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Dear community members,
I created a conda environment for installing MNE. Now I want to install
freesurfer in this same environment to use freesurfer in combination with
MNE.
Does anyone have already installed and configured freesurfer in an
mris_spherical_average will use the surface-based registration (?h.sphere.reg)
to map the labels to whatever your output subject is and do the averaging in
that space. You can specify fsaverage by -o fsaverage on the
mris_spherical_average command line. You shouldn’t need to do anything other
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My apologies, Bruce, now I’m more confused. We paint the sulci on the native
surfaces in Freeview. Then we register them to fsaverage. We want to register
them to fsaverage because we are interested in creating an average map that
would represent
Oh yes, that is your problem. mris_spherical_average assumes they are in
subject space
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Kristi Drudik
Sent: Friday, February 26, 2021 2:52 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Sulcal probability maps
Can you load the label onto that subject also?
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Kristi Drudik
Sent: Friday, February 26, 2021 2:37 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Sulcal probability maps
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Dear Douglas,
And is there a recommended way to compute a z value from the cluster
p-value?
With voxel-wise measure of z value, do you mean a z value of a particular
voxel, for instance, the voxel with the maximum p value in a cluster?
Thank you very
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Hello Andrew,
Please accept my apologies for such a detailed response, I had a health issue,
and I was just able to test what you suggested.
When I use the wget command, again I have an error: -bash: wget: command not
found
Any ideas on how to
Hello,
I am moving a 6mm volume from MNI152 to fsaverage for group analysis and I get
the following warning:
mri_vol2surf --src MNI_6mm.nii.gz --out surf_sm4_lh.mgh --mni152reg --hemi lh
--interp nearest --surf-fwhm 4
WARNING: the voxel resolution in the source volume (6,6,6) differs from
can you send the full screen output as text? Also, try it on 1 subject first.
The output should look like the input. Generally this error means some of your
surfaces are out of date (that is, you reran recon-all and didn't regenerate
everything, like the label files)
cheers
Bruce
fname is the name of the file you want to load for every subject (the label
file name in your case). Subject 1 is the FS id of the first subject you want
to load (followed by subject 2, ...)
cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf
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Hi Bruce,
Thank you for your reply! What is the difference between and
. I’m having some trouble running this command.
Best,
Kristi
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Fischl, Bruce
Sent: February 25, 2021 11:57 AM
To:
Hi Doug
Thanks for your reply.
They are talairach coordinates as it is mentioned in that paper.
How may I convert the talairach to RAS?
Thanks
MOna
Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
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Hi liangfeng kuang,
I think FreeSurfer is failing to find your subject
as you set the $SUBJECTS_DIR to .../kuang_dev_results
but your actual subject is in .../kaung_dev_data/... .
Best,
Horsng
> On Feb 26, 2021, at 10:41 PM, Douglas N. Greve wrote:
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Then How FreeSurfer calculates the volume, curvature etc from
Hippocampus and How could I check it?
El vie, 26 feb 2021 a las 14:44, Douglas N. Greve ()
escribió:
> Hippocampus is not part of the surface
>
> On 2/24/2021 10:40 AM, Alberto Del Cerro
You need to add -all to that command (will take 6-8 hours). In the end,
look in the subjectname/stats folder for lots of stats
On 2/25/2021 3:29 AM, Rosalia Dacosta Aguayo wrote:
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Dear all,
I would like to parcellate the brain and calculate the volumes,
Is the point truly talairach or is it mni152 or mni305.
If 152 or 305, then this page will tell you how to do the conversion
https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems
On 2/24/2021 3:26 PM, Nasiriavanaki, Zahra wrote:
Hi Freesurferers
I have some talairach coordinates on
You can't do it in tandem. The 2nd command should work, just don't
include -surf or -label
Also, when you do use -surf, you need a subject and a hemi, eg, -surf
fsaverage lh
On 2/24/2021 12:03 PM, Erin Moe wrote:
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>
> Hi Doug,
> Thank you for the advice! I
Hippocampus is not part of the surface
On 2/24/2021 10:40 AM, Alberto Del Cerro Leon wrote:
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Hello Freesurfers, I am doing an AAL atlas on freesurfer using
mri_vol2surf and editing the labels manually. However when I was
editing the labels in tksurfer the
Do you mean from an individual subject to MNI152 or from fsaverage?
On 2/24/2021 6:32 AM, 况况 wrote:
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Dear Community,
I want to acquire each amygdala subnuclei volumes' mask to from
freesurfer(fsaverage space) to spm(MNI space). what should i do? can
you
Not sure, the command line looks correct. Can you run it with -debug as
the first flag? Capture the output in a file (don't take a picture).
On 2/24/2021 6:14 AM, 况况 wrote:
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hello,
i downloaded dev version, input
Look for those commands in the subject/scripts/recon-all.cmd to verify.
It is possible that the table is not up-to-date
On 2/23/2021 10:52 AM, THIBEAU SUTRE Elina wrote:
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Thank you for your answer!
I actually found a .gcs version of the atlas here
There is no z value for the cluster itself, but you could take the
cluster p-value and use it to compute a z value. Or do you want a
voxel-wise measure of z value?
On 2/24/2021 4:00 AM, Agurne Sampedro Calvete wrote:
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Dear Freesurfer experts,
In
On 2/23/2021 11:37 PM, miracle ozzoude wrote:
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Thanks Doug. I appreciate it. I have more questions.
1) Aren't both models answering the same question regardless of which
side of the equation cortical thickness or syndromes is placed?
Similar questions,
Yes (excluding ventricles, of course)
On 2/23/2021 3:27 PM, Barletta, Valeria wrote:
Thanks a lot. One more thing, is the total brain volume
"BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles" ?
Valeria Barletta, MD
Massachusetts General Hospital
149 13th Street, Charlestown MA
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