subject:"\[Freesurfer\] aparc \& wm underestimation"

Re: [Freesurfer] aparc & wm underestimation

2024-03-29 Thread Douglas N. Greve

Oh, I see you are using 7.1.1. You can upgrade to 7.4.1. This will not 
change the basic recon-all output and you'll have access to those new 
features.


On 3/16/2024 4:21 PM, Stanica, Maria wrote:


External Email - Use Caution

We checked and the ?h.orig surface looks right. We tried the -expert 
options file that you suggested anyway, but it exited with errors 
unfortunately and didn’t work. Is there anything else we can try?


Thanks again for your help!

Best,

Maria

*From: *freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 


*Date: *Wednesday, March 6, 2024 at 9:20 AM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] aparc & wm underestimation

This is difficult to debug remotely. The first thing to look at is the 
?h.orig surface. Does that look more-or-less right? If not, then it 
means that the wm.mgz is wrong. If it does not look right, it means 
that the surface placement algorithm is pushing the surface into 
subcortical gray. One way to overcome this is to create a 
brain.finalsurfs.manedit.mgz by copying the brain.finalsurfs.mgz, then 
edit the brain.finalsurfs.manedit.mgz to set those areas where the 
surface is off to 255. Then create an expert options file with

WhitePreAparc --rip-bg-no-annot --restore-255  --outvol mrisps.wpa.mgz
PlaceWhiteSurf --restore-255 --outvol mrisps.white.mgz
T1PialSurf --restore-255 --outvol mrisps.pial.mgz
And pass that to recon-all with the -expert option

On 3/5/2024 7:10 PM, Stanica, Maria wrote:

*External Email - Use Caution *

Yes, the problem is that the white surface on the left side of the
image is extending too far into subcortical gray matter. We did
delete the control points and ran some white matter edits, but the
image I sent you is after we applied those edits (it was even
worse before). I don’t see any other wm edits we can make to the
image. It didn’t resolve our issue enough to make the image usable
for our analyses, so I wanted to see if there was anything else we
could do to resolve the problem.

Thank you!

*From: *freesurfer-boun...@nmr.mgh.harvard.edu

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
*Date: *Tuesday, March 5, 2024 at 9:11 AM
*To: *freesurfer@nmr.mgh.harvard.edu

<mailto:freesurfer@nmr.mgh.harvard.edu>
    *Subject: *Re: [Freesurfer] aparc & wm underestimation

Just to make sure I understand, the problem is that the white
surface on the left side of the image is extending too far into
subcortical gray matter, right? This can be difficult to fix, but
the right fix is to edit the wm.mgz. Make sure to delete your
control points as that is not the right fix. Also, remember that
the surfaces in this area may always be inaccurate if you can see
where the boundary is.

On 3/3/2024 6:09 PM, Stanica, Maria wrote:

*External Email - Use Caution *

This is after the most recent round of edits for one of the
subjects.

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu <mailto:mstan...@uab.edu>

Pronouns: she/her/hers

Image

*From: *freesurfer-boun...@nmr.mgh.harvard.edu

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
*Date: *Sunday, March 3, 2024 at 3:38 PM
*To: *freesurfer@nmr.mgh.harvard.edu

<mailto:freesurfer@nmr.mgh.harvard.edu>
    *Subject: *Re: [Freesurfer] aparc & wm underestimation

Can you send pictures of the slices showing the problem?

On 3/3/2024 3:18 PM, Stanica, Maria wrote:

*External Email - Use Caution *

Hello FS developers,

I ran my subjects through skullstripping and recon-all.
Everything processed correctly (and exited without
errors), except 4 images which have an underestimation in
coronal subcortical region. The underestimation is
significant and goes on for about 10-12 slices (for one
image it was 153-162, for another it was 150-164).

After searching the list, we attempted control points,
which ended up not working (I don’t believe this was the
right method to correct the error). Then we tried white
matter edits, and one of the images was resolved, but the
other 3 did not get better. Is there anything else we
could do to try to resolve the issue? I can provide any
other information needed. Any help would be appreciated!

 1. Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64

Re: [Freesurfer] aparc & wm underestimation

2024-03-16 Thread Stanica, Maria

External Email - Use Caution

We checked and the ?h.orig surface looks right. We tried the -expert options 
file that you suggested anyway, but it exited with errors unfortunately and 
didn’t work. Is there anything else we can try?

Thanks again for your help!

