Dear Freesurfers, after finishing autorecon2, I was inspecting brainmask.mgz with wm.mgz as the aux volume. I noticed that the segmentation has classified some of the subcortical nuclei (thalamus, putamen etc) as csf instead of graymatter (they appear white as opposed to black in the wm volume). What is the best way to correct this problem? If I have to manually correct this, would I need to remove these misclassified csf voxels and by doing so, would they then become gray matter after I save the main and aux volumes? appreciate any help,
Binyam
Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 4444 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601
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Hi Binyam,
don't worry about the subcortical regions in the wm.mgz (they were actually classified as white matter, but it won't matter)
Bruce
On Wed, 21 Mar 2007, Binyam Nardos wrote:
Dear Freesurfers, after finishing autorecon2, I was inspecting brainmask.mgz with wm.mgz as the aux volume. I noticed that the segmentation has classified some of the subcortical nuclei (thalamus, putamen etc) as csf instead of graymatter (they appear white as opposed to black in the wm volume). What is the best way to correct this problem? If I have to manually correct this, would I need to remove these misclassified csf voxels and by doing so, would they then become gray matter after I save the main and aux volumes? appreciate any help,
Binyam
Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 4444 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601
The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments.
Bruce, thanks for the quick response. I have to bug you one more time, I have attached a screenshot of the wm volume, would you correct the voxels classified as csf (on the top left corner) which, on the brainmask volume, appear as graymatter, or should I altogether stop worrying about gray matter structures misclassified as csf? thanks a lot, Binyam
Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 4444 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601
The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 3/21/2007 4:35 PM To: Binyam Nardos Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] gray matter misclassified as csf
Hi Binyam,
don't worry about the subcortical regions in the wm.mgz (they were actually classified as white matter, but it won't matter)
Bruce
On Wed, 21 Mar 2007, Binyam Nardos wrote:
Dear Freesurfers, after finishing autorecon2, I was inspecting brainmask.mgz with wm.mgz as the aux volume. I noticed that the segmentation has classified some of the subcortical nuclei (thalamus, putamen etc) as csf instead of graymatter (they appear white as opposed to black in the wm volume). What is the best way to correct this problem? If I have to manually correct this, would I need to remove these misclassified csf voxels and by doing so, would they then become gray matter after I save the main and aux volumes? appreciate any help,
Binyam
Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 4444 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601
The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments.
the wm.mgz is a binary segmentation of white and non-white, so there is no distinction between CSF and gm. There is some autofilling of various structures to get the topology of the gray/white interface close to spherical (e.g. ventricles, basal ganglia, etc...), but you should only bother editing if the final white and pial surfaces are not correct On Wed, 21 Mar 2007, Binyam Nardos wrote:
Bruce, thanks for the quick response. I have to bug you one more time, I have attached a screenshot of the wm volume, would you correct the voxels classified as csf (on the top left corner) which, on the brainmask volume, appear as graymatter, or should I altogether stop worrying about gray matter structures misclassified as csf? thanks a lot, Binyam
Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 4444 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601
The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments.
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wed 3/21/2007 4:35 PM To: Binyam Nardos Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] gray matter misclassified as csf
Hi Binyam,
don't worry about the subcortical regions in the wm.mgz (they were actually classified as white matter, but it won't matter)
Bruce
On Wed, 21 Mar 2007, Binyam Nardos wrote:
Dear Freesurfers, after finishing autorecon2, I was inspecting brainmask.mgz with wm.mgz as the aux volume. I noticed that the segmentation has classified some of the subcortical nuclei (thalamus, putamen etc) as csf instead of graymatter (they appear white as opposed to black in the wm volume). What is the best way to correct this problem? If I have to manually correct this, would I need to remove these misclassified csf voxels and by doing so, would they then become gray matter after I save the main and aux volumes? appreciate any help,
Binyam
Binyam Nardos Cognitive Rehabilitation Research Group Washington University School of Medicine Box # 8505 4444 Forest Park Blvd St. Louis, MO 63108 Office: (314) 454-7795 Fax: (314) 286-1601
The contents of this e-mail message and any attachments are intended solely for the addressee(s) named in this message. This communication is intended to be and to remain confidential and may be subject to applicable physician/patient and/or work product privileges. If you are not the intended recipient of this message, or if this message has been addressed to you in error, please immediately alert the sender by reply e-mail and then delete this message and its attachments.
freesurfer@nmr.mgh.harvard.edu
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Binyam Nardos -
Bruce Fischl