Index

Name

mri_concat

Description

Concatenates input data sets.

Synopsis

mri_concat.bin

Arguments

Optional Flagged Arguments

--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

Example

  mri_concat --i f1.mgh --i f2.mgh --o cout.mgh
  mri_concat f1.mgh f2.mgh --o cout.mgh
  mri_concat f*.mgh --o cout.mgh
  mri_concat f*.mgh --o coutmn.mgh --mean
  mri_concat f*.mgh --o coutdiff.mgh --paired-diff
  mri_concat f*.mgh --o coutdiff.mgh --paired-diff-norm
  mri_concat f*.mgh --o coutdiff.mgh --paired-diff-norm1

Conjunction takes the min of the abs across frames at each voxel. The output value at the voxel is the min, including the true sign of the min. Eg, if the two frames are:

Reference

Nichols, Brett, Andersson, Wager, and Poline NeuroImage, Volume 25, Issue 3, 15 April 2005, 653-660

Reporting Bugs

Report bugs to freesurfer@nmr.mgh.harvard.edu

mri_concat (last edited 2017-11-22 18:41:12 by MorganFogarty)