External Email - Use Caution
Dear FreeSurfer experts:
I am working on a manual for my lab and I would like to clarify the two points below (to which I couldn’t find answers in the online FS content available):
* When editing the wm.mgz fails, can control points (CPs) be used to correct pial errors cause by lesions (e.g., perivascular spaces, microbleeds, WMH). I understand the FS tutorial recommends against this, however at times it seems that only editing the wm.mgz will not be sufficient (Figure 1 below)
* Should white matter voxels with 0 intensity in the wm.mgz (inside the white surface) be filled in, even when these voxels do not affect white matter surface segmentation whatsoever? (Figure 2 below).
* Would the cerebral white matter volumetric data (wmparc.stats) be affected by these 0 intensity voxels?
Thanks so much for you help! Nárlon Cássio
Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSFHR/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon [cid:0757C5B4-5E01-42A4-8BE6-6C5779C2D024][cid:E4FD3068-0778-4057-850B-40E9EB3318C8]
External Email - Use Caution
Hi colleagues, Just following up on this if anyone has an input =)
Thanks Nárlon Cássio
Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSFHR/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon
On Jun 7, 2021, at 3:38 PM, Boa Sorte Silva, Narlon <narlon.silva@ubc.camailto:narlon.silva@ubc.ca> wrote:
[CAUTION: Non-UBC Email]
External Email - Use Caution
Dear FreeSurfer experts:
I am working on a manual for my lab and I would like to clarify the two points below (to which I couldn’t find answers in the online FS content available):
* When editing the wm.mgz fails, can control points (CPs) be used to correct pial errors cause by lesions (e.g., perivascular spaces, microbleeds, WMH). I understand the FS tutorial recommends against this, however at times it seems that only editing the wm.mgz will not be sufficient (Figure 1 below)
* Should white matter voxels with 0 intensity in the wm.mgz (inside the white surface) be filled in, even when these voxels do not affect white matter surface segmentation whatsoever? (Figure 2 below).
* Would the cerebral white matter volumetric data (wmparc.stats) be affected by these 0 intensity voxels?
Thanks so much for you help! Nárlon Cássio
Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSFHR/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon <Fig_1.jpg><Fig_2.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1Jo00ZEvZJ2OOVtzPX2nQDYfKz-G6loTyOXN_5NscrX43uv...
On 6/7/2021 6:38 PM, Boa Sorte Silva, Narlon wrote:
External Email - Use Caution
Dear FreeSurfer experts:
I am working on a manual for my lab and I would like to clarify the two points below (to which I couldn’t find answers in the online FS content available):
- When editing the wm.mgz fails, can control points (CPs) be used to correct pial errors cause by lesions (e.g., perivascular spaces, microbleeds, WMH). I understand the FS tutorial recommends against this, however at times it seems that only editing the wm.mgz will not be sufficient (Figure 1 below)
Definitely do not put control points in anything that is not healthy WM. Not sure what your issue is in Fig 1. It looks like a lesion right next to cortex. Here, it is probably very difficult to tell where cortex begins and the lesions ends. In 7.2, you will have the option of putting repositioning points that allow you to place a point where you want the surface to go.
- Should white matter voxels with 0 intensity in the wm.mgz (inside the white surface) be filled in, even when these voxels do not affect white matter surface segmentation whatsoever? (Figure 2 below).
It does not hurt, but it is not needed.
- Would the cerebral white matter volumetric data (wmparc.stats) be affected by these 0 intensity voxels?
No, not at all. The wm.mgz is only used for surface placement.
Thanks so much for you help! Nárlon Cássio
*Nárlon Cássio Boa Sorte Silva* PhD (He, Him, His) CIHR and MSFHR/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Thanks!
Nárlon Cássio
Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSFHR/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon
On Jun 24, 2021, at 8:03 AM, Douglas N. Greve <dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu> wrote:
[CAUTION: Non-UBC Email]
On 6/7/2021 6:38 PM, Boa Sorte Silva, Narlon wrote:
External Email - Use Caution
Dear FreeSurfer experts:
I am working on a manual for my lab and I would like to clarify the two points below (to which I couldn’t find answers in the online FS content available):
* When editing the wm.mgz fails, can control points (CPs) be used to correct pial errors cause by lesions (e.g., perivascular spaces, microbleeds, WMH). I understand the FS tutorial recommends against this, however at times it seems that only editing the wm.mgz will not be sufficient (Figure 1 below)
Definitely do not put control points in anything that is not healthy WM. Not sure what your issue is in Fig 1. It looks like a lesion right next to cortex. Here, it is probably very difficult to tell where cortex begins and the lesions ends. In 7.2, you will have the option of putting repositioning points that allow you to place a point where you want the surface to go.
* Should white matter voxels with 0 intensity in the wm.mgz (inside the white surface) be filled in, even when these voxels do not affect white matter surface segmentation whatsoever? (Figure 2 below).
It does not hurt, but it is not needed.
* Would the cerebral white matter volumetric data (wmparc.stats) be affected by these 0 intensity voxels?
No, not at all. The wm.mgz is only used for surface placement.
Thanks so much for you help! Nárlon Cássio
Nárlon Cássio Boa Sorte Silva PhD (He, Him, His) CIHR and MSFHR/PARF Postdoctoral Research Fellow Aging, Mobility, and Cognitive Health Lab Djavad Mowafaghian Centre for Brain Health Department of Physical Therapy, Faculty of Medicine University of British Columbia Vancouver, Canada Twitter: @BoaNarlon <Fig_1.jpg><Fig_2.jpg>
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1rWttTfdUocWs5S3Rz8ipBLWcQUBqr3pldAV568MxoBT7KH...
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1rWttTfdUocWs5S3Rz8ipBLWcQUBqr3pldAV568MxoBT7KH... 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 http://secure-web.cisco.com/1tSAQ_PE-053F2xp5cjgWq1S596BFBgxw_3HgYBCMY7VIOti... . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. 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@nmr.mgh.harvard.edu
-
Boa Sorte Silva, Narlon -
Douglas N. Greve