Dear List,
I have a similar problem with getting accurate pial and white matter surfaces in monkey inferior temporal, frontal and occipital regions. In those areas surfaces are not recognized properly. I tried putting control points with limited success. In my case most of the missed white matter voxels have the intensity value of 110. As was mentioned somewhere in the list, is it useless to have control points on the voxels with the value of 110? I would very much appreciate it if you could suggest any other ways to correct this problem.
Thanks, Kazu
Hi Paul,
The inferior temporal regions are the trickiest, especially in low quality scans - without seeing any images, you may have achieved as close as you are going to get.
Be careful with control points, more is not always better, quality over quantity, you want to be sure you have put them in correct locations, not on partial volumed voxels, and only in regions that are
supposed to be wm.
While adding voxels to the wm volume will have some impact on where the final surface lays, it is also dependant on finding the best intensity gradient. If your scans are lower quality with intensity troubles that will likely trump any edits you've made.
If you'd like to upload one of your subjects I am happy to take a look
at it
- although I will be out of town all next week so it might take me a
while to get to it.
Jenni
-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Greenberg Sent: Friday, January 05, 2007 7:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] control points and white matter edits
Hi all,
I'm having trouble getting accurate white and pial surfaces in inferior temporal regions on a few lower quality scans with significant intensity variation. I've added hundreds of control points and drawn in white matter in these regions when control points failed to recover unlabeled cortex, but when re-running the scripts with either -autorecon2-wm, or -autorecon2-cp, followed by -autorecon3
the surfaces are still not accurate. Are there other interventions I can to to get more accurate surfaces? If you manually add white matter why will the regenerated white matter surfaces not always
extend around the hand drawn parts?
Thanks, Paul
yes, they won't do anything if the wm is already 110. Check to see if there is a topological defect there.
On Thu, 18 Jan 2007, Tanji, Kazuyo (NIH/NIMH) [F] wrote:
Dear List,
I have a similar problem with getting accurate pial and white matter surfaces in monkey inferior temporal, frontal and occipital regions. In those areas surfaces are not recognized properly. I tried putting control points with limited success. In my case most of the missed white matter voxels have the intensity value of 110. As was mentioned somewhere in the list, is it useless to have control points on the voxels with the value of 110? I would very much appreciate it if you could suggest any other ways to correct this problem.
Thanks, Kazu
Hi Paul,
The inferior temporal regions are the trickiest, especially in low quality scans - without seeing any images, you may have achieved as close as you are going to get.
Be careful with control points, more is not always better, quality over quantity, you want to be sure you have put them in correct locations, not on partial volumed voxels, and only in regions that are
supposed to be wm.
While adding voxels to the wm volume will have some impact on where the final surface lays, it is also dependant on finding the best intensity gradient. If your scans are lower quality with intensity troubles that will likely trump any edits you've made.
If you'd like to upload one of your subjects I am happy to take a look
at it
- although I will be out of town all next week so it might take me a
while to get to it.
Jenni
-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Greenberg Sent: Friday, January 05, 2007 7:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] control points and white matter edits
Hi all,
I'm having trouble getting accurate white and pial surfaces in inferior temporal regions on a few lower quality scans with significant intensity variation. I've added hundreds of control points and drawn in white matter in these regions when control points failed to recover unlabeled cortex, but when re-running the scripts with either -autorecon2-wm, or -autorecon2-cp, followed by -autorecon3
the surfaces are still not accurate. Are there other interventions I can to to get more accurate surfaces? If you manually add white matter why will the regenerated white matter surfaces not always
extend around the hand drawn parts?
Thanks, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
There is no apparent topological wm or gm defect in those areas. Is there anything else I can do, like manually draw the contour?
Thanks, Kazu
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 18, 2007 9:33 AM To: Tanji, Kazuyo (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] control points and white matter edits
yes, they won't do anything if the wm is already 110. Check to see if there is a topological defect there.
On Thu, 18 Jan 2007, Tanji, Kazuyo (NIH/NIMH) [F] wrote:
Dear List,
I have a similar problem with getting accurate pial and
white matter
surfaces in monkey inferior temporal, frontal and occipital
regions.
In those areas surfaces are not recognized properly. I
tried putting
control points with limited success. In my case most of the missed white matter voxels have the intensity value of 110. As was
mentioned
somewhere in the list, is it useless to have control points on the voxels with the value of 110? I would very much appreciate
it if you
could suggest any other ways to correct this problem.
Thanks, Kazu
Hi Paul,
The inferior temporal regions are the trickiest, especially in low quality scans - without seeing any images, you may have
achieved as
close as you are going to get.
