Usage: 3dSynthesize options Reads a ‘-cbucket’ dataset and a ‘.xmat.1D’ matrix from 3dDeconvolve, and synthesizes a fit dataset using selected sub-bricks and matrix columns.
- -cbucket ccc = Read the dataset ‘ccc’, which should have been
- output from 3dDeconvolve via the ‘-cbucket’ option.
- -matrix mmm = Read the matrix ‘mmm’, which should have been
- output from 3dDeconvolve via the ‘-x1D’ option.
- -select sss = Selects specific columns from the matrix (and the
corresponding coefficient sub-bricks from the cbucket). The string ‘sss’ can be of the forms:
baseline = All baseline coefficients. polort = All polynomial baseline coefficients
(skipping -stim_base coefficients).
- allfunc = All coefficients that are NOT marked
- (in the -matrix file) as being in the baseline (i.e., all -stim_xxx values except those with -stim_base)
- allstim = All -stim_xxx coefficients, including
- those with -stim_base.
- all = All coefficients (should give results
- equivalent to ‘3dDeconvolve -fitts’).
something = All columns/coefficients that match
this -stim_label from 3dDeconvolve [to be precise, all columns whose ] [-stim_label starts with ‘something’] [will be selected for inclusion. ]
- digits = Columns can also be selected by
- numbers (starting at 0), or number ranges of the form 3..7 and 3-7. [A string is a number range if it] [comprises only digits and the ] [characters ‘.’ and/or ‘-‘. ] [Otherwise, it is used to match ] [a -stim_label. ]
More than one ‘-select sss’ option can be used, or you can put more than one string after the ‘-select’, as in this example:
- 3dSynthesize -matrix fred.xmat.1D -cbucket fred+orig
- -select baseline FaceStim -prefix FS
which synthesizes the baseline and ‘FaceStim’ responses together, ignoring any other stimuli in the dataset and matrix.
-dry = Don’t compute the output, just check the inputs.
- -TR dt = Set TR in the output to ‘dt’. The default value
- of TR is read from the header of the matrix file.
-prefix ppp = Output result into dataset with name ‘ppp’.
- -cenfill xxx = Determines how censored time points from the
- 3dDeconvolve run will be filled. ‘xxx’ is one of:
zero = 0s will be put in at all censored times nbhr = average of non-censored neighboring times none = don’t put the censored times in at all
(in which case the created dataset is) (shorter than the input to 3dDeconvolve)If you don’t give some -cenfill option, the default operation is ‘zero’. This default is different than previous versions of this program, which did ‘none’.
- **N.B.: You might like the program to compute the model fit
- at the censored times, like it does at all others. This CAN be done if you input the matrix file saved by the ‘-x1D_uncensored’ option in 3dDeconvolve.
NOTES: – You could do the same thing in 3dcalc, but this way is simpler
and faster. But less flexible, of course.
– The output dataset is always stored as floats. – The -cbucket dataset must have the same number of sub-bricks as
the input matrix has columns.
– Other similar applications are left to your imagination. – To see the column labels stored in matrix file ‘fred.xmat.1D’, type
the Unix command ‘grep ColumnLabels fred.xmat.1D’; sample output:
- # ColumnLabels = “Run#1Pol#0 ; Run#1Pol#1 ; Run#2Pol#0 ; Run#2Pol#1 ;
FaceStim#0 ; FaceStim#1 ; HouseStim#0 ; HouseStim#1”which shows the 4 ‘-polort 1’ baseline parameters from 2 separate imaging runs, and then 2 parameters each for ‘FaceStim’ and ‘HouseStim’.
– When using a ‘raw’ matrix, you’ll probably also want the ‘-TR’ option. – When putting more than one string after ‘-select’, do NOT combine
these separate strings togther in quotes. If you do, they will be seen as a single string, which almost surely won’t match anything.
– Author: RWCox – March 2007
++ Compile date = Dec 16 2015