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Hi Doug & Gaurav,
There are some instructions for running recon-all on skull stripped brains in
the FAQ’s on the wiki
https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Ihavealreadyskull-strippeddata.CanIsubmitittorecon-all.3F
pasted
script from Freesurfer 7.0. We have someone working to
integrate it into the same python framework as SAMSEG and segment_subfields but
we are limited by available developer time.
BW,
Henry
From: Georgios Argyropoulos
Date: Friday, 12 April 2024 at 11:04
To: Tregidgo, Henry
Cc: freesurfer
: Georgios Argyropoulos
Date: Thursday, 11 April 2024 at 17:24
To: freesurfer@nmr.mgh.harvard.edu , Tregidgo,
Henry
Subject: Re: [Freesurfer] Question on using thalseg_1.1.h5
⚠ Caution: External sender
Many thanks and apologies, Henry - I figured it out... I stupidly replaced your
improved
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Hi Georgios,
This isn’t an error that I’ve personally come across before. Would you mind
answering a few questions and we’ll see if we can get this running for you.
1. Can I ask which operating system you are running FreeSurfer on?
2. Have
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Hi Adrian,
For features added after June 2023 you will need to use a development or "dev"
version of freesurfer.
Download and installation instructions can be found at
elogo%2FdefaultAvatar.png]
zlseu2109
zlseu2...@163.com
Replied Message
FromTregidgo, Henry <mailto:h.tregi...@ucl.ac.uk>
Date07/10/2023 21:41
To freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject Re: [Freesurfer]
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The Pt is one of a few nuclei that can sometimes not make it into the final
visualisation (others being the Pc and Vm). For these very small nuclei, their
posterior probabilities (soft segmentation) generated by the Bayesian
segmentation algorithm
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I believe these are describing the regional image values extracted from the
bias corrected and normalised input image. They give the mean, standard
deviation, minimum, maximum and range for each ROI.
The relevant image should be saved as
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Hi,
Thank you for your interest in our tool. Currently these three nuclei are not
segmented by the network implementation, but they will be segmented by the
Bayesian tool once we have integrated it into FreeSurfer.
The Pc, VM and Pt are the three
