Advanced Event-related fMRI Example Data Set
============================================
Repetition priming for famous and nonfamous faces
Created R. Henson 8/7/00
WDCN & ICN, UCL
[log in to unmask]
Modified for SPM2 by R. Henson 13/5/03
One subject's data from Henson et al. (2002) Cerebral Cortex -
FOR TEACHING PURPOSES ONLY (to illustrate facilities of SPM) -
PLEASE DO NOT CITE WITHOUT PERMISSION
Experiment
----------
2x2 factorial event-related fMRI
One session (one subject)
(Famous vs. Nonfamous) x (1st vs 2nd presentation) of faces against
baseline of chequerboard
2 presentations of 26 Famous and 26 Nonfamous Greyscale photographs,
for 0.5s, randomly intermixed, for fame judgment task (one of two
right finger key presses).
Parameteric factor "lag" = number of faces intervening between
repetition of a specific face + 1
Minimal SOA=4.5s, with probability 2/3 (ie 1/3 null events)
Continuous EPI (TE=40ms,TR=2s) 24 descending slices (64x64 3x3mm2),
3mm thick, 1.5mm gap
Following images are in the Data directory...
sM03953_0005_*.{img,hdr,mat}
------------------------
351 Analyze format functional images (*img contain data, *hdr is Analyze header)
64x64x24 3mmx3mmx4.5mm voxels
< View images with button on main SPM window - Note orbitofrontal
and inferior temporal drop-out and ghosting (Effects:brighten if necessary) >
usM03953_0005_*.{img,hdr,mat}
-----------------------------
Coregister all images to first, and then unwarp and reslice
using sinc interpolation (*mat files contain orientation information)
Type:
Select in the upper left SPM window
'Number of subjects' - 1
'Num Sessions for subject 1' - 1
Select all 351 sM03953_0005_*.{img} and press 'Done'
Pull down menu - 'Model field changes w.r.t'- select 'Pitch & Roll'
Pull down menu - select 'Create what?' - select 'All images + mean'
Output:
u* resliced, unwarped files
mean* mean of resliced files (for normalisation)
rp_sM03953_0005_0006.txt
movement parameters (6x351 values)
spm2.ps
graphical output of translations and rotations
ausM03953_0005_* .{img,hdr,mat}
-------------------------------
351 functional images temporally realigned to middle slice 12 (of 24)
using sinc interpolation (top slice = 24 = acquired first)
Type:
Press in the upper middle SPM window
'Number of subjects/sessions' - 1
Select all usM03953_0005_*.img and press 'Done'
Pull down menu - select 'Descending (first slice = top)'
Prompt - Reference Slice - enter '12' (default)
Prompt - Interscan interval (TR) - enter '2.0'
Prompt - Acquisition time (TA) - enter '1.9...' (default)
Output:
au* files interpolated realigned images
< Can use to create difference image between ausM03953_0005_0100.img
and usM03953_0005_0100.img to see effect of interpolation about middle slice >
wausM03953_0005_*.{img,hdr,mat}
-------------------------------
Normalised interpolated realigned functional images
The normalisation parameters are generated from the mean realigned
image, normalised to the EPI template using affine and nonlinear warps
Optional: To save filespace, can change default voxel size to 3x3x3,
rather than interpolating to 2x2x2:
Press in SPM main window
Pull down menu - 'Spatial Normalization'
Pull down menu - 'Defaults for - writing normalized'
Pull down menu - 'Preserve concentrations'
Pull down menu: Bounding box - 'Default'
Pull down menu: Voxel sizes - '3 3 3'
Pull down menu: Interpolation - 'Trilinear'
Pull down menu: To wrap images - 'no wrap'
Type:
Press near upper, middle SPM window
Pull down menu - 'Determine Parameters and Write Normalised'
Select 'Template image' - EPI.img
Select 'Source image, subj1' - meanusM03953_0005_0006.img
Select 'Images to write' - meanusM03953_0005_0006.img
AND
all 351 ausM03953_0005_*.img
Select 'Source image,subj2' - press Done (ie select nothing; tells SPM no more subjects)
Output:
wau* files normalised, interpolated, realigned functionals
wmeanusM03953_0005_0006.img
normalised mean realigned functional
meanusM03953_0005_0006_sn3d.mat
normalisation parameters
spm2.ps
graphical output of normalisation process (appended)
< View normalised images with button - Note interpolation
to new voxel sizes and image dimensions >
< View normalisation transformations in spm2.ps (second page) >
< Check registration with button - select
wmeanusM03953_0005_0006.img, EPI.img in SPM Templates dir and
single_sub_T1.img in SPM Canonical dir >
swausM03953_0005_*.{img,hdr,mat}
--------------------------------
Smoothed normalised realigned images
Smoothed with an isotropic Gaussian kernel with FWHM = 8mm (for statistical inference using theory of Gaussian fields)
Type:
Press in upper right SPM window
Prompt - smoothing FWHM - enter '8'
Select all wausM03953_0005_*.img and press 'Done'
Output:
swaus* Smoothed normalised images
OPTIONAL step: normalising structural image
-------------------------------------------
Coregister mean EPI and structural T1 images
Type:
Press in upper right SPM window
Prompt - No. subjects enter - '1'
Pull down menu - 'Coregister only'
Select target image - 'meanusM03953_0005_0006.img'
Select object image - 'sM03953_0007.img'
Select other images -