Hi ALL,
I have the problem that when I try to dump out the 64 values per voxel into a file using 3dmaskdump, the dumped values with corresponding spatial coordinates don’t match when I upload the file I dumped into AFNI GUI and go to the spatial coordinate position there. The following are the commands I used:
(1) whereami -mask_atlas_region TT_Daemon:right:47 -prefix trmiddle
(2) 3dresample -master DeconIMGAMpulse+tlrc -prefix testRmiddle -input trmiddle+tlrc
(3) 3dmaskdump -mask testRmiddle+tlrc -noijk -xyz -o testRmiddledump
Also if you 3dinfo the files you get:
DeconIMGAMpulse:
-79.5 79.5 3.0 54
-79.5 109.5 3.0 64
-63.5 83.5 3.0 50
trmiddle:
-80 80 1.0 161
-80 110 1.0 191
-65 85 1.0 151
testRmiddle:
-79.5 79.5 3.0 54
-79.5 109.5 3.0 64
-63.5 83.5 3.0 50
The file DeconIMGAMpulse+tlrc is an old file from 2011. I don’t know if that makes a difference. What stupid thing am I doing? Thanks for your help!
-Linda
Maybe I don’t understand the question, but I think the confusion comes from differences in the grids between your two kinds of datasets. The whereami output is on the grid of the Talairach Daemon atlas, and the resampled data is at a coarser resolution of 3mm and offset by 0.5 from the Talairach atlas. The "Jump to xyz " function in AFNI jumps to a coordinate based on the underlay dataset. The 3dinfo output shows the extent coordinates and voxel sizes, and that all seems expected.
Thank you Daniel since I was confused and I am glad I am not doing anything wrong. Now I can continue with my analysis. Thanks! -Linda