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

-  ⇤ ← Revision 3 as of 2008-04-29 11:45:10 → 
  Size: 905
  Editor: localhost
  Comment: converted to 1.6 markup
+   ← Revision 9 as of 2017-11-22 18:41:12 → ⇥
  Size: 3978
  Editor: MorganFogarty
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 1:
-USAGE: mri_concat
+'''Index'''
<<TableOfContents>>
-Line 3:
+Line 4:
-   --i invol <--i invol ...> (don't need --i) 
   --o out
+= Name =
mri_concat
-Line 6:
+Line 7:
-   --paired-diff : compute paired diff (1-2, 3-4, etc)
 
   --paired-diff-norm : same as paired-diff but scale by TP1,2 average
+= Description =
Concatenates input data sets.
 Line 10:
-   --paired-diff-norm1 : same as paired-diff but scale by TP1
+= Synopsis =
mri_concat.bin
-Line 12:
+Line 13:
-   --paired-diff-norm2 : same as paired-diff but scale by TP2
+= Arguments =
-Line 14:
+Line 15:
-   --mean : compute mean of concatenated volumes
+== 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 ||
-Line 16:
+Line 64:
-   --help      print out information on how to use this program
+= 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:
-Line 18:
+Line 76:
-   --version   print out version and exit
+   +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
-Line 20:
+Line 81:
-Concatenates input data sets.
EXAMPLES:
  mri_concat --i f1.mgh --i f2.mgh --o cout.mgh
-Line 24:
+Line 82:
-  mri_concat f1.mgh f2.mgh --o cout.mgh
+= Reference =
Nichols, Brett, Andersson, Wager, and Poline
NeuroImage, Volume 25, Issue 3, 15 April 2005, 653-660
-Line 26:
+Line 86:
-  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
+= Reporting Bugs =
Report bugs to freesurfer@nmr.mgh.harvard.edu