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|| --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 || |
Index
Contents
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 |
Examples
Example 1
See Also
Reporting Bugs
Report bugs to freesurfer@nmr.mgh.harvard.edu