Hi Jakob,
I believe we fixed the bug in FS 7.4 release. Can you give it a try?
Best,
Yujing
From: freesurfer-boun...@nmr.mgh.harvard.edu
On Behalf Of Litsch, Jakob Benjamin
Sent: Wednesday, December 6, 2023 10:40 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Segmentation error
External Email - Use Caution
Hi there,
Just want to check if you get the recon-all files that I sent for an entire
subject?!
I am also wondering if the problem with the segmentation can be related to
the small size of aged Portuguese brains considering the expected size
based for
Hi Gabriela
can you check the skull stripping and see if the cerebellum was removed
in the initial run? Did you have to adjust the skull stripping at any time?
It looks like the cerebellum is completely unlabeled, which usually
indicates a skull strippin problem
Bruce
On Mon, 22 Apr 2013, HO
total brain volume would be a more conservative normalization - it would
test the hypothesis that some brain regions are atrophying faster than
average.
cheers
Bruce
On Thu, 27 Oct 2011, Gergely Orsi wrote:
Yes.
This was our guess also, the problem is that these subject were scanned with
an
Yes.
This was our guess also, the problem is that these subject were scanned with
an old MPRAGE sequence that has only 160 slices and 0.94mm slice thickness,
thus it does not provide full brain coverage, part of the cerebellum is
missing for the big headed subjects.
That is the main reason for th
you can also check the accuracy of the registration used to compute the
eTIV with:
cd $SUBJECTS_DIR/$subject/mri/transforms
tkregister2 --lta talairach_with_skull.lta \
--targ $FREESURFER_HOME/average/RB_all_withskull_2008-03-26.gca \
--mov ../nu_noneck.mgz --reg junk.reg.dat
doug
Gergel
I think your acquisition is cutting off some cerebellum, and in any case
has a very steep intensity drop off in the cerebellum and brainstem. Is it
slab selective in that direction? You might try increasing the size of the
slab or lengthening your slab-select pulse, or including some oversamplin
SZEMAN2.tar.gz have just been uploaded.
Thank you
Gergo
2011/10/25 Gergely Orsi
> Yes of course, just a minute.
>
>
> 2011/10/25 Bruce Fischl
>
>> I meant canyou tar and gzip the subject and ftp it to us
>>
>> On Tue, 25 Oct 2011, Gergely Orsi wrote:
>>
>> Here you are:
>>>
>>> # Title Segme
Yes of course, just a minute.
2011/10/25 Bruce Fischl
> I meant canyou tar and gzip the subject and ftp it to us
>
> On Tue, 25 Oct 2011, Gergely Orsi wrote:
>
> Here you are:
>>
>> # Title Segmentation Statistics
>> #
>> # generating_program mri_segstats
>> # cvs_version $Id: mri_segstats.c,v
I meant canyou tar and gzip the subject and ftp it to us
On Tue, 25 Oct
2011, Gergely Orsi wrote:
Here you are:
# Title Segmentation Statistics
#
# generating_program mri_segstats
# cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 nicks Exp $
# cmdline mri_segstats --seg mri/ase
Here you are:
# Title Segmentation Statistics
#
# generating_program mri_segstats
# cvs_version $Id: mri_segstats.c,v 1.33.2.5 2009/02/11 22:38:51 nicks Exp $
# cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask
mri/brain
can you send us an example of one that is way off?
On Tue, 25 Oct 2011,
Gergely Orsi wrote:
Dear Bruce and others,
We have just ran into strange ICV volumes.
For all our 100+ subjets, the total icv is around 1500cm3 (around 1300-1700).
For the new group (only 7 subjects) the average ICV is
Dear Bruce and others,
We have just ran into strange ICV volumes.
For all our 100+ subjets, the total icv is around 1500cm3 (around
1300-1700).
For the new group (only 7 subjects) the average ICV is around 1200 (ranging
from 900-1500).
This is almost microcephalia, but they are normal.
If we
Thank you very much Bruce!
Have a nice day/night.
2011/10/3 Bruce Fischl
> The stuff outside the pial surface won't affect things, which is one of the
> reasons we prefer the surface-based measured of cortical morphometry.
>
> Similarly, we don't use the surface-based stuff in the hippocampus,
The stuff outside the pial surface won't affect things, which is one of
the reasons we prefer the surface-based measured of cortical morphometry.
Similarly, we don't use the surface-based stuff in the hippocampus, so you
should be all set (since many of the cortical assumptions aren't valid
th
Hi Alfredo
It must be a topological defect. You will need to find and correct it in the
wm.mgz
Cheers
Bruce
On Jun 8, 2011, at 7:42 PM, Alfredo Damasceno
wrote:
> Alfredo
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Hi Gonzalo,
sorry, I don't understand. What do you mean by "right-hippocampus of
T1.mgz"? T1.mgz isn't a label volume, it doesn't have a right-hippocampus
measure in it.
cheers
Bruce
On Thu, 5 Nov 2009, Gonzalo Rojas wrote:
> Hi:
>
> Which is the error of the volumes that appears in aseg.s
Hi:
Which is the error of the volumes that appears in aseg.stats ?... are
they quantifiable ?... Because I notice that the right-hippocampus (for
example) that appears in aseg.auto.mgz is bigger than the
right-hippocampus of T1.mgz image...
Sincerely,
--
Gonzalo Rojas Costa
Department
Hi Martin,
can you show the orig surface also? This is probably due to a topological
defect being incorrectly fixed. You can load the ?h.orig.nofix (or
inflated.nofix) surface and read in the ?h.defect_labels curvature file to
see if there was a defect in these regions. Does the white matter c
Great. Thanks!!
-Original Message-
From: florent segonne [mailto:[EMAIL PROTECTED]
Sent: Wed 5/18/2005 1:22 AM
To: Fornito, Alexander
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Segmentation error
Hello Alex,
This warning message appears during the watershed segmentation process.
The final brain shape is compared to a statistical atlas and the correctness
of the segmentation (of the shape) is evaluated.
It turns out that the validation is often too restrictive and often
generates a usele
Hi,
When running segment_subject, I get a meesage saying THE SEGMENTATION IS
PROBABLY NOT CORRECT at the validation stage. Any hints as to what might be
causing this and how to fix?
Thanks,
Alex
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