Hi, FreeSurfer experts
I am posting it here again since I still have not had the issue solved. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached files). It is strange that such a problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. I also checked the orig.nofix with defects_label overlaied as suggested by Bruce and I do not see red marks close to the region (see attached file). So I wonder if anyone would help on solving the issue.
Many thanks in advance
Leon
----- Forwarded Message ----- From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Leon leonado78@yahoo.com Sent: Friday, May 25, 2012 11:23 AM Subject: Re: [Freesurfer] wm surface does not follow wm.mgz
Hi Leon
can you cc the list so others can answer? I don't have any experience with monkey recons so I'm not going to be able to be all that helpful. Check the filled.mgz and see if the surface follows it, and if so we'll have to figure out why that region is being turned on in the filled cheers Bruce
On Fri, 25 May 2012, Leon wrote:
Hi, Bruce
I checked the orig.nofix and do not see any obvious defect there (see the attached file). Do you have any suggestions on how I should check the defects other than visual check? I loaded the defect_label and there is no red label near this region.
Thank you! Leon
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Leon leonado78@yahoo.com Sent: Wednesday, May 23, 2012 7:28 PM Subject: Re: [Freesurfer] wm surface does not follow wm.mgz
That almost certainly means there is a topological defect there. Check the orig.nofix
Cheers Bruce
On May 23, 2012, at 2:49 PM, Leon leonado78@yahoo.com wrote:
Hi, FreeSurfer experts
I have seen similar posts before but did not think that I could solve the issue based on the answers from the previous posts. So I am posting it here again. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached file). It is strange that such problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. So I wonder if anyone would help on solving this issue.
Thanks in advance! Leon
<RightPreCentralGyri.jpg>
_______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Hi Leon,
if I recall correctly the wm surface is looking at intensity gradients in the brain.finalsurfs.mgz (I think). So please have a look at that file and see whether you have some weird issues in that file. The orig surface is created from the wm.mgz and so will reflect edit you made there. BTW I think the filled is created from wm.mgz, so I guess it is guaranteed to match the orig surface… I do wonder why your wm.mgz shows so much structure, as I am under the impression the wm.mgz should basically be of the wm voxel value (I am wondering about the basal ganglia /caudate intensity I guess)
Best Sebastian
On May 25, 2012, at 10:15 AM, Leon wrote:
Hi, FreeSurfer experts
I am posting it here again since I still have not had the issue solved. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached files). It is strange that such a problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. I also checked the orig.nofix with defects_label overlaied as suggested by Bruce and I do not see red marks close to the region (see attached file). So I wonder if anyone would help on solving the issue.
Many thanks in advance
Leon
----- Forwarded Message ----- From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Leon leonado78@yahoo.com Sent: Friday, May 25, 2012 11:23 AM Subject: Re: [Freesurfer] wm surface does not follow wm.mgz
Hi Leon
can you cc the list so others can answer? I don't have any experience with monkey recons so I'm not going to be able to be all that helpful. Check the filled.mgz and see if the surface follows it, and if so we'll have to figure out why that region is being turned on in the filled cheers Bruce
On Fri, 25 May 2012, Leon wrote:
Hi, Bruce
I checked the orig.nofix and do not see any obvious defect there (see the attached file). Do you have any suggestions on how I should check the defects other than visual check? I loaded the defect_label and there is no red label near this region.
Thank you! Leon
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Leon leonado78@yahoo.com Sent: Wednesday, May 23, 2012 7:28 PM Subject: Re: [Freesurfer] wm surface does not follow wm.mgz
That almost certainly means there is a topological defect there. Check the orig.nofix
Cheers Bruce
On May 23, 2012, at 2:49 PM, Leon leonado78@yahoo.com wrote:
Hi, FreeSurfer expertsI have seen similar posts before but did not think that I could solve the issue based on the answers from the previous posts. So I am posting it here again. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached file). It is strange that such problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. So I wonder if anyone would help on solving this issue.
