--i inputvol

input volume

Input data. Format must be something readable by mri_convert (eg, mgh, mgz, img, nii, nii.gz). Alternately, one can synthesize white gaussian noise with --synth and --synth-frames in which case inputvol is used as a dimension template.

--o outputvol

save input after smoothing

Save input after smoothing. See also --save-detended and --save-unmasked.

--smooth-only

smooth and save, do not compute fwhm (--so)

Does not attempt to compute FWHM. Smooths the input, saves to outputvol, and exists. Respects --save-unmasked, but not --save-detended. This allows for data sets with fewer than 10 frames to be smoothed.

--save-detended

save input after smoothing, masking, and detrending

--save-unmasked

Save input after smoothing and detrending, but do not mask while
smoothing. Note that the output will be different even inside
the mask because the smoother handles voxels on the boundary
of the mask differently than those at the center.

--mask maskvol

binary mask

Compute FWHM only over voxels in the given mask. Format can be anything accepted by mri_convert. If smoothing is to be done, it will only be done inside the mask. It is strongly recommended that a masked be used (see also --auto-mask and --save-unmasked).

--mask-thresh absthresh

threshold for mask (default is .5)

Threshold mask at thresh. Default is 0.5 (ie, it expects a binary mask).

--auto-mask rthresh

compute mask

Compute a mask based on a fraction (rthresh) of the global mean. If
rthresh is 0.1, then all voxels in the mean image above 0.1*globalmean
are in the mask.

--nerode n

erode mask n times prior to computer fwhm

Erode mask n times (ie, make it smaller). Occurs after any mask inversion.

--mask-inv

invert mask

Invert mask, ie, compute FWHM only over voxels outside the given mask.

--out-mask outmask

save final mask to outmask

--ar1 ar1path

save apatial AR1 volume

--X x.mat

matlab4 detrending matrix

Detrend/residualize data with the matrix in x.mat. Ie,
y = (I-inv(X'*X)*X')*y, where y is the input. x.mat must
be a matlab4 matrix. Not with --detrend.

--detrend order

polynomial detrending (default 0)

Detrend data with polynomial of given order. Not with --X. Note:<<BR>>if neither --X nor --detrend are specified, then detrending
order of 0 is used (ie, the mean is removed).

--sqr

compute square of input before smooething

--fwhm fwhm

smooth by fwhm before measuring

Smooth BY fwhm mm before estimating the fwhm. This is mainly good for
debuggging. But with --out can also be used to smooth data.

--gstd gstd

same as --fwhm but specified as the stddev

--to-fwhm tofwhm

smooth to fwhm

Smooth TO tofwhm mm. This is idea proposed by Lee Friedman
( lfriedman10@comcast.net ) and fBIRN (www.birn.net) as a way to
reduce variation across data sets, particularly when the data
may have come from different scanners. The method implemented
here uses an iterative approach in which the data are smoothed
BY varying amounmts until the resulting fwhm is within a certain
tolerance of tofwhm. By default, the tolerance is 0.5 mm, but
can be changed with --to-fwhm-tol. It will iterate at most 20
times (can be changed with --to-fwhm-nmax). An error will be
returned if the tofwhm is less than the inherent fwhm or the max
number of iterations is exceeded. The minimization is done with
a Golden Section Search (see Numerical Recipes in C).

--to-fwhm-tol tolerance

smooth to fwhm +/- tol (default .5mm)

Keep iterating the tofwhm search until the result is within tol
of the desired fwhm (or until the maximum number of iterations
is reached).

--to-fwhm-nmax nitersmax

maximum number of iterations (default 20)

--to-fwhm-file file

save to-fwhm params in file

Save some results of the tofwhm minimization to file. Good for
debugging. Results also saved in summary file.

--sum sumfile

summary/log

Prints summary to ascii sumfile. Send this file when requesting
help or more information.

--dat datfile

only the final fwhm estimate

--synth

Synthesize input with white gaussian noise. Ten frames are used by default,
but this can be changed with --synth-frames. Uses input volume as template.
This functionality is useful for degugging. Eg, when using --synth and --fwhm,
it should measure the resulting fwhm to be that passed by --fwhm. Can do
the same with --to-fwhm.

--synth-frames nframes

default is 10

Synthesize input with white gaussian noise with the given number of frames.
Implies --synth.

--nframesmin n

require at least this many frames

--ispm

input is spm-analyze. Set --i to stem.

--in_nspmzeropad nz

zero-padding for spm-analyze

--debug

turn on debugging

--checkopts

don't run anything, just check options and exit

--help

print out information on how to use this program

--version

print out version and exit