Re: [Freesurfer] Freesurfer white matter overestimated

[Douglas N. Greve]

Can you include an image with and without the surfaces? Make sure to 
include slices where you think the white surface extends too far.


On 2/28/2024 9:13 AM, Luisa Klahn wrote:


External Email - Use Caution

Dear Douglas,
Please find the nu.mgz screenshot attached.
Best,
Luisa



*Von:* Luisa Klahn 
*Gesendet:* Montag, 26. Februar 2024 08:53
*An:* dgr...@mgh.harvard.edu 
*Betreff:* Re: [Freesurfer] Freesurfer white matter overestimated
Dear Douglas,
Please find attached the pictures for the following issue:
I am processing structural data from a 3T scanner using Freesurfer
version 7.3.2. For some subjects, the grey matter looks very thin, and
the white matter looks overestimated. I'll attach screenshots of the
brainmask, wm mask, and T1 including wm and pial surface lines.
I have tried to set control points into the wm but this did not change
the results.
Does anyone have an idea? Would it be possible to change the intensity
settings in the recon-all command?

Thanks for helping!
Best,
Luisa
___
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 
<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] Freesurfer white matter overestimated

[Douglas N. Greve]

It looks like the volume has very poor contrast. What volume are you 
displaying it on? Can you take a pic on the nu.mgz?


On 2/26/2024 2:53 AM, Luisa Klahn wrote:


External Email - Use Caution

Dear Douglas,
Please find attached the pictures for the following issue:
I am processing structural data from a 3T scanner using Freesurfer
version 7.3.2. For some subjects, the grey matter looks very thin, and
the white matter looks overestimated. I'll attach screenshots of the
brainmask, wm mask, and T1 including wm and pial surface lines.
I have tried to set control points into the wm but this did not change
the results.
Does anyone have an idea? Would it be possible to change the intensity
settings in the recon-all command?

Thanks for helping!
Best,
Luisa
___
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] Freesurfer white matter overestimated

[Douglas N. Greve]

Hi, no snapshots were attached.

On 2/1/2024 6:02 AM, Luisa Klahn wrote:


External Email - Use Caution

Hello!
I am processing structural data from a 3T scanner using Freesurfer 
version 7.3.2. For some subjects, the grey matter looks very thin, and 
the white matter looks overestimated. I'll attach screenshots of the 
brainmask, wm mask, and T1 including wm and pial surface lines.
I have tried to set control points into the wm but this did not change 
the results.


Does anyone have an idea? Would it be possible to change the intensity 
settings in the recon-all command?


Thanks for helping!
Luisa

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
___
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. 

[Freesurfer] Freesurfer white matter overestimated

[Luisa Klahn]

External Email - Use Caution

Hello!
I am processing structural data from a 3T scanner using Freesurfer version 
7.3.2. For some subjects, the grey matter looks very thin, and the white matter 
looks overestimated. I'll attach screenshots of the brainmask, wm mask, and T1 
including wm and pial surface lines.
I have tried to set control points into the wm but this did not change the 
results.

Does anyone have an idea? Would it be possible to change the intensity settings 
in the recon-all command?

Thanks for helping!
Luisa
___
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.