Please note this is a work in progress... the information provided is not complete.

This is a list of the values contained within the defaults structure that SPM2b references. The settings that you can change are in bold, and a summary of how this setting effects your analysis is listed below it.

To change a certain setting you must allow yourself access to the SPM global structure, by typing: global defaults;

Once you have access to the structure you can now change values by assining a new element to the specified default, i.e. defaults.logfile = 'MY_LOGFILE.log';

If the bolded value is indented, you must access it via the non-indented words above it, i.e. defaults.segment.affreg.smosrc = 10

If you have any questions feel free to contact Andrew Fox at asfox@wisc.edu.

Defaults

grid: 0.4000
Sets a grid size?

cmdline: 0
Turns the command line prompt on/off. (0=off, 1=on)

logfile: ''
Selects a log file to write SPM command history to.

printstr: 'print -dpsc2 -painters -append -noui spm2.ps'
Determines the command used to print spm2 information. (log file?)

analyze: [1x1 struct]

multivol: 0
Turns analyze multi-volume reading on/off. (0=off, 1=on)
flip: 0
Determines how SPM will deal with the L/R orientation of the images. (0 = RisR, 1 = RisL)
You want to make sure that this option is set such that when displaying your images R is R. Though SPM will change how your data looks in SPM it will not change the files, such that if you have flip=1, your images will be stored in RisL format, but will appear as RisR format within SPM.

stats: [1x1 struct]

maxmem: 1048576
Description
maxres: 64
Description
fmri: [1x1 struct]

ufp: 0.0010
Description
t: 16
Number of time bins per scan. (?)
t0: 1
First time bin. (?)
% With longs TRs you may want to shift the regressors so that they are
% aligned to a particular slice. This is effected by resetting the
% values of defaults.stats.fmri.t and defaults.stats.fmri.t0 in
% spm_defaults. defaults.stats.fmri.t is the number of time-bins per
% scan used when building regressors. Onsets are defined
% in temporal units of scans starting at 0. defaults.stats.fmri.t0 is
% the first time-bin at which the regressors are resampled to coincide
% with data acquisition. If defaults.stats.fmri.t0 = 1 then the
% regressors will be appropriate for the first slice. If you want to
% temporally realign the regressors so that they match responses in the
% middle slice then make defaults.stats.fmri.t0 =
% defaults.stats.fmri.t/2 (assuming there is a negligible gap between
% volume acquisitions. Default values are defaults.stats.fmri.t = 16
% and defaults.stats.fmri.t0 = 1.

pet: [1x1 struct]

ufp: 0.0500
Description

realign: [1x1 struct]

estimate: [1x1 struct]

quality: 0.7500
A fairly arbitraty quality selector for the realignment that allows you to adjust the quality vs. speed tradeoff. (1.0 = best quality, 0.0 = best speed)
weight: 0
Turns weight masking on/off. Weight masking will allow you to mask out certain portions of your data when attempting realignment. (0=off, 1=on)
interp: 2
Description
wrap: [0 0 0]
This option allows you to choose to wrap images around if they are coregistered beyond the voxel space. Ideally it should not be necessary, however, it is suggested that you wrap in Y if you are dealing with un-resliced MRI images where phase encoding is in the Y direction.
???? 0 = no wrap? 1 = wrap?

write: [1x1 struct]

mask: 1
Description
interp: 4
Description
wrap: [0 0 0]
This option allows you to choose to wrap images around if they are coregistered beyond the voxel space. Ideally it should not be necessary, however, it is suggested that you wrap in Y if you are dealing with un-resliced MRI images where phase encoding is in the Y direction.

coreg: [1x1 struct]

estimate: [1x1 struct]

cost_fun: 'nmi'
Allows you to select a different cost function for the way that SPM will determine success in the coregistration procedure.

