Hi,
I am running Hippocampal subfield processing stream and I think I got all the appropriate "posterior_*.mgz files" I need to get the stats, but I am not seeing "nonPartialVolumeStatsRight.txt" anywhere as described in the wiki under $subjectsdir. What I am seeing is "volumeStats_left.txt" and "volumeStats_right.txt" files under the "$subject/mri" directory and one of the text files look like this. ------------------------------------ volumeInVoxels: Left-Hippocampus: 2616.97 left_presubiculum: 4050 left_CA1: 2880.55 left_CA2_3: 8120.59 left_fimbria: 212.439 left_subiculum: 5985.02 left_CA4_DG: 4459.07 left_hippocampal_fissure: 358.59 -------------------------------------
If I look at the end of the "hippo-subfields.log" file, it is saying it is skipping the partial volume segmentation (see below).
--------------------------- ... Debug: Off Observers: none Matrix: -0.5 0 0 0 0 0.5 0 -0.5 0 Offset: [41.7047, -40.8148, -4.10007] Center: [0, 0, 0] Translation: [41.7047, -40.8148, -4.10007] Inverse: -2 0 0 0 0 -2 0 2 0 Singular: 0 spacing: [0.5, 0.5, 0.5] origin: [41.7047, -40.8148, -4.10007] direction: -1 0 0 0 0 1 0 -1 0
done! Skipping the partial volume segmentation part -------------------------------------------
Can please someone tell me what I am missing? Also, what do I need to do to extract the values to a spreadsheet? Should I use asegstats2table? under '-help' it doesn't say which options it should be used to get the subfields.
Thank you so much for the help in advance.
Cheers, Yoon