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I am trying to create a 3D brain model from a *.nii file (here: test.niiI),
which I have copied to the subjects folder.
A) Using the command line, the following error messages appear:
Phils-MacBook:~ cnaehle$ recon-all -s brain -all -i
/Applications
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You don’t have permission to write to the default location of
SUBJECTS_DIR as set in the freesurfer shell environment, i.e.,
/Applications/freesurfer/7.4.1/subjects. The example subject data there
is on purpose meant to be read only along with the
Sorry, I deleted the original thread. Can you remind me of the original
problem?
On 1/13/2025 4:51 PM, Michael Eyre wrote:
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Hi, thanks for your response, apologies for late reply.
nu.mgz looks fine
When I run tkregisterfv --s subject --fstal : orig.mgz(
That recon-all.log file says it returned without error:
"recon-all -s E0001 finished without error at Mon Dec 23 12:20:40 KST 2024"
what's the problem?
On 1/13/2025 10:26 PM, 박경일 wrote:
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Dear FS Development Team,
I recently encountered an error while runn
That flag is to perform only the subcortical segmentation, but there are
are steps leading up to it that need to be done. If all you want is a
subcortical seg, then you can just run
mri_synthseg --i orig.mgz --o synthseg.mgz
On 1/15/2025 8:42 AM, Sara Rapuc wrote:
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it says finished without error
On 1/15/2025 5:13 PM, 박경일 wrote:
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Dear FS Development Team,
I recently encountered an error while running the recon-all process.
This is the first time I’ve experienced an issue with this routine
process. Please refer to the
It says that it cannot find /run/media/user/2TB/freesurfer/ASegStatsLUT.txt
does that file exist on your system?
On 1/16/2025 6:20 PM, 박경일 wrote:
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Dear FS Development Team,
I recently encountered an error while running the recon-all process.
This is the
You can edit the brain.finalsurfs.manedit.mgz to remove those voxels.
You may need to removed them from the wm.mgz and filled.mgz
On 1/21/2025 1:41 PM, Eszter Boros wrote:
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Dear FreeSurfer Team,
We are editing some longitudinal data using FreeSurfer 7.4.1
you can use the two stage model
On 1/15/2025 1:52 PM, Eszter Boros wrote:
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Dear FreeSurfer Team,
We are analyzing some longitudinal data (baseline [0], 6 months, 1
year, 1.5 years) using FreeSurfer 7.4.1.
We already analyzed two timepoints (basline[0] and
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Please let us know which freeeusfer release you installed using the
CentOS8 RPM file, e.g., as downloaded
from https://secure-web.cisco.com/1pEbxYZrDQAhBusbNo8pVT0Cdze9IJw2Pdh5Um6RyCRHAsipkgTH9ILKiFEaPYHAKtDWDhlXD5eGZ0jgd5Ma7Mg96D9WUrGdcC7yOD6wlvc_yj
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I have installed freesurfer on RHEL8. When I try to run the freeview, I get the
following error:
This application failed to start because no Qt platform plugin could be
initialized. Reinstalling the application may fix this problem.
Available platfo
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