If you want to keep the original orientation, you can specify
--conform-dc. Would that fix your problem?
On 12/21/2023 9:30 AM, Dipterix Wang wrote:
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Dear FreeSurer Wizards,
I'm trying to run the recon-all command on one of my template brains
such that th
Yes, that is correct
On 12/20/2023 2:07 PM, Edwards, Vincent wrote:
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Hi,
I'm following up on my quick question from this time last week.
I have several brains that I sent through recon-all using Freesurfer
7. If I wanted to use Freeview on Freesurfer vers
btw, you can get fornix segmentation from mri_sclimbic_seg
On 12/15/2023 11:34 AM, Huang, Yujing wrote:
Can you try ‘mri_segstats’? It will compute statistics on segmented
volumes - https://surfer.nmr.mgh.harvard.edu/fswiki/mri_segstats
Yujing
*From:* Ahsan Ali
*Sent:* Friday, December 1
Try using DOSS (--fsgd your.fsgd doss) instead of DODS (which is the
default).
On 12/8/2023 12:03 PM, Martin Juneja wrote:
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Hello FreeSurfer experts,
In my case-control study, I have a dataset of 5 healthy controls (HCs)
and one patient (PAT). I was wonde
I think that will work, but there are better tools for this kind of
thing. If you have 7.4, you can use mri_binarize, like
mri_binarize -dilate-vertex vno surf radius outmask
where vno is the center vertex, surf is the surface (eg, white), radius
is the desired radius of the cicrle, and outmask
On 12/13/2023 7:47 AM, Dawn Matthews wrote:
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Hello Freesurfer team and thank you for your continued responses to
questions. My questions pertain to mri_cc, and subsegmentation of the
corpus callosum. In prior runs of version 6.0, it seems that aseg
out
Yes, that is correct.
On 12/13/2023 3:01 AM, Edwards, Vincent wrote:
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Hello,
I have several brains that I sent through recon-all using Freesurfer
7. If I wanted to use Freeview on Freesurfer version 5 to do
pial/wm/and control point edits, would I be able
Have you tried using the "intermediate" option (--int) in bbregister?
The intermediate volume should be a whole brain volume and it should
share a RAS space with the slab volume (eg, if they were acquired in the
same session; load both the slab and the intermediate in freeview to see
if they ar
We usually use the white surface because its placement is independent of
the placement of the pial surface (and so independent of thickness and
volume), but it is really an empirical question.
On 12/12/2023 11:26 PM, free_learner wrote:
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Dear experts,
Sur
tksurfer was deprecated years ago, though it's replacement (freeview)
does not seem to have that capability either.
On 12/12/2023 2:29 PM, Lee, Jeungchan wrote:
Hi Freesurfers,
I’m using TkSurfer to visualize my results and want to add a
horizontal color scale bar. I used [ -colorscalebarfla
I have not worked with the Brainnetome atlas so I don't know what it
will take. Maybe talk to the Brainnetome developers?
On 12/12/2023 11:05 AM, Blanca Zufiria Gerbolés wrote:
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Dear all,
I would like to extract the cortical thickness, subcortical volumes
Have you seen this page
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems ?
On 12/10/2023 8:55 AM, Hyunchul Lee wrote:
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Hello,
I've just started using Freesurfer this week and I'm quite confused
about coordinate systems.
Specifically, I have SEEG
Not sure what you mean by the background. You can try binarizing the
electrodes (mri_binarize), then load it as a segmentation.
On 12/8/2023 5:47 PM, Datta, Aditya wrote:
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Hi,
Is there any way to clear background for a volume file from the
command line. I
sorry, what is the dura flag you are talking about? Also, dura generally
interferes with the placement of the pial surface, not the white (ie,
white-gray boundary) surface.
On 12/7/2023 2:20 PM, Akkoyunlu, Beyza wrote:
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Hi,
I have longitudinal data with M
You should load
$chronic_CMI_volume_path/"$sub_base"_chronic-CMI_4-1.nii.gz into
freeview with the surfaces, eg
cd subject/mri
freeview nu.mgz
$chronic_CMI_volume_path/"$sub_base"_chronic-CMI_4-1.nii.gz -f
../surfs/?h.white ../surfs/?h.pial
and see if the lesion maps between the white and pia
No, sorry, that was only available in the old tksurfer/tkmedit. We have
not implemented it in freeview.
On 12/6/2023 6:37 PM, Tejaswi D. Sudhakar wrote:
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Hello,
I am to generate a plot to visualize the slopes between classes for
group analysis.
I would
You are right that using all the scans will bias toward tp2. I think I
would just run the cross for each time point using all the data you
have. This will not bias the base because an average of the images
within each time point will be used to make the base. If possible, you
will want to make
What volume and what surface? You can recon-all the MNI152NLIN2009cAsym
to generate surfaces, then they will be in registration directly
On 12/6/2023 10:30 AM, Lee, Jeungchan wrote:
Hi Freesurfers,
I was wondering if there is a registration matrix (from volumetric to
surface) for MNI152NLIN2
Hi Yunus
The ones with “pial” in them are from the pial surface for things like
curvature and surface area, the ones without are from the white surface. The
rest of the name indicates which cortical parcellation the statistics are
summarized in (e.g. the lh.aparc.pial.stats contains statistics
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hi freesurfers,I wanted to know what is the difference between
'.aparc.a2009s.stats', '.aparc.DKTatlas.stats', '.aparc.pial.stats', and
'.aparc.stats' in the stats directory of freesurfer results?thanks,Yunus
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