3dmaskave for slices in y direction

AFNI Message Board
1

I want to get an average beta value for each slice along an ROI. I saw that 3dmaskave’s -slice option only goes in the z-direction, but in my data slices are in the y-direction. I am currently trying to do it using 3dmaskdump, but that gives me many betas and I would need to average them afterwards. Is there a better way to do this? this is my current 3dmaskdump command to get values from where y=17:

3dmaskdump -mask …/…/ROIs.nii_ANTS+tlrc. -mrange 13 24 -xyz -cmask ‘-a …/…/ROIs.nii -expr 1-bool(j-17)’ -o test stats.101_ANTS+tlrc.

2

The slice direction is the definition of the z direction,
however slices are stored on disk. Can you be more
specific as to what you mean by slices being in the y
direction? Did you resample/reorient the data?

  • rick
3

to my knowledge I haven’t resampled/reoriented the data. Here is the orientation info when I 3dinfo my data:
Data Axes Tilt: Plumb
Data Axes Orientation:
first (x) = Anterior-to-Posterior
second (y) = Superior-to-Inferior
third (z) = Left-to-Right [-orient ASL]

Is that what you would expect?

I’m confused about how to determine which slices I want. When the z-value changes in the AFNI window, the cursor moves along the dorsal/ventral axis as seen here: Image 1[/url] [url=http://imgur.com/kjl0b1L]Image 2. That’s not what I think of as slices-- I would expect the cursor to move in an anterior-posterior direction. It’s possible that I’m thinking about this the wrong way, but I’d appreciate your input!

4

The coordinates in the AFNI GUI are actually
irrelevant, as they are given in a “standard”
orientation (either RAI or LPI, say). That is
so that a brain looks like a brain, and those
coordinates mean the same thing across
subjects and datasets per subject.

Your slices are left to right, so that is what
3dmaskave would use with the -slices option.

So you were planning to class 3dmaskave
repeatedly, once for each slice? That should
work.

  • rick
5

To be clear, I was trying to run 3dmaskave on chunks of slices in the anterior to posterior dimension. I didn’t want LTR or inferior to superior slices, so I reoriented the data. I didn’t realize that slices are in the z-dimension by default. so I made anterior/posterior the z dimension and then ran 3dmaskave. thanks for your help!