You probably don't have write permission to that folder.
Also, you can try
mri_segstats --qa-stats subject subject.qa.dat
Run mri_segstats with --help to understand what is in the qa.dat file
On 2/17/2023 7:43 PM, MANSON ERIC NAAB wrote:
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Thank you once
Yes, but you have to get it started in about the right place.
On 2/23/2023 9:47 AM, Fischl, Bruce R.,PHD wrote:
Hi Sebastien
I believe that Doug has had success using bbregister for this. You
might give it a try
Cheers
Bruce
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
*On Behalf Of
Under "Render" select "Mesh"
Under "Annotation" hit the View/Edit button. From there you can turn any
annotation on or off.
On 2/22/2023 2:34 PM, Leonardo Tozzi wrote:
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Dear Experts,
I would like to use Freeview to achieve the following.
I would like to
If you are using 7.X, you can run
tkmeditfv subject norm.mgz -defects
This will load a "segmentation" with the defects in the volume, an
annotation (surface segmentation) showing them on the surface, and a
point set that you can go to any of the points.
On 2/21/2023 7:21 PM, KennethSPrice
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Hi,
The latest post I could find about substantia nigra segmentation in
FreeSurfer is from May 2020
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Hello Elmira,
You can try downloading an installing the 7.3.2 package file,
freesurfer-darwin-macOS-7.3.2.pkg, from
These are segments in the wmparc.mgz file. Originally, I called these
centrum semiovale, but I realized that, while they might overlap heavily
with CS, it they were really just voxels left unsegmented by the main
process and I did not really know that they were a good segmentation of CS.
On
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Dear,
Please, request to pass code to open the file
FS_7_2_0_Ubuntu_18_04_06.ova.7z
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Dear Team,
I'm about to install Freesurfer in a VirtualBox VM under Windows.,
following the instructions in
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Dear Freesurfer team,
I was wondering if FS has a way to segment the centrum semiovale?
The freesurfer colorLUT table mentions "Centrum semiovale is also labled
with 5001 (left) and 5002 (right)." (see
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Hello, I'd like to request the password for FS_7_2_0_ubuntu_18_04_06.ova.7z
in
order to install the virtual image and run Freesurfer in a Virtualbox VM.
Thank you!
Omar Ahmed
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Hi Inga,
Did you infant_recon_all run through without any errors? If you see the regular
FS directory structure in your subejct directory that woudl mean the
infant_recon_all successfull completed. If there is only a "work" directory
there, that means the process quit in the middle of the
Hi Inga,
Sorry, I missed this message on the mailing list.
This is a new issue to me, so I will take a look at the label fusion step.
And yes, we are working on including T2w images in the pipeline as at the
newborn stage it would help with the GM/WM segmentation accuracy.
Best, Lilla
Hi Chris,
Are you setting the environment path correctly? It seems that infant_recon_all
cannot find the relevant folder.
Best, Lilla
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Sayre, Christopher
Sent: Wednesday, January 25, 2023 9:13 AM
To:
Hi Jee Won,
Currently the infant stream does not allow for a rerun after manual edits.
Editing the thalamus though would not impact the surface computations though.
Best, Lilla
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Kang, Jee Won
Sent:
You'll probably have to use matlab, eg,
[vertices, label, colortable] = read_annotation(filename)
ind = find(label==yourlabel);
beta = fast_vol2mat(MRIread('beta.nii.gz'));
yourlabelbeta = beta(:,ind);
On 3/6/2023 10:08 AM, Huang, Yujing wrote:
Hi Andy,
Can you try the mask option?
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Hi everyone,
Could someone please direct me to the workaround instructions on installing
Freesurfer on Mac M1 ultra on OS 13.0 Ventura?
Thank you,
Elmira
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can you send an example?
On 2/17/2023 9:38 AM, Federica Di Antonio wrote:
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Dear experts,
I hope this email finds you well.
I run the pvc correction with mri_gtmpvc for subjects data obtained
with two different PET tracers.
In gtm.stats.dat, for every
On 2/17/2023 9:21 AM, Federica Di Antonio wrote:
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Dear Freesurfer experts,
I'm using PETsurfer. I've done the standard pipeline for all my
subjects, using the cvs registration.
I was wondering (maybe it's very stupid) when the standard pipeline
"uses"
when you say that it is better cortex segmentation, do you mean better
than the aseg.mgz=aparc+aseg.mgz or better than the aseg.presurf.mgz? Do
you mean in general or just near the WMH? The aseg/aparc+aseg use the
surfaces to refine the gray/white boundary, and usually the surfaces do
a much
On 2/15/2023 5:35 PM, Antonio #30 wrote:
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Hello again,
I would like to ask one last thing.
How can the class averages computed from csdbase.y.ocn.dat not match
the gamma.mgh values in the cluster?
e.g. How can gamma show +29 in a vertex that is part of
I think it is basically the same procedure as the other segmentations,
ie, a set of 40 subjects' whole brains were manually labeled, many of
them had WMH, then it is just the normal Bayesian labeling as in Bruce
Fischl's 2002 Neuron paper.
On 2/13/2023 12:37 PM, Alberto Del Cerro Leon wrote:
That one looks like there was a massive failure of the registration. One
thing you can try is to add -samseg-reg to the command line. This will
use samseg to do this registration, which may be more robust. Is there
anything amiss with your image?
On 2/13/2023 10:25 AM, Goeckner, Bryna wrote:
Hi Andy,
Can you try the mask option?
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_glmfit
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Andy Kim
Sent: Tuesday, February 28, 2023 10:47 PM
To: freesurfer
Subject: [Freesurfer] How to get individual betas (parameter
Hi Philipp, by default, those parameters are not used anymore as we are
using ANTS N4 (though this is not obvious). There is no separate
parameter set for for 3T for N4. It is still possible to use the old
MNI N3 code, so we have kept it in there.
On 2/25/2023 2:58 PM, Saemann, Philipp
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Hi,
I do not have the pass code to open the Ubuntu compressed image with
Freesurfer, can you provide me with that?
Thank you very much.
Best regards,
Chloe
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Hi,
You can find sources on Freesurfer Wiki -
https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki
Here the page about conducting an at-home FreeSurfer Course -
https://surfer.nmr.mgh.harvard.edu/fswiki/TeachYourselfFreeSurfer
Best,
Yujing
-Original Message-
From:
Hi Tracy,
I’m wondering if you have any success with other subjects. Can you attach the
failed recon-all.log?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Tracy Riggins
Sent: Sunday, March 5, 2023 1:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer]
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