Dear AFNI experts,
I created the left hippocampal mask from FreeSurfer segementation and tried to extract FA values using 3dmaskave, which showed the below error.
++ WARNING: file /Users/titus/.afni.log is now 7359264127 (7.4 billion) bytes long!
++ 3dmaskave: AFNI version=AFNI_19.3.11 (Nov 1 2019) [64-bit]
*+ WARNING: If you are performing spatial transformations on an oblique dset,
such as /Data/EPC/practice/ROI/EPC001.pre/lhipp.nii.gz,
or viewing/combining it with volumes of differing obliquity,
you should consider running:
3dWarp -deoblique
on this and other oblique datasets in the same session.
See 3dWarp -help for details.
++ Oblique dataset:/Data/EPC/practice/ROI/EPC001.pre/lhipp.nii.gz is 29.999701 degrees from plumb.
++ Oblique dataset:/Data/EPC/practice/EPC001/EPC001.pre/dwi/FA.nii.gz is 29.999701 degrees from plumb.
*+ WARNING: Input dataset /Data/EPC/practice/EPC001/EPC001.pre/dwi/FA.nii.gz grid mismatch from mask.
Try the following command for grid comparison:
3dinfo -header_line -prefix -same_all_grid /Data/EPC/practice/ROI/EPC001.pre/lhipp.nii.gz /Data/EPC/practice/EPC001/EPC001.pre/dwi/FA.nii.gz
When running 3dinfo -header_line -prefix -same_all_grid /Data/EPC/practice/ROI/EPC001.pre/lhipp.nii.gz /Data/EPC/practice/EPC001/EPC001.pre/dwi/FA.nii.gz, it showed the below.
prefix =dim? =delt? =ornt? =cent? =obl?
lhipp.nii.gz 0 0 1 0 1
FA.nii.gz 0 0 1 1 1
I also tried 3dresample using the below command.
3dresample -rmode NN -master /Data/EPC/practice/EPC001/EPC001.pre/dwi/FA.nii.gz -inset /Data/EPC/practice/ROI/EPC001.pre/lhipp.nii.gz -prefix /Data/EPC/practice/ROI/EPC001.pre/lhipp_resampled.nii.gz
But, the 3dinfo -header showed the same results. Could you please advise how to solve this issue? I also attached the screenshot of the left hippocampal mask overlay and FA underlay, which I think there is no issue in terms of segementation.
Best,
JW
