masking with 3dcalc

AFNI Message Board
1

Hello,

I am doing a seed based analysis on resting state data and instead or looking at correlations within the entire brain, we wanted to restrict the analysis to neocortex. I figured I would adjust my mask in 3dDeconvolve to analyze just neocortex (as indicated below ***) but in order to create that mask, I would have to add 100 or so ROIs. Is there a way that I could say, rather, (this atlas - regions (x+y+z)) rather than regions 1+2+3…100. Or even an easier way with 3dautomask or something?

this is the way I normally generate ROIs
3dcalc -a $atlas -expr “equals(a,34)+equals(a,33)” -prefix ${ROI}.nii

3dDeconvolve -input $dset
-mask anat_mask_rs+tlrc’[0]'\ ***** Change anat_mask to neoctx_mask*******
-polort -1
-jobs 8 -float
-num_stimts 1
-stim_file 1 ${s}_${ROI}.1D
-stim_label 1 ${ROI}
-tout -rout -bucket ${s}buc${ROI} -overwrite

Thanks as always!!

2

I’m not sure if I completely understand,

Do you want the output to be a binary mask, starting from an entire atlas but chopping away a couple pieces? If so, you could do something like:


3dcalc -a $atlas -expr "step(a) - step(equals(a,34) + equals(a,33))" -prefix  NEW_MASK

which makes everywhere in $atlas > 0 have a value of 1, and then subtracts 1 from regions #34 and #33, pushing those locations back to zero and hence out of the mask.

Or, if you wanted to maintain ROI numbering from the atlas, you could adjust the command to be:


3dcalc -a $atlas -expr "a*(step(a) - step(equals(a,34)+equals(a,33)))" -prefix  NEW_MASK2

(and then you could reattach the labeltable).

–pt

ps: Only the first step() in each command should be needed, because the other #ed regions shouldn’t/can’t overlap, by definition, but I left it in in case other criteria came up.

3

This might be a good example for when to use amongst()
in 3dcalc. For example, see the output of:

afni_proc.py -help | grep -B 1 amongst

as in:

3dcalc -a aparc+aseg.nii -datum byte -prefix FT_WM.nii \
       -expr 'amongst(a,2,7,16,41,46,251,252,253,254,255)'

I am not sure whether there is any limit on the number
of terms. Perhaps if the last term survives, all is well.

  • rick
4

Ok… thanks Paul. That’s exactly what I want to do, I just didn’t realize I could say step(a) to reference the entire $atlas… that is what it’s doing, correct? I am a little confused about the difference between example 1 and 2, however. The second example is keeping the ROIs information in the output mask?

5

Thanks Rick! So, in that example, each of those numbers would represent an annotated region in atlas (a) and be output in the FT_WM.nii file to represent “white matter”(WM), say?

6

In my example, the output would be 0/1.
If you want the values to be the same as
in the input (i.e. a restricted atlas, as Paul
did), multiply by ‘a’:

-expr ‘a*amongst(a,…)’

  • rick
7

Hi-

Yes, the first example makes a binary mask (1s inside, 0s outside) where, say, regions [1…32] and [35…100] were, while the seond example makes a subset atlas containing just regions [1…32] and [35…100], each containing their original integer value.

If you have string labels associated with each integer (seeing a name when you click on a value in AFNI), then you would want to copy the labeltable from the initial atlas over to the newly created file.

–pt