If it came from running recon-all, then it is corrected for bias fields.
Note that B1 is a particular type of bias field (often quite minor at 3T
and below).
On 3/18/2021 2:25 PM, Arman Avesta wrote:
External Email - Use Caution
Hi FreeSurfer gang,
I'm using ADNI's pre-processed dat
External Email - Use Caution
Hi FreeSurfer gang,
I'm using ADNI's pre-processed data to train a neural network. Specifically,
for each included subject I'm using FreeSurfer Cross-Sectional brainmask.mgz
(as input).
My question is: are these ADNI pre-processed brainmask.mgz volum
fully I'll be able to fix it when he's back early next week.
Will let you know
Many thanks again,
Iwo
From: Allison Stevens
To: Iwo Bohr
Cc: Freesurfer@nmr.mgh.harvard.edu
Sent: Friday, 29 May, 2009 13:58:54
Subject: Re: [Freesurfer] brainmask.mg
Thanks Pedro, I was just thinking about it.
Iwo
From: Pedro Paulo de Magalhães Oliveira Junior
To: Iwo Bohr
Cc: Freesurfer@nmr.mgh.harvard.edu
Sent: Friday, 29 May, 2009 14:26:01
Subject: Re: [Freesurfer] brainmask.mgz recan-all and nu_correct error
Iwo
To
Iwo
To find where Perl is type:
*which perl*
---
Pedro Paulo de M. Oliveira Junior
2009/5/29 Allison Stevens
> Iwo,
> If you do
> ls $FREESURFER_HOME/bin
>
> Do you see mri_nu_correct.mni there?
>
> If you do, this message might help you:
> http://www.mail-archive.com/freesurfer@nmr.mgh.harva
Iwo,
If you do
ls $FREESURFER_HOME/bin
Do you see mri_nu_correct.mni there?
If you do, this message might help you:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg06793.html
Essentially, you have to make sure the nu_correct uses perl so you need to
make sure it knows where it's
Hello everybody,
Since I was corresponding with a few persons separetly, it required resending
the same information to all of them.
So I am getting back to the general forum with my still unsolved problem.
To recap: when I run recaon-all pipeline as below:
[iwob...@huxley FMRI]$ recon-all -autor
It's the volume created after the first normalization and skull stripping.
Allison
On Wed, 12 Nov 2008, Alexa Nardelli wrote:
Hey, I was just wondering if the brainmask.mgz file is the image after
normalization?
Thanks
Alexa
___
Freesurfer mailing
Hey, I was just wondering if the brainmask.mgz file is the image after
normalization?
Thanks
Alexa
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Freesurfer@nmr.mgh.harvard.edu
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Hi Petr,
I would try to be consistent throughout the study, even if this means
redoing some parts.
cheers,
Bruce
On Thu, 26 Jun 2008 [EMAIL PROTECTED] wrote:
Hi!
Have a couple of questions regarding manual edits correcting the
pial-surface.
Have found out, in some of our data sets, that th
Hi!
Have a couple of questions regarding manual edits correcting the
pial-surface.
Have found out, in some of our data sets, that the brain.mgz file has been
used instead of the brainmask.mgz during edits to correct the pial
surface. Seems that this protocol has been inherited from pre-version 3.
Hi Cate,
there is a section on the wiki about troubleshooting the skullstripping.
Try some of those recommendations first (mostly changing the preflooding
height). If the cerebellum is messed up, then the aseg probably won't work
well which can hurt the whole processing stream.
cheers,
Bruce
Hi,
I ran autorecon1 on a group of data consisting of a single set of mprage
DICOMs per subject, acquired on a Siemens Allegra 3T scanner. Several of
the brainmask.mgz images had large portions of the brainstem and cerebellum
removed. A couple had portions of the neck which were not removed. Th
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