Hi Yoon,
when you run the script kvlQuantifyHippocampalSubfieldSegmentations.sh, it
goes along the volumeStats_left.txt and volumeStats_right.txt to build a large
table with all the volumes. The output files
(nonPartialVolumeStatsLeft.txt/nonPartialVolumeStatsRight.txt) should be in
your subjects directory $subject.
Regarding the partial volume segmentation, it's not fully implemented / tested
yet.
Cheers,
/Eugenio
Juan Eugenio Iglesias
Postdoctoral researcher BCBL
www.jeiglesias.com
www.bcbl.eu
Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer
----- Original Message -----
From: "Yoonho Chung" <yoonho.ch...@yale.edu>
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, August 15, 2014 10:33:19 PM
Subject: [Freesurfer] Hippocampal Subfields missing
nonPartialVolumeStatsRight.txt file
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
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