Be careful with control points, more is not always better, quality over quantity, you want to be sure you have put them in correct locations, not on partial volumed voxels, and only in regions that are
supposed to be wm.
While adding voxels to the wm volume will have some impact
on where
the final surface lays, it is also dependant on finding the best intensity gradient. If your scans are lower quality with
intensity
troubles that will likely trump any edits you've made.
If you'd like to upload one of your subjects I am happy to take a look
at it
- although I will be out of town all next week so it might
take me a
while to get to it.
Jenni
-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Greenberg Sent: Friday, January 05, 2007 7:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] control points and white matter edits
Hi all,
I'm having trouble getting accurate white and pial surfaces in inferior temporal regions on a few lower quality scans with significant intensity variation. I've added hundreds of control points and drawn in white matter in these regions when
control points
failed to recover unlabeled cortex, but when re-running
the scripts
with either -autorecon2-wm, or -autorecon2-cp, followed by -autorecon3
the surfaces are still not accurate. Are there other
interventions I
can to to get more accurate surfaces? If you manually add white matter why will the regenerated white matter surfaces not always
extend around the hand drawn parts?
Thanks, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
is the wm properly labeled there in the wm.mgz?
On Thu, 18 Jan 2007, Tanji, Kazuyo (NIH/NIMH) [F] wrote:
There is no apparent topological wm or gm defect in those areas. Is there anything else I can do, like manually draw the contour?
Thanks, Kazu
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 18, 2007 9:33 AM To: Tanji, Kazuyo (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] control points and white matter edits
yes, they won't do anything if the wm is already 110. Check to see if there is a topological defect there.
On Thu, 18 Jan 2007, Tanji, Kazuyo (NIH/NIMH) [F] wrote:
Dear List,
I have a similar problem with getting accurate pial and
white matter
surfaces in monkey inferior temporal, frontal and occipital
regions.
In those areas surfaces are not recognized properly. I
tried putting
control points with limited success. In my case most of the missed white matter voxels have the intensity value of 110. As was
mentioned
somewhere in the list, is it useless to have control points on the voxels with the value of 110? I would very much appreciate
it if you
could suggest any other ways to correct this problem.
Thanks, Kazu
Hi Paul,
The inferior temporal regions are the trickiest, especially in low quality scans - without seeing any images, you may have
achieved as
close as you are going to get.
Be careful with control points, more is not always better, quality over quantity, you want to be sure you have put them in correct locations, not on partial volumed voxels, and only in regions that are
supposed to be wm.
While adding voxels to the wm volume will have some impact
on where
the final surface lays, it is also dependant on finding the best intensity gradient. If your scans are lower quality with
intensity
troubles that will likely trump any edits you've made.
If you'd like to upload one of your subjects I am happy to take a look
at it
- although I will be out of town all next week so it might
take me a
while to get to it.
Jenni
-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Greenberg Sent: Friday, January 05, 2007 7:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] control points and white matter edits
Hi all,
I'm having trouble getting accurate white and pial surfaces in inferior temporal regions on a few lower quality scans with significant intensity variation. I've added hundreds of control points and drawn in white matter in these regions when
control points
failed to recover unlabeled cortex, but when re-running
the scripts
with either -autorecon2-wm, or -autorecon2-cp, followed by -autorecon3
the surfaces are still not accurate. Are there other
interventions I
can to to get more accurate surfaces? If you manually add white matter why will the regenerated white matter surfaces not always
extend around the hand drawn parts?
Thanks, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Does it turn gray in the wm.mgz if the wm is properly labeled? If so, it is not labeled properly in those areas.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 18, 2007 9:58 AM To: Tanji, Kazuyo (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] control points and white matter edits
is the wm properly labeled there in the wm.mgz?
On Thu, 18 Jan 2007, Tanji, Kazuyo (NIH/NIMH) [F] wrote:
There is no apparent topological wm or gm defect in those areas. Is there anything else I can do, like manually draw the contour?
Thanks, Kazu
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 18, 2007 9:33 AM To: Tanji, Kazuyo (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] control points and white matter edits
yes, they won't do anything if the wm is already 110.
Check to see if
there is a topological defect there.
On Thu, 18 Jan 2007, Tanji, Kazuyo (NIH/NIMH) [F] wrote:
Dear List,
I have a similar problem with getting accurate pial and
white matter
surfaces in monkey inferior temporal, frontal and occipital
regions.
