'''Index'''
<<TableOfContents>>

= 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:

   +2.1 and +3.4 --> +2.1
   -2.1 and -3.4 --> -2.1
   +2.1 and -3.4 --> +2.1
   -2.1 and +3.4 --> -2.1


= 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