Thanks in advance! Leon
<RightPreCentralGyri.jpg> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
<OrigNoFix_vs_WM.jpg><RightPreCentralGyri.jpg>_______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Hi, Sebastian and Bruce I think I have found the reason: there are low intensity values at the precentral region (~1) that are almost invisible when viewed using the gray color scheme in FS. When I converted the wm.mgz to nifti format and viewed it in FSL using red-yellow color scheme. They are readily shown there.
Is there any option in tkmedit that can show volume images with different color schemes such as red-yellow or blue, green? I found the option very helpful in detecting unwanted voxels with low intensity values when I am working on the data in FSL.
Thank you for your help! Leon
________________________________ From: Sebastian Moeller sebastian.moeller1@rwth-aachen.de To: Leon leonado78@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 1:28 PM Subject: Re: [Freesurfer] Fw: wm surface does not follow wm.mgz
Hi Leon,
if I recall correctly the wm surface is looking at intensity gradients in the brain.finalsurfs.mgz (I think). So please have a look at that file and see whether you have some weird issues in that file. The orig surface is created from the wm.mgz and so will reflect edit you made there. BTW I think the filled is created from wm.mgz, so I guess it is guaranteed to match the orig surface… I do wonder why your wm.mgz shows so much structure, as I am under the impression the wm.mgz should basically be of the wm voxel value (I am wondering about the basal ganglia /caudate intensity I guess)
Best Sebastian
On May 25, 2012, at 10:15 AM, Leon wrote:
Hi, FreeSurfer experts
I am posting it here again since I still have not had the issue solved. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached files). It is strange that such a problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. I also checked the orig.nofix with defects_label overlaied as suggested by Bruce and I do not see red marks close to the region (see attached file). So I wonder if anyone would help on solving the issue.
Many thanks in advance
Leon
----- Forwarded Message ----- From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Leon leonado78@yahoo.com Sent: Friday, May 25, 2012 11:23 AM Subject: Re: [Freesurfer] wm surface does not follow wm.mgz
Hi Leon
can you cc the list so others can answer? I don't have any experience with monkey recons so I'm not going to be able to be all that helpful. Check the filled.mgz and see if the surface follows it, and if so we'll have to figure out why that region is being turned on in the filled cheers Bruce
On Fri, 25 May 2012, Leon wrote:
Hi, Bruce
I checked the orig.nofix and do not see any obvious defect there (see the attached file). Do you have any suggestions on how I should check the defects other than visual check? I loaded the defect_label and there is no red label near this region.
Thank you! Leon
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Leon leonado78@yahoo.com Sent: Wednesday, May 23, 2012 7:28 PM Subject: Re: [Freesurfer] wm surface does not follow wm.mgz
That almost certainly means there is a topological defect there. Check the orig.nofix
Cheers Bruce
On May 23, 2012, at 2:49 PM, Leon leonado78@yahoo.com wrote:
Hi, FreeSurfer experts
I have seen similar posts before but did not think that I could solve the issue based on the answers from the previous posts. So I am posting it here again. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached file). It is strange that such problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. So I wonder if anyone would help on solving this issue.
Thanks in advance! Leon
<RightPreCentralGyri.jpg>
_______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
<OrigNoFix_vs_WM.jpg><RightPreCentralGyri.jpg>_______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
Hi Leon
you can either change the windowing in tkmedit, or load the wm.mgz as an overlay of segmentation in either tkmedit or freeview.
cheers Bruce On Fri, 25 May 2012, Leon wrote:
Hi, Sebastian and Bruce I think I have found the reason: there are low intensity values at the precentral region (~1) that are almost invisible when viewed using the gray color scheme in FS. When I converted the wm.mgz to nifti format and viewed it in FSL using red-yellow color scheme. They are readily shown there.