In those areas surfaces are not recognized properly. I
tried putting
control points with limited success. In my case most of
the missed
white matter voxels have the intensity value of 110. As was
mentioned
somewhere in the list, is it useless to have control
points on the
voxels with the value of 110? I would very much appreciate
it if you
could suggest any other ways to correct this problem.
Thanks, Kazu
Hi Paul,
The inferior temporal regions are the trickiest,
especially in low
quality scans - without seeing any images, you may have
achieved as
close as you are going to get.
Be careful with control points, more is not always
better, quality
over quantity, you want to be sure you have put them in correct locations, not on partial volumed voxels, and only in
regions that
are
supposed to be wm.
While adding voxels to the wm volume will have some impact
on where
the final surface lays, it is also dependant on finding the best intensity gradient. If your scans are lower quality with
intensity
troubles that will likely trump any edits you've made.
If you'd like to upload one of your subjects I am happy
to take a
look
at it
- although I will be out of town all next week so it might
take me a
while to get to it.
Jenni
-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Greenberg Sent: Friday, January 05, 2007 7:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] control points and white matter edits
Hi all,
I'm having trouble getting accurate white and pial surfaces in inferior temporal regions on a few lower quality scans with significant intensity variation. I've added hundreds of control points and drawn in white matter in these regions when
control points
failed to recover unlabeled cortex, but when re-running
the scripts
with either -autorecon2-wm, or -autorecon2-cp, followed by -autorecon3
the surfaces are still not accurate. Are there other
interventions I
can to to get more accurate surfaces? If you manually add white matter why will the regenerated white matter surfaces not always
extend around the hand drawn parts?
Thanks, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
yes, the wm.mgz should be nonzero there. If it's not,check the brainmask.mgz and make sure it wasn't removed by the skullstripping On Thu, 18 Jan 2007, Tanji, Kazuyo (NIH/NIMH) [F] wrote:
Does it turn gray in the wm.mgz if the wm is properly labeled? If so, it is not labeled properly in those areas.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 18, 2007 9:58 AM To: Tanji, Kazuyo (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] control points and white matter edits
is the wm properly labeled there in the wm.mgz?
On Thu, 18 Jan 2007, Tanji, Kazuyo (NIH/NIMH) [F] wrote:
There is no apparent topological wm or gm defect in those areas. Is there anything else I can do, like manually draw the contour?
Thanks, Kazu
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Thursday, January 18, 2007 9:33 AM To: Tanji, Kazuyo (NIH/NIMH) [F] Cc: freesurfer@nmr.mgh.harvard.edu Subject: RE: [Freesurfer] control points and white matter edits
yes, they won't do anything if the wm is already 110.
Check to see if
there is a topological defect there.
On Thu, 18 Jan 2007, Tanji, Kazuyo (NIH/NIMH) [F] wrote:
Dear List,
I have a similar problem with getting accurate pial and
white matter
surfaces in monkey inferior temporal, frontal and occipital
regions.
In those areas surfaces are not recognized properly. I
tried putting
control points with limited success. In my case most of
the missed
white matter voxels have the intensity value of 110. As was
mentioned
somewhere in the list, is it useless to have control
points on the
voxels with the value of 110? I would very much appreciate
it if you
could suggest any other ways to correct this problem.
Thanks, Kazu
Hi Paul,
The inferior temporal regions are the trickiest,
especially in low
quality scans - without seeing any images, you may have
achieved as
close as you are going to get.
Be careful with control points, more is not always
better, quality
over quantity, you want to be sure you have put them in correct locations, not on partial volumed voxels, and only in
regions that
are
supposed to be wm.
While adding voxels to the wm volume will have some impact
on where
the final surface lays, it is also dependant on finding the best intensity gradient. If your scans are lower quality with
intensity
troubles that will likely trump any edits you've made.
If you'd like to upload one of your subjects I am happy
to take a
look
at it
- although I will be out of town all next week so it might
take me a
while to get to it.
Jenni
-----Original Message----- From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of Paul Greenberg Sent: Friday, January 05, 2007 7:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] control points and white matter edits
Hi all,
I'm having trouble getting accurate white and pial surfaces in inferior temporal regions on a few lower quality scans with significant intensity variation. I've added hundreds of control points and drawn in white matter in these regions when
control points
failed to recover unlabeled cortex, but when re-running
the scripts
with either -autorecon2-wm, or -autorecon2-cp, followed by -autorecon3
the surfaces are still not accurate. Are there other
interventions I
can to to get more accurate surfaces? If you manually add white matter why will the regenerated white matter surfaces not always
extend around the hand drawn parts?
Thanks, Paul
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Tanji, Kazuyo (NIH/NIMH) [F]