Best,
Maria

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Date: Wednesday, March 6, 2024 at 9:20 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] aparc & wm underestimation
This is difficult to debug remotely. The first thing to look at is the ?h.orig 
surface. Does that look more-or-less right? If not, then it means that the 
wm.mgz is wrong. If it does not look right, it means that the surface placement 
algorithm is pushing the surface into subcortical gray. One way to overcome 
this is to create a brain.finalsurfs.manedit.mgz by copying the 
brain.finalsurfs.mgz, then edit the brain.finalsurfs.manedit.mgz to set those 
areas where the surface is off to 255. Then create an expert options file with
WhitePreAparc --rip-bg-no-annot --restore-255  --outvol mrisps.wpa.mgz
PlaceWhiteSurf --restore-255 --outvol mrisps.white.mgz
T1PialSurf --restore-255 --outvol mrisps.pial.mgz
And pass that to recon-all with the -expert option
On 3/5/2024 7:10 PM, Stanica, Maria wrote:

External Email - Use Caution
Yes, the problem is that the white surface on the left side of the image is 
extending too far into subcortical gray matter. We did delete the control 
points and ran some white matter edits, but the image I sent you is after we 
applied those edits (it was even worse before). I don’t see any other wm edits 
we can make to the image. It didn’t resolve our issue enough to make the image 
usable for our analyses, so I wanted to see if there was anything else we could 
do to resolve the problem.

Thank you!


From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Date: Tuesday, March 5, 2024 at 9:11 AM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] aparc & wm underestimation
Just to make sure I understand, the problem is that the white surface on the 
left side of the image is extending too far into subcortical gray matter, 
right? This can be difficult to fix, but the right fix is to edit the wm.mgz. 
Make sure to delete your control points as that is not the right fix. Also, 
remember that the surfaces in this area may always be inaccurate if you can see 
where the boundary is.
On 3/3/2024 6:09 PM, Stanica, Maria wrote:

External Email - Use Caution
This is after the most recent round of edits for one of the subjects.

Maria Stǎnicǎ, B.A. | Graduate Student
Medical/Clinical Psychology Doctoral Program
UAB |The University of Alabama at Birmingham
mstan...@uab.edu<mailto:mstan...@uab.edu>
Pronouns: she/her/hers
[Image]



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Date: Sunday, March 3, 2024 at 3:38 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] aparc & wm underestimation
Can you send pictures of the slices showing the problem?
On 3/3/2024 3:18 PM, Stanica, Maria wrote:

External Email - Use Caution
Hello FS developers,

I ran my subjects through skullstripping and recon-all. Everything processed 
correctly (and exited without errors), except 4 images which have an 
underestimation in coronal subcortical region. The underestimation is 
significant and goes on for about 10-12 slices (for one image it was 153-162, 
for another it was 150-164).

After searching the list, we attempted control points, which ended up not 
working (I don’t believe this was the right method to correct the error). Then 
we tried white matter edits, and one of the images was resolved, but the other 
3 did not get better. Is there anything else we could do to try to resolve the 
issue? I can provide any other information needed. Any help would be 
appreciated!


  1.  Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
  2.  Operating System: Red Hat Enterprise Linux 7
  3.  OS Version: 7.9 (Maipo)

Best,
Maria

Maria Stǎnicǎ, B.A. | Graduate Student
Medical/Clinical Psychology Doctoral Program
UAB |The University of Alabama at Birmingham
mstan...@uab.edu<mailto:mstan...@uab.edu>
Pronouns: she/her/hers
[Image]




___

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Re: [Freesurfer] aparc & wm underestimation

2024-03-06 Thread Douglas N. Greve

This is difficult to debug remotely. The first thing to look at is the
?h.orig surface. Does that look more-or-less right? If not, then it
means that the wm.mgz is wrong. If it does not look right, it means that
the surface placement algorithm is pushing the surface into subcortical
gray. One way to overcome this is to create a
brain.finalsurfs.manedit.mgz by copying the brain.finalsurfs.mgz, then
edit the brain.finalsurfs.manedit.mgz to set those areas where the
surface is off to 255. Then create an expert options file with

WhitePreAparc --rip-bg-no-annot --restore-255 --outvol mrisps.wpa.mgz
PlaceWhiteSurf --restore-255 --outvol mrisps.white.mgz
T1PialSurf --restore-255 --outvol mrisps.pial.mgz
And pass that to recon-all with the -expert option

On 3/5/2024 7:10 PM, Stanica, Maria wrote:

External Email - Use Caution

Yes, the problem is that the white surface on the left side of the
image is extending too far into subcortical gray matter. We did delete
the control points and ran some white matter edits, but the image I
sent you is after we applied those edits (it was even worse before). I
don’t see any other wm edits we can make to the image. It didn’t
resolve our issue enough to make the image usable for our analyses, so
I wanted to see if there was anything else we could do to resolve the
problem.

Thank you!