% For inter-modal registration, use:
% 'mi' - Mutual Information
% 'nmi' - Normalised Mutual Information
% 'ecc' - Entropy Correlation Coefficient
% For within modality, you could use:
% 'ncc' - Normalised Cross Correlation
sep: [4 2]
Description
tol: [1x12 double]
Description
0.0200
0.0200
0.0200
0.0010
0.0010
0.0010
0.0100
0.0100
0.0100
0.0010
0.0010
0.0010
fwhm: [7 7]
Amount of smoothing? ?????

write: [1x1 struct]

interp: 1
Description
wrap: [0 0 0]
This option allows you to choose to wrap images around if they are coregistered beyond the voxel space. Ideally it should not be necessary, however, it is suggested that you wrap in Y if you are dealing with un-resliced MRI images where phase encoding is in the Y direction.
mask: 0
Description

normalise: [1x1 struct]

estimate: [1x1 struct]

smosrc: 8
Smoothing of source image. (in mm)
smoref: 0
Smoothing of template image (in mm)
regtype: 'mni'
Description
weight: ''
A file that will weight the normalization procedure...
???? Which image? - Template image I think.
cutoff: 25
Description
nits: 16
This is the number of iterations SPM2 will perform when searching for the best set of non-linear basis functions. In practice it does not take 16 iterations but it is generally preferred, unless time is of the essence.
reg: 1
Description
wtsrc: 0
Toggles weighting the source image. (0=off, 1=on)

write: [1x1 struct]

preserve: 0
This allows you to adjust the procedure for combining voxels after normalization. SPM99 always preserved the concentrations, and this would be considered the standard way to normalize, however, "preserve total" will preserve the total amount of signal in a given area regardless of whether it expands or contracts. For example, if you have 6 voxels that all have a value of 1 that are combined into 1 voxel: using "preserve concentration" the value of that voxel will be 1, and using "preserve total" the value of that voxel will be 6. (0=preserve concentrations, 1=preserve totals)
bb: [2x3 double]
Determines the number of mm that will be included in the output image, measured from the origin (which should be set as the Anterior Commisure). If you are normalizing to MNI space, using the default bounding box will generally include all of the brain, but get rid of surrounding space (i.e. where the skull is).
-78 -112 -50
78 76 85
vox: [2 2 2]
Voxel size in mm (x y z) that the normalization procedure will output. It makes sense to preserve the voxel-sizes of your data, but since SPM2b converts your data into cubic voxels when normalizing (CHECK THIS) you should be sure to choose the most common or smallest original voxel size to minimize the warping of your data.
interp: 1
Description
wrap: [0 0 0]
This option allows you to choose to wrap images around if they are coregistered beyond the voxel space. Ideally it should not be necessary, however, it is suggested that you wrap in Y if you are dealing with un-resliced MRI images where phase encoding is in the Y direction.

segment: [1x1 struct]

estimate: [1x1 struct]

priors: [3x30 char]
The path names for the prior probability maps that SPM will use during the segmentation procedure.
W:\dev\spm2b\apriori\gray.mnc
W:\dev\spm2b\apriori\white.mnc
W:\dev\spm2b\apriori\csf.mnc

reg: 0.0100
Description
cutoff: 30
Description
samp: 3
Description
bb: [2x3 double]
Determines the number of mm that will be included in the output image, measured from the origin (which should be set as the Anterior Commisure). If you are normalizing to MNI space, using the default bounding box will generally include all of the brain, but get rid of surrounding space (i.e. where the skull is).
-88 -122 -60
88 86 95
affreg: [1x1 struct]

smosrc: 8
Number of mm to smooth the source image before attempting the affine transformation into mni space (to match the prior probability maps).
regtyp: 'mni'
Description
weight: ''
Description

write: [1x1 struct]

cleanup: 1
Attempt to clean up the probability maps be removing voxels that have a high probability of being of a different type.
wrt_cor: 1
Directs SPM as to whether it should write the corrected image or not. (0=no, 1=yes)

bias: [1x1 struct]

nbins: 256
Description
reg: 0.0100
Description
cutoff: 30
Description

modality: 'FMRI'
Selects the modality you are working with, in order to give the appropriate statistical options. ('FMRI' or 'PET')

SWD: 'W:\dev\spm2b'
Description

TWD: 'C:\DOCUME~1\fox\LOCALS~1\Temp\'
Description