3dMatch, written by PA Taylor (Nov., 2012), part of FATCAT (Taylor & Saad,
2013) in AFNI.
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
Find similar subbricks and rearrange order to ease comparison
Comparison simply done by comparing (weighted) correlation maps of
values, which may include thresholding of either refset or inset
values. The weighting is done by squaring each voxel value (whilst
maintaining its original sign). The Dice coefficient is also calculated
to quantify overlap of regions.
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ COMMANDS:
3dMatch -inset FILE1 -refset FILE2 {-mask FILE3} {-in_min THR1} \
{-in_max THR2} {-ref_min THR3} {-ref_max THR4} -prefix FILE4 \
{-only_dice_thr}
where:
-inset FILE1 :file with M subbricks of data to match against another
file.
-refset FILE2 :file with N subbricks, serving as a reference for
FILE1. N=M is *not* a requirement; matching is done
based on squares of values (with signs preserved), and
both best fit of in->ref and ref->in are calculated
and output.
-mask FILE3 :a mask of regions to include in the correlation of
data sets; technically not necessary as relative
correlation values shouldn't change, but the magnitudes
would scale up without it. Dice coeff values should not
be affected by absence or presence of wholebrain mask.
-in_min THR1 :during the correlation/matching analysis, values below
THR1 in the `-inset' will be zeroed (and during Dice
coefficient calculation, excluded from comparison).
(See `-only_dice_thr' option, below.)
-in_max THR2 :during the correlation/matching analysis, values above
THR2 in the `-inset' will be zeroed (and during Dice
coefficient calculation, excluded from comparison).
-ref_min THR3 :during the correlation/matching analysis, values below
THR3 in the `-refset' will be zeroed (and during Dice
coefficient calculation, excluded from comparison).
(See `-only_dice_thr' option, below.)
-ref_max THR4 :during the correlation/matching analysis, values above
THR4 in the `-refset' will be zeroed (and during Dice
coefficient calculation, excluded from comparison).
-prefix FILE4 :prefix out output name for both *BRIK/HEAD files, as
well as for the *_coeff.vals text files (see below).
-only_dice_thr :if option is included in command line, the thresholding
above is only applied during Dice evaluation, not
during spatial correlation.
+ OUTPUTS, named using prefix;
*_REF+orig :AFNI BRIK/HEAD file with the same number of subbricks
as the `-refset' file, each one corresponding to a
subbrick of the `-inset' file with highest weighted
correlation. Any unmatched `-inset' subbricks are NOT
appended at the end. (For example, you could underlay
the -ref_set FILE2 and visually inspect the comparisons
per slice.)
*_REF_coeff.vals :simple text file with four columns, recording the
original brick number slices which have been
reordered in the output *_REF+orig file. Cols. 1&2-
orig `-refset' and `-inset' indices, respectively;
Col. 3- weighted correlation coefficient; Col 4.-
simple Dice coefficient.
*_IN+orig :AFNI BRIK/HEAD file with the same number of subbricks
as the `-inset' file, each one corresponding to
a subbrick of the `-refset' file with highest weighted
correlation. Any unmatched `-refset' subbricks are NOT
appended at the end. (For example, you could underlay
the -inset FILE1 and visually inspect the comparisons
per slice.)
*_IN_coeff.vals :simple text file with four columns, recording the
original brick number slices which have been
reordered in the output *_IN+orig file. Cols. 1&2-
orig `-inset' and `-refset' indices, respectively;
Col. 3- weighted correlation coefficient; Col 4.-
simple Dice coefficient.
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
+ EXAMPLE:
3dMatch \
-inset CORREL_DATA+orig \
-refset STANDARD_RSNs+orig \
-mask mask+orig \
-in_min 0.4 \
-ref_min 2.3 \
-prefix MATCHED \
-only_dice_thr
* * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * *
If you use this program, please reference the introductory/description
paper for the FATCAT toolbox:
Taylor PA, Saad ZS (2013). FATCAT: (An Efficient) Functional
And Tractographic Connectivity Analysis Toolbox. Brain
Connectivity 3(5):523-535.
