Sorry, I don't understand what you are asking. Can you elaborate?
On 1/19/2024 4:37 PM, Na, Xiaoxu wrote:
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Hi Dr. Doug,
Thanks for your prompt reply!
I’m sorry it was not clear. Basically, I would like to extract the
cortical volume for each subject using a pre-defined ROI. As I have
already created the surface ROI, thanks to your answer on the official
website, I have no further question now on ROI.
This group analysiscan’s further survive the multiple correction using
the mri_glmfit-sim that you gave me years ago, so there is no file
like cache.th40.neg.sig.ocn.annot as before.
Instead, I tried to create a ROI and run command line as $mri_segstats
--seg mask1.sm1.bin.mgh --exlude 0 --i
groupAnalysis/lh.volume.g2v2.10.mgh --avgwf lh.volume.mask1.dat, where
mask1.sm1.bin.mgh is the ROI and groupAnalysis/lh.volume.g2v2.10.mgh
is the mris_proc processed file from a group of subjects. It did
extract something, 1 number for each subject, but I believe there is a
ratio or scalar between the actual volume of that vertex and those
show in lh.volume.g2v2.10.mgh. Is there anywhere I can figure out
where this ratio/scalar is? Thank you so much!
Regards,
Xiaoxu
*From:*freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. Greve
*Sent:* Friday, January 19, 2024 3:16 PM
*To:* freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] FW: Create a Binarized ROI for Surface
On 1/19/2024 3: 45 PM, Na, Xiaoxu wrote: External Email - Use Caution
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
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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>
<mailto: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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