: Thursday, February 16, 2023 8:38 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Infant Freesurfer - manual edits
External Email - Use Caution
Dear Freesurfer experts,
Hello, I have started experimenting with Infant Freesurfer (version 4a14499),
and we have run
+
From: "Kang, Jee Won"
Subject: Re: [Freesurfer] Infant Freesurfer - manual edits
To: "freesurfer@nmr.mgh.harvard.edu"
Message-ID:
Content-Type: text/plain; charset="iso-8859-1"
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Dear Freesurfer ex
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Dear Freesurfer experts,
Hello, I have started experimenting with Infant Freesurfer (version 4a14499),
and we have run into a problem with very poor segmentation of the thalamus in
one of our subjects.
Is there a way to incorporate manual edits,
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Hi Dr Bruce,
I ran surface based analysis between one subject and a group of controls. The
problem is that I don't expect any difference in this region at least visually
(i.e. by looking at the CC in controls and compare it with the subject's data).
Hi John
is this causing a problem for you? What type of analysis do you want to
do that is impacted by this? If you upload the subject we will take a look,
but these regions are typically excluded from the surface analysis as they
are non-cortical anyway.
cheers
Bruce
On Wed, 30 May 2018,
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Hi Dr Bruce.
I highly appreciate your quick response. kindly see attached is another view.
The boundaries of the corpus callosum are not correctly defined on multiple
slices. Can this be fixed by setting control points in the CC regions?
Thanks
Hi John
I'm not sure I understand exactly what you are referring to. We
automatically fill in the ventricles so that they are contained within
the interior of the ?h.white surfaces. Is that what you thought was
incorrect?
cheers
Bruce
On Wed, 30 May 2018, John Anderson wrote:
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Dear FS experts,
My question is very basic and I appreciate your help.
I ran recon-all on a low quality T1 image. I'd like to fix the segmentation
error (attached).
Wm.mgz seems to be fine and the wm intensity is ~110. Can this error be fixed
by
/PialEdits_freeview
Antonin Skoch
Hi David,
Thank you for the feedback! I followed your advice's and everything has been
resolved. Highly appreciated!Cheers,
John
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Original Message
Subject: Re: [Freesurfer] manual edits
Local Time
Hi David,
Thank you for the feedback! I followed your advice's and everything has been
resolved. Highly appreciated!
Cheers,
John
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Original Message
Subject: Re: [Freesurfer] manual edits
Local Time: April 12, 2017 11
"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] manual edits
Dear Freesurfer experts,
I am not an expert in manual edits, so I highly appreciate any feedback
regarding the issues in my questions below. I ran the following command line
“recon-all
Hi Kaiming
those look pretty good. It's impossible to tell for sure from a single
slice.
Bruce
On Wed, 4 Dec 2013, Kaiming Yin wrote:
Dear guys,
I have a simple question in the manual edits parts.
I am using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 with Ubuntu 13.10,
for a
yes, the first one looks like an issue, psossibley a topological defect
fixed in the wrong way. What is the resolution of this data? The second one
looks like the surface dips into the cerebellum. What is the aseg like? The
3rd one looks ok, but I'm not positive that I understand what you are
Thanks, the resolution is: 1*1*1 (see below):
data_type INT16
dim1 160
dim2 240
dim3 256
dim4 1
datatype 4
pixdim11.00
pixdim21.00
pixdim31.00
pixdim42.299523
cal_max0.
Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Tue 11/6/2007 8:49 PM
To: Watson, Christopher
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Manual edits to aseg.mgz/brainmask.mgz
Hi Chris,
what type of acquisition are you using? Dura can be really hard to deal
] Manual edits to aseg.mgz/brainmask.mgz
Hi Chris,
what type of acquisition are you using? Dura can be really hard to deal
with, as it can look just like gm, depending on your MR parameters, and
it is can also be physically adjacent to gm. That said, it's only
usually a
problem in localized areas
Hello all,
I was wondering if there is a quick way to make edits to multiple slices
of the aseg.mgz (or the brainmask.mgz) volume.
Specifically, I am working on my first subject, and it seems that on
almost every slice, pieces of the dura/skull/arachnoid/what-have-you get
segmented as cortex
Hi Chris,
what type of acquisition are you using? Dura can be really hard to deal
with, as it can look just like gm, depending on your MR parameters, and
it is can also be physically adjacent to gm. That said, it's only usually a
problem in localized areas. What resolution is your data? We
.
-Original Message-
From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Tue 11/6/2007 8:49 PM
To: Watson, Christopher
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Manual edits to aseg.mgz/brainmask.mgz
Hi Chris,
what type of acquisition are you using? Dura can be really hard
PROTECTED]
Sent: Tue 11/6/2007 8:49 PM
To: Watson, Christopher
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Manual edits to aseg.mgz/brainmask.mgz
Hi Chris,
what type of acquisition are you using? Dura can be really hard to deal
with, as it can look just like gm, depending on your MR
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