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Dear freesurfer experts,
I want to create 3D models (fbx or ply file) of the pial files including
the annotation/coloring that is loaded.
I tried to use mris_convert to make the pial file that was saved with
the annotation to convert the surface into
External Email - Use CautionDear Freesurfer experts,I was trying this command: $ recon-all -s Desikan -i /path/to/nii -all, to generate the anno files.But it ends up with the errors of MRInormFindControlPoints: could not find enough control points The .nii file I am using is the vol
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Hi Yang
The input to recon-all should be a T1-weighted MRI volume. I think what you are
giving it instead is a label volume
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Man YANG
Sent: Wednesday, June 14, 2023 6:52 AM
To:
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I’m not sure if I understood what you are trying to show. If you want to show
the cortical thickness on top of the pial surface, you can load it as an
overlay.
Ruopeng
On Jun 14, 2023, at 7:30 AM, Malav Shah
mailto:malav.s...@bccn-berlin.de>> wrote
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Thanks for your reply, Wang.
Sorry if the question was not clear. I will try to elaborate better.
Here is a cropped image from the previous screenshot. This is a T2 sequence,
and with a manipulated contrast, so the overall brightness is very high.
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Hi Loïc,
Uncertain if this will address the error you are receiving, but after looking
over your analysis.info files and the analysis script, it looks like you are
trying to analyze each individual retinotopy run (polar or eccen) separately?
If that
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Hi all,
I am running Freesurfer 7.3.2 on T1 images (LPI orientation) with
176*256*256 FOV, 1mm isotropic resolution.
I saw that the Ants N4 bias correction is done after the FOV is expanded to
256*256*256, not on the original image. Shouldn't t
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Hi Yujing,
Thanks. I am wondering about the reason why Freesurfer converts data types
to uchar. Doesn't this affect the non-uniformity bias correction
that follows?
Best,
Ruifeng
On Tue, Jun 13, 2023 at 9:37 AM Huang, Yujing
wrote:
> Extern
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Hello,
I am looking to run a MANCOVA to examine cortical gray matter differences
across three groups (accounting for several covariates), and I was hoping
to get input on whether I am setting up my design matrix correctly.
Groups: 3
Covariates: Age (d
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Hello,
I produced an m3z warp file with mri_gradunwarp.
Now I need to 0 out all displacement in the z direction, while keeping
everything else the same since I need to combine multiple warps from images
with different geometries.
I see two strateg
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Why can’t you visualize it on the pial surface? Any error message when you
attempt to do that? Can you elaborate?
On Jun 14, 2023, at 12:12 PM, Malav Shah
mailto:malav.s...@bccn-berlin.de>> wrote:
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Thanks for yo
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Dear Freesurfers,
A workaround was previously posted for Apple M1/2 processors to download and
run the 7.3.2 release of Freesurfer (here
https://secure-web.cisco.com/1rgq3XWhrkT5IzQbYknPjjI7Mi7jKtIiJWP1SE_KD5koSQ-3iSHZ30Nk2GI7phyDpowICRBD3HLzAMmu61OF
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Thank you for the prompt response and looking into the issue. I just checked
with the University IT, unfortunately FreeSurfer v7.4 and v7.3 requires
Centos7.X + above, whereas the Artemis HPC operating system at my university is
based on Centos 6.9,
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The link to msg 74015 did not work for me in the freesurfer mail list archive,
so I don’t know how that relates to what you are inquiring about. But
the freesurfer Intel Mac binaries generally run (automatically) using the
built-in Rosetta emulatio
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Thank you so much,
I previously used the workaround to uninstall and reinstall tensorflow that was
posted on the forum on 12th December 2022 for 7.3.2. This workaround worked for
the development version also this evening, but several tools are failin
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