How to export values in stats as brik file using mask

AFNI Message Board
1

Hi Gurus,

Is there any way to export values, say T values or correlation coefficients, in stats file as a BRIK file using a ROI mask?
I’m not familiar with AFNI codes, so I will really appreciate it if you can show me a sample script.

2

Hi-

Sure, there are lots of ways to do this kind of thing. The details matter a bit—is your ROI a lone mask region in its own volume, or is it in a “map” of ROIs and you are picking one out?

My guess is “3dcalc” is what you want. You can use subbrick selectors on a dset to pull out specific information. For example, to select the volume with index=7 in a 4D dataset (NB: index counting starts at 0, as in C and Python), you could write it in a 3dcalc expression as: DSET"[7]". Note the use of quotes, so the shell doesn’t interpret the square brackets before AFNI gets a hold of it. From part of 3dcalc’s help


INPUT DATASET NAMES
-------------------
This program accepts datasets that are modified on input according to the
following schemes:
  'r1+orig[3..5]'                                    {sub-brick selector}
  'r1+orig<100..200>'                                {sub-range selector}
  'r1+orig[3..5]<100..200>'                          {both selectors}

So, if you wanted to get the [7]th volume from DSET_STATS, and multiply it by a DSET_ROI mask, you could do:


3dcalc \
    -a DSET_STATS"[7]" \
    -b DSET_ROI \
    -expr 'a*step(b)"  \
    -prefix DSET_OUT

Many AFNI statistics file outputs have string labels attached per volume, to record from whence they came (see “3dinfo DSET” or “3dinfo -verb DSET”). You can use these labels to select the volume as well; if your [7]th volume has the label “AAA#0_Coef”, you could write the equivalent expression to the above as:


3dcalc \
    -a DSET_STATS"[AAA#0_Coef]" \
    -b DSET_ROI \
    -expr 'a*step(b)"  \
    -prefix DSET_OUT

If DSET_ROI has lots of values, and you want the ROI with value 4, then you could use:


3dcalc \
    -a DSET_STATS"[7]" \
    -b DSET_ROI"<4>" \
    -expr 'a*step(b)"  \
    -prefix DSET_OUT

Note the different bracket being used to select by value for the “b” dset.

As you are getting familiar with this, checking your results in the GUI is key… and you can also check back here with questions.

For more general info:

–pt

3

Thank you very much for your reply!