*From: *freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve

*Date: *Tuesday, March 5, 2024 at 9:11 AM
*To: *freesurfer@nmr.mgh.harvard.edu
*Subject: *Re: [Freesurfer] aparc & wm underestimation

Just to make sure I understand, the problem is that the white surface
on the left side of the image is extending too far into subcortical
gray matter, right? This can be difficult to fix, but the right fix is
to edit the wm.mgz. Make sure to delete your control points as that is
not the right fix. Also, remember that the surfaces in this area may
always be inaccurate if you can see where the boundary is.

On 3/3/2024 6:09 PM, Stanica, Maria wrote:

*External Email - Use Caution *

This is after the most recent round of edits for one of the subjects.

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu <mailto:mstan...@uab.edu>

Pronouns: she/her/hers

Image

*From: *freesurfer-boun...@nmr.mgh.harvard.edu

<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
Douglas N. Greve
<mailto:dgr...@mgh.harvard.edu>
*Date: *Sunday, March 3, 2024 at 3:38 PM
*To: *freesurfer@nmr.mgh.harvard.edu

<mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject: *Re: [Freesurfer] aparc & wm underestimation

Can you send pictures of the slices showing the problem?

On 3/3/2024 3:18 PM, Stanica, Maria wrote:

*External Email - Use Caution *

Hello FS developers,

I ran my subjects through skullstripping and recon-all.
Everything processed correctly (and exited without errors),
except 4 images which have an underestimation in coronal
subcortical region. The underestimation is significant and
goes on for about 10-12 slices (for one image it was 153-162,
for another it was 150-164).

After searching the list, we attempted control points, which
ended up not working (I don’t believe this was the right
method to correct the error). Then we tried white matter
edits, and one of the images was resolved, but the other 3 did
not get better. Is there anything else we could do to try to
resolve the issue? I can provide any other information needed.
Any help would be appreciated!

1. Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
2. Operating System: Red Hat Enterprise Linux 7
3. OS Version: 7.9 (Maipo)

Best,

Maria

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu <mailto:mstan...@uab.edu>

Pronouns: she/her/hers

Image

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Re: [Freesurfer] aparc & wm underestimation

2024-03-05 Thread Stanica, Maria

External Email - Use Caution

Yes, the problem is that the white surface on the left side of the image is 
extending too far into subcortical gray matter. We did delete the control 
points and ran some white matter edits, but the image I sent you is after we 
applied those edits (it was even worse before). I don’t see any other wm edits 
we can make to the image. It didn’t resolve our issue enough to make the image 
usable for our analyses, so I wanted to see if there was anything else we could 
do to resolve the problem.

Thank you!


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Date: Tuesday, March 5, 2024 at 9:11 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] aparc & wm underestimation
Just to make sure I understand, the problem is that the white surface on the 
left side of the image is extending too far into subcortical gray matter, 
right? This can be difficult to fix, but the right fix is to edit the wm.mgz. 
Make sure to delete your control points as that is not the right fix. Also, 
remember that the surfaces in this area may always be inaccurate if you can see 
where the boundary is.
On 3/3/2024 6:09 PM, Stanica, Maria wrote:

External Email - Use Caution
This is after the most recent round of edits for one of the subjects.

Maria Stǎnicǎ, B.A. | Graduate Student
Medical/Clinical Psychology Doctoral Program
UAB |The University of Alabama at Birmingham
mstan...@uab.edu<mailto:mstan...@uab.edu>
Pronouns: she/her/hers
[Image]



From: 
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of Douglas N. Greve 
<mailto:dgr...@mgh.harvard.edu>
Date: Sunday, March 3, 2024 at 3:38 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 
<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] aparc & wm underestimation
Can you send pictures of the slices showing the problem?
On 3/3/2024 3:18 PM, Stanica, Maria wrote:

External Email - Use Caution
Hello FS developers,

I ran my subjects through skullstripping and recon-all. Everything processed 
correctly (and exited without errors), except 4 images which have an 
underestimation in coronal subcortical region. The underestimation is 
significant and goes on for about 10-12 slices (for one image it was 153-162, 
for another it was 150-164).

After searching the list, we attempted control points, which ended up not 
working (I don’t believe this was the right method to correct the error). Then 
we tried white matter edits, and one of the images was resolved, but the other 
3 did not get better. Is there anything else we could do to try to resolve the 
issue? I can provide any other information needed. Any help would be 
appreciated!


  1.  Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
  2.  Operating System: Red Hat Enterprise Linux 7
  3.  OS Version: 7.9 (Maipo)

Best,
Maria

Maria Stǎnicǎ, B.A. | Graduate Student
Medical/Clinical Psychology Doctoral Program
UAB |The University of Alabama at Birmingham
mstan...@uab.edu<mailto:mstan...@uab.edu>
Pronouns: she/her/hers
[Image]




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Re: [Freesurfer] aparc & wm underestimation

2024-03-05 Thread Douglas N. Greve

Just to make sure I understand, the problem is that the white surface on
the left side of the image is extending too far into subcortical gray
matter, right? This can be difficult to fix, but the right fix is to
edit the wm.mgz. Make sure to delete your control points as that is not
the right fix. Also, remember that the surfaces in this area may always
be inaccurate if you can see where the boundary is.

