Hi everybody.
I have done all the auto-recon steps on my data, and I have some questions about the quality of the resulting images. I am aware of the troubleshooting tutorials, but I don't think these are covering my questions.
I have uploaded some images of the surfaces and segmentations of a subject to http://freesurfer.nikolasborrel.com, and my question is about the spikes in the inflated surfaces. I have selected two spikes on the surface (green mark), one for each hemisphere, and have found the corresponding location in tkmedit in each of the three directions (s,h,c).
For the spike in the left hemisphere (spike1_lh), I can't see what should be causing the spike. The segmentation looks correct.
For the spike in the right hemisphere (spike_rh), it seems like there are many 'isles of segmentations, but are these causing the spike? If yes, how should these isles be corrected?
Finally, how smooth is the inflated surface expected to be in a 'correct' case? Should a small amount of spikes be allowed, as long as they are not 'too severe'?
I can upload more images if needed, thanks in advance!
Kind regards Nikolas
Hi Nikolas
the spiked by themselves aren't a problem, it's only if the surface isn't accurately following the true gray/white boundary that you need to intervene. It's a bit hard to tell in this case without being able to scroll back and forth, but I suspect the segmentation is a bit inaccurate in this region, which results in an incorrectly fixed topological defect. If you want to, you can tar and gzip the entire subject dir and ftp it for us and I'll take a look.
cheers Bruce
On Tue, 1 Feb 2011, Nikolas Borrel-Jensen wrote:
Hi everybody.
I have done all the auto-recon steps on my data, and I have some questions about the quality of the resulting images. I am aware of the troubleshooting tutorials, but I don't think these are covering my questions.
I have uploaded some images of the surfaces and segmentations of a subject to http://freesurfer.nikolasborrel.com, and my question is about the spikes in the inflated surfaces. I have selected two spikes on the surface (green mark), one for each hemisphere, and have found the corresponding location in tkmedit in each of the three directions (s,h,c).
For the spike in the left hemisphere (spike1_lh), I can't see what should be causing the spike. The segmentation looks correct.
For the spike in the right hemisphere (spike_rh), it seems like there are many 'isles of segmentations, but are these causing the spike? If yes, how should these isles be corrected?
Finally, how smooth is the inflated surface expected to be in a 'correct' case? Should a small amount of spikes be allowed, as long as they are not 'too severe'?
I can upload more images if needed, thanks in advance!
Kind regards Nikolas
You can also run the defect-seg program to help locate the places where the automatic topology fixer fixed defects. Run it with --help to get more info.
doug
Bruce Fischl wrote:
Hi Nikolas
the spiked by themselves aren't a problem, it's only if the surface isn't accurately following the true gray/white boundary that you need to intervene. It's a bit hard to tell in this case without being able to scroll back and forth, but I suspect the segmentation is a bit inaccurate in this region, which results in an incorrectly fixed topological defect. If you want to, you can tar and gzip the entire subject dir and ftp it for us and I'll take a look.
cheers Bruce
On Tue, 1 Feb 2011, Nikolas Borrel-Jensen wrote:
Hi everybody.
I have done all the auto-recon steps on my data, and I have some questions about the quality of the resulting images. I am aware of the troubleshooting tutorials, but I don't think these are covering my questions.
I have uploaded some images of the surfaces and segmentations of a subject to http://freesurfer.nikolasborrel.com, and my question is about the spikes in the inflated surfaces. I have selected two spikes on the surface (green mark), one for each hemisphere, and have found the corresponding location in tkmedit in each of the three directions (s,h,c).
For the spike in the left hemisphere (spike1_lh), I can't see what should be causing the spike. The segmentation looks correct.
For the spike in the right hemisphere (spike_rh), it seems like there are many 'isles of segmentations, but are these causing the spike? If yes, how should these isles be corrected?
Finally, how smooth is the inflated surface expected to be in a 'correct' case? Should a small amount of spikes be allowed, as long as they are not 'too severe'?
I can upload more images if needed, thanks in advance!
Kind regards Nikolas
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks for the fast reply. I have uploaded the entire subject directory and would appreciate if you could take a look.
/Nikolas
On Tue, Feb 1, 2011 at 3:17 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Nikolas
the spiked by themselves aren't a problem, it's only if the surface isn't accurately following the true gray/white boundary that you need to intervene. It's a bit hard to tell in this case without being able to scroll back and forth, but I suspect the segmentation is a bit inaccurate in this region, which results in an incorrectly fixed topological defect. If you want to, you can tar and gzip the entire subject dir and ftp it for us and I'll take a look.
cheers Bruce
On Tue, 1 Feb 2011, Nikolas Borrel-Jensen wrote:
Hi everybody.
