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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 analysis can’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 MailScanner
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to
be
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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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