Same as with any other input file type. See our tutorials
On 03/02/2017 11:30 AM, yusif Al-kheder wrote:
> Thank you,
> How would I go on about using the segmentation with nifti mri files.
>
> Youssif
>
>> On Mar 2, 2017, at 11:24 AM, Douglas N Greve
>> wrote:
>>
>>
>>
>>> On 03/02/2017 11:18 A
Thank you,
How would I go on about using the segmentation with nifti mri files.
Youssif
> On Mar 2, 2017, at 11:24 AM, Douglas N Greve
> wrote:
>
>
>
>> On 03/02/2017 11:18 AM, yusif Al-kheder wrote:
>> Hello,
>> Is it possible to segment the brain into these parts if possible using
>> fre
On 03/02/2017 11:18 AM, yusif Al-kheder wrote:
> Hello,
> Is it possible to segment the brain into these parts if possible using
> freesurfer;
> Cerebellum -- yes
> Midbrain -- not really (something called ventral diencphalon that overlaps a
> little)
> Pons -- no, but it is a target we will h
Hello,
Is it possible to segment the brain into these parts if possible using
freesurfer; Cerebellum
Midbrain
Pons
Medulla Oblongata
Hippocampus
Thalamus
Hypothalamus
Anterior and Posterior Commissura
Corpus Callosum
Hypophysis
Dura Mater
Youssif
___
1:34 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity
change
Hi Batool
you don't need -all and -autorecon2-cp -aurorecon3 (-all is both of those
and more). It must have generated some output. Is there a recon-all.log in
the freesurferfol
is...@nmr.mgh.harvard.edu]
> Sent: Thursday, December 01, 2016 5:21 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity
> change
>
> sure, good luck
> Bruce
> On Thu, 1 Dec 2016, Rizvi, Batool wrote:
>
>>
: Thursday, December 01, 2016 5:21 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity
change
sure, good luck
Bruce
On Thu, 1 Dec 2016, Rizvi, Batool wrote:
> Sounds great, thanks again for your help and will try out your
> recommend
.edu
> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, December 01, 2016 4:27 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity
> change
>
> yes, you ca
: Thursday, December 01, 2016 4:27 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity
change
yes, you can remove the control.dat file and run autorecon2-cp and
autorecon3. Should only take a couple of hours depending on your
processor
On Thu, 1 Dec
on behalf of Bruce Fischl
> [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, December 01, 2016 4:04 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity
> change
>
> the problme is that you have several control points i
urfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, December 01, 2016 4:04 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity
change
the problme is that you have several control points in v
Sent: Thursday, December 01, 2016 2:31 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity
> change
>
> hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not
> really possible to diagnose fr
t; [fis...@nmr.mgh.harvard.edu]
> Sent: Thursday, December 01, 2016 2:31 PM
> To: Freesurfer support list
> Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity
> change
>
> hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's n
d.edu] on behalf of Bruce Fischl
[fis...@nmr.mgh.harvard.edu]
Sent: Thursday, December 01, 2016 2:31 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] white matter segmentation incorrect after intensity
change
hmmm, that's awfully bright. Is it also bright on the orig.mgz? It&#x
hmmm, that's awfully bright. Is it also bright on the orig.mgz? It's not
really possible to diagnose from a single slice from a single subject. If
you tar, gzip and upload the subject one of us will take a look
cheers
Bruce
On Thu, 1
Dec 2016, Rizvi, Batool wrote:
Hi FreeSurfer experts,
; [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
> Sent: Tuesday, May 24, 2016 6:45 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] White matter segmentation
>
> see
> https://urldefense.proofpoint.com/v2/url?u=http-3A__ww
ision --interp nearest
Thanks,
Fari
-Original Message-
From: freesurfer-boun...@nmr.mgh.harvard.edu
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve
Sent: Tuesday, May 24, 2016 6:45 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] White matter segment
see
http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg47157.html
On 05/24/2016 05:44 PM, Mahmoudi, Fariborz wrote:
>
> Dear All,
>
> I want to segment white matter into 131xx and 141xx label series. I
> used aparc.a2009s but it just gave me cortex labels (111xx and 121xx).
> Can
Dear All,
I want to segment white matter into 131xx and 141xx label series. I used
aparc.a2009s but it just gave me cortex labels (111xx and 121xx). Can anyone
guide me how could I do this?
Regards,
Fari
CONFIDENTIALITY NOTICE: This email contains information
mri_binarize is a freesurfer command-line program and --wm is an option
to that program.
On 10/03/2014 02:09 AM, Leise Borg wrote:
>
> Hi FreeSurfer
>
> I need the white matter segmentations, and I've looked at some e-mail
> correspondence and one answer I think I can use is the following:
>
>
Hi FreeSurfer
I need the white matter segmentations, and I've looked at some e-mail
correspondence and one answer I think I can use is the following:
If you just want white matter, then better to create a mask from the
aparc+aseg.mgz with mri_binarize with the --wm flag.
doug
I just don't underst
: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] white matter segmentation
Hi Bruce,
I am running the latest version of Freesurfer.
I am sorry but I am still not really sure as to how to fix the wrong
segmentation. Even if I see that there was an error before the
topology correction (which
Hi Bruce,
I am running the latest version of Freesurfer.
I am sorry but I am still not really sure as to how to fix the wrong
segmentation. Even if I see that there was an error before the
topology correction (which basically means that the correction made it
worse?), how and where do I correct it
Hi Jenny,
it's probably the topology correction that is causing your problem. What
version are you running? Look for a topological error in that region (i.e.
a hole or a handle). You can usually see the defects on the
?h.inflated.nofix surface. Load it with:
tksurfer -orig orig.nofix $subjec
Hi Bruce,
thanks for the quick response.
I am still not quite sure though where to do the edits. On the
brainmask? I originally thought that I have to do the edits of the
white matter segmentation on the wm.mgz. However, on the wm.mgz the
white matter segmentation looks fine (i.e., the superior t
Hi Jenny,
the ?h.white is pretty much our final say one where the gray/white
boundary is, and is usually substantially more accurate than the wm.mgz.
Your dataset has a lot of motion artifact, but mostly looks okay except for
the superior temporal gyrus, which has been chopped. You'll need to
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