Is there any option in tkmedit that can show volume images with different color schemes such as red-yellow or blue, green? I found the option very helpful in detecting unwanted voxels with low intensity values when I am working on the data in FSL.
Thank you for your help! Leon
From: Sebastian Moeller sebastian.moeller1@rwth-aachen.de To: Leon leonado78@yahoo.com Cc: FreeSurfer freesurfer@nmr.mgh.harvard.edu Sent: Friday, May 25, 2012 1:28 PM Subject: Re: [Freesurfer] Fw: wm surface does not follow wm.mgz
Hi Leon,
if I recall correctly the wm surface is looking at intensity gradients in the brain.finalsurfs.mgz (I think). So please have a look at that file and see whether you have some weird issues in that file. The orig surface is created from the wm.mgz and so will reflect edit you made there. BTW I think the filled is created from wm.mgz, so I guess it is guaranteed to match the orig surface? I do wonder why your wm.mgz shows so much structure, as I am under the impression the wm.mgz should basically be of the wm voxel value (I am wondering about the basal ganglia /caudate intensity I guess)
Best Sebastian
On May 25, 2012, at 10:15 AM, Leon wrote:
Hi, FreeSurfer experts
I am posting it here again since I still have not had the issue solved.
Basically, I find that white matter surface does not follow the wm.mgz file (see the attached files). It is strange that such a problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. I also checked the orig.nofix with defects_label overlaied as suggested by Bruce and I do not see red marks close to the region (see attached file). So I wonder if anyone would help on solving the issue.
Many thanks in advance
Leon
----- Forwarded Message ----- From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Leon leonado78@yahoo.com Sent: Friday, May 25, 2012 11:23 AM Subject: Re: [Freesurfer] wm surface does not follow wm.mgz
Hi Leon
can you cc the list so others can answer? I don't have any experience with monkey recons so I'm not going to be able to be all that helpful. Check the filled.mgz and see if the surface follows it, and if so we'll have to figure out why that region is being turned on in the filled cheers Bruce
On Fri, 25 May 2012, Leon wrote:
Hi, Bruce
I checked the orig.nofix and do not see any obvious defect there (see
the
attached file). Do you have any suggestions on how I should check the defects other than visual check? I loaded the defect_label and there is
no
red label near this region.
Thank you! Leon
_
From: Bruce Fischl fischl@nmr.mgh.harvard.edu To: Leon leonado78@yahoo.com Sent: Wednesday, May 23, 2012 7:28 PM Subject: Re: [Freesurfer] wm surface does not follow wm.mgz
That almost certainly means there is a topological defect there. Check
the
orig.nofix
Cheers Bruce
On May 23, 2012, at 2:49 PM, Leon leonado78@yahoo.com wrote:
Hi, FreeSurfer experts
I have seen similar posts before but did not think that I could solve the issue based on the answers from the previous posts. So I am posting it here again. Basically, I find that white matter surface does not follow the wm.mgz file (see the attached file). It is strange that such problem is only located at the precentral gyrus. I checked the white matter original surface and the inflated surface and they look fine. I also went through wm.mgz slice by slice to see if there is abrupt gradient between slices and it doe not seem to have that either. So I wonder if anyone would help on solving this issue.
Thanks in advance! Leon
<RightPreCentralGyri.jpg>
_______________________________________________ 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 Partners Compliance HelpLine at http://www.partners.org/complianceline . 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.
<OrigNoFix_vs_WM.jpg><RightPreCentralGyri.jpg>_____________________________
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
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . 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.
-- Sebastian Moeller
telephone: +1-626-325-8598 /+1-626-395-6523 / +1-626-395-6616 fax: 626-395-8826 German GSM: +49 - 15 77 - 1 90 31 41 mobile: +1-626-325-8598 +1-626-807-5242 US CDMA: +1-626-807-5242 moeller@caltech.edu
Division of Biology MC 114-96 California Institute of Technology 1200 East California Boulevard CA 91125, Pasadena USA
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Leon -
Sebastian Moeller