Hi Michelle
the wm segmentation is kind of irrelevant - it's the ?h.white surfaces
that matter (and maybe not even those if you only care about subcortical
things)
cheers
Bruce
On Fri, 25 Aug 2017, Michelle VanTieghem wrote:
Hi Bruce,
I got this to work, but we are still having the same pr
Hi,
As a related question, we have been using FSL 5.3.
I would like to use LME methods. I noticed that FSL 5.3 "Allows processing
of subjects with single time point through the longitudinal stream to
include them without bias into statistical analysis (LME)."
but the Matlabs LME tools are only men
Hi Bruce,
I got this to work, but we are still having the same problem wth
over-inclusion of pial matter in the white matter segmentations even when
using skullstrip from other packages (AFNI , FSL, ANTs).
I am mainly interested in the subcortical volumes, and I want to do a
longitudinal analysi
are you sure you created the brainmask with -rl orig.mgz? It should have
the same dimensions afterwards.
On Wed, 9 Aug 2017, Michelle VanTieghem
wrote:
-bash-4.1$ mri_info orig.mgz
Volume information for orig.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1., 1.0
-bash-4.1$ mri_info orig.mgz
Volume information for orig.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1., 1., 1.
type: UCHAR (0)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
can you send us the output of mri_info on orig.mgz and brainmask.mgz
created with the -rl flag? And also send us the full screen output of the
command that fails?
thanks
Bruce
On Wed, 9 Aug 2017, Michelle VanTieghem
wrote:
Hi,
I originally used
mri_convert orig.mgz afni_stripped_volume.b
Hi,
I originally used
mri_convert orig.mgz afni_stripped_volume.brik brainmask.mgz
and I re-did it using the -rl flag as you recommended.
it did not influence anything, same problem.
I'd appreciate any trouble shooting tips.
Thanks,
M
On Mon, Aug 7, 2017 at 5:45 PM, Bruce Fischl
wrote:
> w
what viewer did you check in? If not freeview, look at it in freeview
On
Mon, 7 Aug 2017, Michelle VanTieghem wrote:
Hi,
After checking the images in the viewer, it appears that 001.mgz and
brainmask.mgz are in the correct orientation, but brain.mgz (created by
freesurfer) is rotated 90 degre
what was your mri_convert command line? It should be something like
mri_convert -rl orig.mgz afni_stripped_volume.brik brainmask.mgz
cheers
Bruce
On Mon,
7 Aug 2017, Michelle VanTieghem wrote:
Hi Bruce,
Here is what I did. For each subject:
a) used the original (non-skull stripped) brain
Hi,
After checking the images in the viewer, it appears that 001.mgz and
brainmask.mgz are in the correct orientation, but brain.mgz (created by
freesurfer) is rotated 90 degrees. The dimensions of the images don't match
either.
001.mgz and brainmask.mgz are:
dim1 219
dim2 268
Hi Bruce,
Here is what I did. For each subject:
a) used the original (non-skull stripped) brain for the 001.mgz file as
input - located in the Subnum/mri directory
b) used mri_convert to get the afni skull-stripped brains and renamed them
"brainmask.mgz" , located in the Subnum/mri directory.
c) T
no, you don't use brainmask as input, you just put it in the subject's
mri dir. recon-all should then recognize that it is different than
brainmask.auto.mgz, assume it has been manually edited, and preserve
those edits
On Tue, 18 Jul 2017, Michelle VanTieghem wrote:
Hi,
Yes, I am trying to u
Hi,
Yes, I am trying to use skull stripping from another package, since -gcut
option did not work on our data for appropriate skull stripping, and as a
result there is too much pial matter included as white matter.
a) Is brainmask.mgz an appropriate input file for recon-all -all? for
example, sho
I think if you convert the afni's skull stripping to .mgz format and put
it in mri/brainmask.mgz we will recognize that it is different from
brainmask.auto.mgz and use it instead
cheers
Bruce
On Wed, 12 Jul 2017, Michelle
VanTieghem wrote:
Hi, I am just following up on my previous question.
