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Please provide the following information:- if your host is a virtual
machine (VM, WSL) or on a real physical Linux or Mac system- what OS you are
running- what freesurfer package you installed from
under https://secure-web.cisco.com/13Sxt1nGEBeuhE82
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Hi:
I tried to run freeview, but I got the following error:
"This application failed to start because no Qt platform plugin could be
initialized. Reinstalling the application may fix this problem.
Available platform plugins are: eglfs, linuxfb, min
Dear Nima,
As of today, there is no longitudinal version of recon-all-clinical. It’s a bit
tricky to adapt the standard longitudinal pipeline in FreeSurfer to scans with
thick slices due to the anisotropy of the images, and also due to the deep
learning bits of the pipeline. But you can of cours
where did aseg.nii.gz come from? Is it an individual subject or on the
mni305? If from an individual try
mri_vol2vol --interp nearest --mov aseg.mgz --reg
transforms/talairach.xfm.lta --o aseg.mni305.mgz
On 2/8/2025 11:34 AM, neda afzalian wrote:
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>
> To w
You might be able to use surfa package. It is python so it should work
on windows
On 2/8/2025 2:30 AM, Gonzalo Rojas Costa wrote:
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Hi:
Is there any software for microsoft windows (and/or ubuntu) that
allows you to read mgz file format images, and transfor
The 5th vent, non-wm-hypos, left and right vessel are not worrisome. The
left and right cerebral cortex are probably just a few voxels that did
not get recoded to the surface parcellation. The ento and parahippo are
probably a segmentation error (good that there are only a few of them:)
On 2/
Dear FreeSurfer Team,
I am working with two timepoints for a subject and attempting to create a
template for samseg-long using mri_robust_template. However, I encountered an
error related to voxel size mismatch between the input images. Both timepoint
images are T1W.
The command I ran is:
mri_r
You can merge them together with a combination of mris_annotation2label
to split the annotation into different labels, then merge the labels you
want with mri_mergelabels, then use mris_anatomical_stats to compute a
stats file. Alternatively, and probably easier, is just to compute an
average o
I think what you are doing is fine. Those meshes were made over 25 years
ago, so the details you seek are probably lost
On 2/5/2025 7:26 PM, Samuel D Anderson wrote:
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Hello,
I am working on generating a vertex mapping file that identifies
corresponding ver
That is a harder problem. I'm not sure what is causing that bright spot.
Artery? B0? The problem is that it is too bright and the algorithm says
"hey, that's not gray matter" and does not know what to do. You can
edit the voxel intensities in the brainmask.finalsurfs.manedit to darken
them so
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Dear all,
I'm hiring a full-time research assistant. Please see below!
The Ohio State University, Dept. of Psychology – Dr. Zeynep Saygin’s Lab, to
assist with neuroscience research on the functional and structural architecture
of the human brain in
Dear Antonio,
NextBrain provides the ICV via SynthSeg 😉
Cheers,
/Eugenio
--
Juan Eugenio Iglesias
http://www.jeiglesias.com
From: freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Antonio Napolitano
Date: Wednesday, February 12, 2025 at 2:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [
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Dear Freesurfer experts,
I have run nextbrain but I am not sure whether it is possible to have the sTIV.
Please, I would need to know how I can compute:
1) histo atlas segmentation with the newest version of Nextbrain along with segm
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