--o out

Output

--i invol

Input

--f listfile

List file has a text list of files (up to 40000)

--paired-sum

Computes paired sum (1+2, 3d+4, ect.)

--paired-avg

Computes paired average (1+2, 3d+4, ect.)

--paired-diff

Computes paired difference (1-2, 3d-4, ect.)

--paired-diff-norm

Same as paired difference but scale by TP1, 2 average

--paired-diff-norm1

Same as paired difference but scale by TP1

--paired-diff-norm2

Same as paired difference but scale by TP2

--norm-mean

Normalize frames by mean of all TP

--norm1

Normalize frames by TP1

--mtx matrix.asc

Multiply by matrix in ascii file

--gmean Ng

Create matrix to average Ng groups, Nper=Ntot/Ng

--combine

Average frames from non-zero voxels. Useful to combine lh.ribbon.mgz and rh.ribbon.mgz.

--keep-datatype

Write output in same datatype as input. Default is to write output in Float format

--abs

Take absolute value of input

--pos

Set input negatives to 0

--neg

Set input positives to 0

--mean

Compute mean of concatenated volumes

--median

Compute median of concatenated volumes

--mean-div-n

Compute mean per nframes (good for variance)

--sum

Compute sum of concatenated volumes

--var

Compute variance of concatenated volumes

--std

Compute standard deviation of concatenated volumes

--max

Compute maximum of concatenated volumes

--max-index

Compute index of maximum of concatenated volumes (1-based)

--max-index-prune

Maximum index setting to 0 any voxel where all frames are 0)

--max-index-add val

Add value to non-zero matrix indices

--min

Compute minimum of concatenated volumes

--rep N

Replicate N times (over frame)

--fnorm

Normalize time series at each voxel and fraction of occurances

--conjunct

Compute voxel-wise conjunction concatenated volumes

--vote

Most frequent value at each voxel and fraction of occurances

--sort

Sort each voxel by ascending frame value

--tar1 dofadjust

Compute temporal ar1

--prune

Set vox to 0 unless all frames are non-zero

--pca

Output is pca. U is output.u.mtx and S is output.stats.dat

--pca-mask mask

Only use voxels whose mask is greater than 0.5

--scm

Computes spatial covariance matrix

--max-bonfcor

Computes max and bonferroni correct (assumes -log10(p))

--mul mulvar

Multiply by mulvar

--add addval

Add addval

--mask maskfile

mask used with --vote or --sort

--rms

Root mean square. square, sum, divide by n frames, square root, eg. combine memprage

--no-check

Do not check inputs (faster)

--help

Prints out information on how to use this program

--version

Prints out version and exits