On 1/19/2024 3:45 PM, Na, Xiaoxu wrote:
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Dear Freesurfer Expert,
While the sphere can only be drawn using that Dr. Doug suggested, the
sphere option would mess up.
Do you need help with this? If so, can you give more info?
I have a further question as using this ROI to extract surface
information from ?h.area and ?h.volume. I’m using the command line as
below:
$mri_segstats --seg mask1.sm1.bin.mgh --exlude 0 --i
groupAnalysis/lh.volume.g2v2.10.mgh --sumwf lh.volume.mask1.dat
However, due to the calculation of surface and volume, we need another
input of sum file (ASCII file), how can I do that before I can run the
above?
Sorry, I don't know what you mean
Another simple question is, what is lh.volume.mgh in the group
analysis folder processed by mris_proc? Is that a simple merge of all
subjects lh.volume file? Why the number is between 0-10, is there any
way I can put ?h.volume or ?h.area back to gain each subject’s real
volume or area value on that surface vertex? Thank you so much!
This is a vertex-wise measure of volume of the cortex at that point. Eg,
a given vertex has an area defined by the mean area of the triangles
that abut it. When this is multiplied by the thickness, you get a
volume measure (we actually compute it differently using a truncated
pyramid, but that's the basic idea). You can use this in a VBM-like
analysis.
Regards,
Xiaoxu
*From:* Na, Xiaoxu
*Sent:* Wednesday, December 13, 2023 4:25 PM
*To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
*Subject:* Create a Binarized ROI for Surface
Dear Freesurfer Expert,
We would like to extract mean Cth values for each subject within a
own-creaded ROI (surface defined), using freeview (for instance). Is
it possible to create a ROI (i.e. spherical surface) surrounding a
particular vertex of an sig.mgh file? (and then extract its mean Cth
values for each subject)?
I think this is not a new question, and it was posted somehow on
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but I’m still encountering questions.
These commands did run, but together they didn’t create a binarized
mask with 1 for the sphere around the coordinates, and 0 for the other
voxels. Would you recommend what I should change? Thank you so much!
$mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness
--pdf sphere --sphere-center -7.4 67.22 60.27 --radius 5 --o
delta.sm00.mgh
$mris_fwhm \
--smooth-only \
--subject fsaverage \
--hemi lh \
--i delta.sm00.mgh \
--niters 10 \
--o delta.sm10.mgh
$mri_binarize --i delta.sm10.mgh --min 10e-5 --o delta.sm10.bin.mgh
Regards,
Xiaoxu
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