Hi,
I am just following up on my previous question.
The -gcut does not appear to make any difference on our skull stripping. I
also saw that you can change flags for watershed option. Do you recommend
this? If so, how would you implement this on freesurfer output that was
already run?
We achieve
Hi Michelle
yes, you can try putting already stripped data through, or I think if you
convert the afni skull stripped volume to $subject/mri/brainmask.mgz
recon-all should recognize that it is different from the auto stripping and
use it instead
cheers
Bruce
On Tue, 4 Jul 2017, Michelle Van
Hello,
I am just following up on this question.
Thanks!
Michelle
On Tue, Jun 27, 2017 at 4:46 PM, Michelle VanTieghem <
michelle.vantieg...@gmail.com> wrote:
> Hi Bruce,
>
> The -gcut does not appear to make any difference on our skull stripping. I
> also saw that you can change flags for water
sure, you can use whatever format we support - we will recognize it by
the extension (e.g. .nii or .nii.gz).
cheers
Bruce
On Tue, 27 Jun 2017, Michelle
VanTieghem wrote:
Hi Bruce,
The -gcut does not appear to make any difference on our skull stripping. I
also saw that you can change flags f
Hi Bruce,
The -gcut does not appear to make any difference on our skull stripping. I
also saw that you can change flags for watershed option. Do you recommend
this? If so, how would you implement this on freesurfer output that was
already run?
We achieve fairly good skull stripping with this data
-gcut should do the trick
cheers
Bruce
On Mon, 12 Jun 2017, Michelle VanTieghem wrote:
Hi,
Thanks for your response. Maybe I am missing something, but I haven't been
able to find any documentation about how to use graph cuts skull stripping
in the freesurfer pipeline. can you please advise?
T
Hi,
Thanks for your response. Maybe I am missing something, but I haven't been
able to find any documentation about how to use graph cuts skull stripping
in the freesurfer pipeline. can you please advise?
Thanks,
Michelle
On Mon, Jun 12, 2017 at 2:48 PM, Bruce Fischl
wrote:
> Hi Michelle
>
> y
Hi Michelle
you can try using the graph cuts skull stripping. It is more aggressive
and more likely to remove more skull/dura (and also to remove some brain)
cheers
Bruce
On Mon,
12 Jun 2017, Michelle VanTieghem wrote:
Hello,
We have assessed freesurfer output for 160+ brains, and about 5
Hello,
We have assessed freesurfer output for 160+ brains, and about 50% have poor
segmentation of pial matter that includes too much skull. Manual edits and
re-running does work to improve the problem, but is very time/labor
intensive for so many scans.
I saw on the freesurfer wiki that you can
uis, MO 63110 Email: mha...@wustl.edu
From: Francesco Siciliano
Date: Wednesday, August 28, 2013 12:36 PM
To: "Harms, Michael"
Subject: RE: [Freesurfer] pial surface editing
My main issue is that the edits I make to brain.finalsurfs.manedit.mgz are not
being
incorporated into the reconfig
From: Francesco Siciliano <sici...@nyspi.columbia.edu>
Date: Wednesday, August 28, 2013 12:36 PM
To: "Harms, Michael" <mha...@wustl.edu>
Subject: RE: [Freesurfer] pial surface editing
My main issue is that the edits I make to brain.finalsurfs.manedit.mgz are not being incorpo
4-747-6173
St. Louis, MO 63110
Email: mha...@wustl.edu
From: Francesco Siciliano <sici...@nyspi.columbia.edu>
Date: Wednesday, August 28, 2013 11:01 AM
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] pial surface editing
Hello,
I am having a few issues with editing the pial surface in freeview. It appears
as though the edits I make to the brainmask are not being taken into account
when I re-run recon-all. I work on a MacBook Pro and have been using
"shift+click" to delete voxels at a brush value of 1 and then s
Hello,
I am having a few issues with editing the pial surface in freeview. It appears
as though the edits I make to the brainmask are not being taken into account
when I re-run recon-all. I work on a MacBook Pro and have been using
"shift+click" to delete voxels at a brush value of 1 and then s
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