On 8/13/2020 10:15 AM, Ellen Ji wrote:
External Email - Use Caution
Thanks Douglas.
recon-all was performed using FS V6. However, we have since upgraded
to V7. Should I stick with what was originally used (mri_aparc2aseg)?
I don't think it will make much of a difference, so do whatever is
easier for you
Here is how the wmparc.mgz was created. Could you verify if my
modified steps below make sense?
wmparc.mgz:
mri_aparc2aseg \
--s subject1 \
--labelwm \
--hypo-as-wm \
--rip-unknown \
--volmask \
--o mri/wmparc.mgz \
--ctxseg aparc+aseg.mgz \
modification for my annotation:
The reason why I added wmparc-dmax 2 is because I want to extend the
annotation, which only includes gm, into the wm. However, when I do
this, there are 2x the labels (gm and wm). Is there any way to do an
extension while maintaining 318 regions? (if I remove the labels post
hoc using mri_binarize, I believe that would just erase all wm, which
isn't what I want).
mri_aparc2aseg \
--s subject1 \
--annot 500_sym.aparc \
--wmparc-dmax 2 \
--labelwm \
--hypo-as-wm \
--o subject1/mri/aparc.500+2mm.nii.gz
Why are you not including --rip-unknown and --volmask? The number of
regions is as expected because it labels cortex as well as the adjacent
WM, but the adjacent WM gets a different segmentation index. You can
merge them back together afterwards if you want.
best,
Ellen
On 8/13/2020 3:39 PM, Douglas N. Greve wrote:
You can look in the recon-all.log file to see how wmparc.mgz is
created. Which version of FS are you using? If V6, then the command
will be mri_aparc2aseg. If V7, then it will mri_surf2volseg. Either
way, modify the command to use your annotation.
On 8/12/2020 5:18 AM, Ellen Ji wrote:
External Email - Use Caution
Dear Freesurfer experts,
I have a surface parcellation (annotation) with 318 labels; see
attachments for each hemi. I wish to extract volume-based features
(FA and MD) corresponding to these 318 labels. I believe I should
perform something like surf2vol to extend the labels into FA space.
However, my surface parcellation is not a surface overlay (which I
need for --so). Any other ways to do this?
I wish for the output to be a single volume-based parcellation of
318 labels, corresponding to the two surface parcellation annotation
files. I will then use this output to get FA measures for each of
the 318 regions.
Thank you,
Ellen
---
Ellen Ji, PhD
Postdoctoral Research Fellow
Psychiatric University Hospital
University of Zürich
ellen...@bli.uzh.ch
homanlab.github.io/ellen/
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