On 3/3/2024 6:09 PM, Stanica, Maria wrote:

External Email - Use Caution

This is after the most recent round of edits for one of the subjects.

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu <mailto:mstan...@uab.edu>

Pronouns: she/her/hers

Image

*From: *freesurfer-boun...@nmr.mgh.harvard.edu
on behalf of Douglas N. Greve

*Date: *Sunday, March 3, 2024 at 3:38 PM
*To: *freesurfer@nmr.mgh.harvard.edu
*Subject: *Re: [Freesurfer] aparc & wm underestimation

Can you send pictures of the slices showing the problem?

On 3/3/2024 3:18 PM, Stanica, Maria wrote:

*External Email - Use Caution *

Hello FS developers,

I ran my subjects through skullstripping and recon-all. Everything
processed correctly (and exited without errors), except 4 images
which have an underestimation in coronal subcortical region. The
underestimation is significant and goes on for about 10-12 slices
(for one image it was 153-162, for another it was 150-164).

After searching the list, we attempted control points, which ended
up not working (I don’t believe this was the right method to
correct the error). Then we tried white matter edits, and one of
the images was resolved, but the other 3 did not get better. Is
there anything else we could do to try to resolve the issue? I can
provide any other information needed. Any help would be appreciated!

1. Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
2. Operating System: Red Hat Enterprise Linux 7
3. OS Version: 7.9 (Maipo)

Best,

Maria

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu <mailto:mstan...@uab.edu>

Pronouns: she/her/hers

Image

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Re: [Freesurfer] aparc & wm underestimation

2024-03-03 Thread Douglas N. Greve


Can you send pictures of the slices showing the problem?

On 3/3/2024 3:18 PM, Stanica, Maria wrote:


External Email - Use Caution

Hello FS developers,

I ran my subjects through skullstripping and recon-all. Everything 
processed correctly (and exited without errors), except 4 images which 
have an underestimation in coronal subcortical region. The 
underestimation is significant and goes on for about 10-12 slices (for 
one image it was 153-162, for another it was 150-164).


After searching the list, we attempted control points, which ended up 
not working (I don’t believe this was the right method to correct the 
error). Then we tried white matter edits, and one of the images was 
resolved, but the other 3 did not get better. Is there anything else 
we could do to try to resolve the issue? I can provide any other 
information needed. Any help would be appreciated!


 1. Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
 2. Operating System: Red Hat Enterprise Linux 7
 3. OS Version: 7.9 (Maipo)

Best,

Maria

*Maria St**ǎ**nic**ǎ**, B.A.| **Graduate Student*

Medical/Clinical Psychology Doctoral Program

UAB |/The University of Alabama at Birmingham/

mstan...@uab.edu 

Pronouns: she/her/hers

Image


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[Freesurfer] aparc & wm underestimation

2024-03-03 Thread Stanica, Maria

External Email - Use Caution

Hello FS developers,

I ran my subjects through skullstripping and recon-all. Everything processed 
correctly (and exited without errors), except 4 images which have an 
underestimation in coronal subcortical region. The underestimation is 
significant and goes on for about 10-12 slices (for one image it was 153-162, 
for another it was 150-164).

After searching the list, we attempted control points, which ended up not 
working (I don’t believe this was the right method to correct the error). Then 
we tried white matter edits, and one of the images was resolved, but the other 
3 did not get better. Is there anything else we could do to try to resolve the 
issue? I can provide any other information needed. Any help would be 
appreciated!


  1.  Freesurfer version: FreeSurfer/7.1.1-centos7_x86_64
  2.  Operating System: Red Hat Enterprise Linux 7
  3.  OS Version: 7.9 (Maipo)

Best,
Maria

Maria Stǎnicǎ, B.A. | Graduate Student
Medical/Clinical Psychology Doctoral Program
UAB |The University of Alabama at Birmingham
mstan...@uab.edu
Pronouns: she/her/hers
[Image]


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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

Re: [Freesurfer] aparc & wm underestimation

Re: [Freesurfer] aparc & wm underestimation

Re: [Freesurfer] aparc & wm underestimation

Re: [Freesurfer] aparc & wm underestimation

Re: [Freesurfer] aparc & wm underestimation

Re: [Freesurfer] aparc & wm underestimation

[Freesurfer] aparc & wm underestimation

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