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Dear Freesurfeer experts,
After running the recon-all, a part of the temporal lobe of one subject was
removed.
I used the watershed algorithm to be less agressive in the skull stripping
step:
recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatl
Hi Manuela
you can certainly do manual editing in freeview
cheers
Bruce
On Thu, 10 Jan 2019, Manuela
Costa wrote:
External Email - Use Caution
Dear all,
We have a subject for whom we would like to do hippocampal subfield and
amygdalar nuclei
segmentation. Unfortunately,
External Email - Use Caution
Dear all,
We have a subject for whom we would like to do hippocampal subfield and
amygdalar nuclei segmentation. Unfortunately, this subject has a large
lesion in the right hemisphere. Looking at the aseg, the segmentation of
the bilateral amygdala a
I see. Yes, that kind of thing is hard. YOu can try the gcuts
skullstripping, which is more aggressive and can sometimes get rid of
this kind of thing, but it also is more likely to strip brain. Or
manually remove those voxels in the brainmask.mgz
cheers
Bruce
On Thu, 22 Jun 2017, Lisa
Delal
Hi Bruce,
Thank you very much for your mail. I am going to specify my question.
In fact, we saw a problem after the recon-all step. The dura was included
in the lh.pial and rh.pial. Indeed, the red demarcation included the
meninges.
I send you an attachment
Cheers
Marine
2017-06-21 18:51
Hi Marine
the brainmask is just a rough estimate of what is brain and what is not.
You don't need to worry if it is not accurate *unless* the lh.pial and/or
rh.pial surfaces end up not being accurate because of dura left in the
brainmask.
cheers
Bruce
On Wed, 21 Jun 2017, Lisa Delalande wrot
Hi,
I am a PhD student and faced a problem with Freesurfer, more specially with
segmentation. First of all, I did a typical qsub command. However, when I
cheked with tkmedit, I saw problems of brainsmask. Indeed, meninges are
often considered as grey matter.
I tried these different commands :
the intensity normalization has a region growing component that is bounded
by intensity gradients. In images like MPRAGE, where SNR is traded for CNR
it can help to raise the threshold for stopping so that more white matter
is included (that's what the -b 20 does, I think the default it 10 or 15
Thanks.
I'll try without expert opts.
But i'm not sure if i can get better results.
Before I found out these expert opts, I ran some images recon2 without
expert opts. And they got poor segmentation.
Actually, some images showed improvement with those options.
I'm curious why these options work for
Can you try it without the expert opts? And what sequence is the data?
On Nov 12, 2012, at 3:35 AM, youngmin huh wrote:
> Hi
> I'm working with some images, and freesurfer didn't properly detect some of
> their white matter boundaries.
> I attached some examples.
> I ran recon2 with expert op
Hi Markus
can you send us an example of where you think the volume is far too low?
Tar and gzip the entire subject dir and put it on our filedrop
cheers
Bruce
On Thu, 5 Jan
2012, Markus Savli wrote:
> Dear Freesurfer Community!
> Recently I started working with Freesurfer and had a number of s
Dear Freesurfer Community!
Recently I started working with Freesurfer and had a number of
subjects processed through the pipeline (recon-all -autorecon-all
-subjid subjname) without error.
So far I am mainly interested in the outcome of the segmentation
of s
Check the skull stripping. This can cause the FS-specific talairach
alignment to fail.
Paltoglou, Aspasia E wrote:
> Dear All,
>
> I am new to freesurfer and I was wondering if you could give me some advice.
>
> I run the freesurfer analysis on the anatomical scan of one subject and I
> noticed
Can you send us the dataset?
On Sep 16, 2009, at 12:18 PM, "Paltoglou, Aspasia E" wrote:
> Dear All,
>
> I am new to freesurfer and I was wondering if you could give me some
> advice.
>
> I run the freesurfer analysis on the anatomical scan of one subject
> and I noticed that in output fil
Dear All,
I am new to freesurfer and I was wondering if you could give me some advice.
I run the freesurfer analysis on the anatomical scan of one subject and I
noticed that in output files from wm.asegedit.mgz onwards, large part of the
brain (frontal lobes) appears to be missing. I checked th
Hi Rachel,
looks like the superior gm is very dark, so some control points in the
superior wm should help. That said, this is much worse than we usually
see.
Let us know how it goes.
cheers,
Bruce
On Tue, 20 May 2008, Dick, Rachel wrote:
Hello,
I'm having some issues with the cortex as
Hello,
I'm having some issues with the cortex as seen in the attached picture.
I know in the more medial regions I can add control points to the white
matter to help the pial line extend further out. However, laterally,
I'm not sure how to include that cortex that is left out. Any help
would
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