down menu - 'Reset All' Output: nsM00223_002.img - the normalized image ---------------- sM00223/nsM00223_seg Data created using the Segment button. Options include lots of nonuniformity correction (saving the corrected image) and stating that the image is spatially normalized. Operations: Press 'number of subjects' - '1' 'Select MRI(s) for subject 1' - nsM00223_002.img 'Are they spatially normalized?' - 'yes' Pull down menu - 'Lots of inhomogeneity correction' Pull down menu - 'Save inhomogeneity corrected images' Outputs: corr_nsM00223_002.img Intensity nonuniformity corrected image. nsM00223_002_seg1.img Grey matter segment nsM00223_002_seg2.img White matter segment nsM00223_002_seg3.img CSF segment spm99.ps Display of segmented images ---------------- sM00223/brain_nsM00223 Output from the XBrain button after entering nsM00223_002_seg1.img and nsM00223_002_seg2.img as inputs. Operations: Press 'Select gray and white matter images' - nsM00223_002_seg1.img - nsM00223_002_seg2.img Pull down menu - 'Save Extracted Brain and Rendering' Outputs: brain_nsM00223_002.img The extracted brain. render_nsM00223_002.mat A render*.mat file that can be used to render results on to. spm99.ps Rendering of extracted brain Directory also includes renderings.tiff which was created via the rendering button and printing using: print -dtiff -noui renderings.tiff ________________________________________________________________________ Geriant Rees, Andrew Holmes & John Ashburner Thu May 13 15:39:19 BST 1999