I have done all the auto-recon steps on my data, and I have some questions about the quality of the resulting images. I am aware of the troubleshooting tutorials, but I don't think these are covering my questions.
I have uploaded some images of the surfaces and segmentations of a subject to http://freesurfer.nikolasborrel.com, and my question is about the spikes in the inflated surfaces. I have selected two spikes on the surface (green mark), one for each hemisphere, and have found the corresponding location in tkmedit in each of the three directions (s,h,c).
For the spike in the left hemisphere (spike1_lh), I can't see what should be causing the spike. The segmentation looks correct.
For the spike in the right hemisphere (spike_rh), it seems like there are many 'isles of segmentations, but are these causing the spike? If yes, how should these isles be corrected?
Finally, how smooth is the inflated surface expected to be in a 'correct' case? Should a small amount of spikes be allowed, as long as they are not 'too severe'?
I can upload more images if needed, thanks in advance!
Kind regards Nikolas
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.
what did you call it? On Tue, 1 Feb 2011, Nikolas Borrel-Jensen wrote:
Thanks for the fast reply. I have uploaded the entire subject directory and would appreciate if you could take a look.
/Nikolas
On Tue, Feb 1, 2011 at 3:17 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
Hi Nikolas
the spiked by themselves aren't a problem, it's only if the surface isn't accurately following the true gray/white boundary that you need to intervene. It's a bit hard to tell in this case without being able to scroll back and forth, but I suspect the segmentation is a bit inaccurate in this region, which results in an incorrectly fixed topological defect. If you want to, you can tar and gzip the entire subject dir and ftp it for us and I'll take a look.
cheers Bruce
On Tue, 1 Feb 2011, Nikolas Borrel-Jensen wrote:
Hi everybody.
I have done all the auto-recon steps on my data, and I have some questions about the quality of the resulting images. I am aware of the troubleshooting tutorials, but I don't think these are covering my questions.
I have uploaded some images of the surfaces and segmentations of a subject to http://freesurfer.nikolasborrel.com, and my question is about the spikes in the inflated surfaces. I have selected two spikes on the surface (green mark), one for each hemisphere, and have found the corresponding location in tkmedit in each of the three directions (s,h,c).
For the spike in the left hemisphere (spike1_lh), I can't see what should be causing the spike. The segmentation looks correct.
For the spike in the right hemisphere (spike_rh), it seems like there are many 'isles of segmentations, but are these causing the spike? If yes, how should these isles be corrected?
Finally, how smooth is the inflated surface expected to be in a 'correct' case? Should a small amount of spikes be allowed, as long as they are not 'too severe'?
I can upload more images if needed, thanks in advance!
Kind regards Nikolas
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.
subj1dir.tar.gz http://freesurfer.nikolasborrel.com/subj1dir.tar.gz in the outermost directory.
On Tue, Feb 1, 2011 at 5:28 PM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
what did you call it?
On Tue, 1 Feb 2011, Nikolas Borrel-Jensen wrote:
Thanks for the fast reply. I have uploaded the entire subject directory
and would appreciate if you could take a look.
/Nikolas
On Tue, Feb 1, 2011 at 3:17 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
Hi Nikolas
the spiked by themselves aren't a problem, it's only if the surface isn't accurately following the true gray/white boundary that you need to intervene. It's a bit hard to tell in this case without being able to scroll back and forth, but I suspect the segmentation is a bit inaccurate in this region, which results in an incorrectly fixed topological defect. If you want to, you can tar and gzip the entire subject dir and ftp it for us and I'll take a look.
cheers Bruce
On Tue, 1 Feb 2011, Nikolas Borrel-Jensen wrote:
Hi everybody.
I have done all the auto-recon steps on my data, and I have some questions about the quality of the resulting images. I am aware of the troubleshooting tutorials, but I don't think these are covering my questions.
I have uploaded some images of the surfaces and segmentations of a subject to http://freesurfer.nikolasborrel.com, and my question is about the spikes in the inflated surfaces. I have selected two spikes on the surface (green mark), one for each hemisphere, and have found the corresponding location in tkmedit in each of the three directions (s,h,c).
For the spike in the left hemisphere (spike1_lh), I can't see what should be causing the spike. The segmentation looks correct.
For the spike in the right hemisphere (spike_rh), it seems like there are many 'isles of segmentations, but are these causing the spike? If yes, how should these isles be corrected?
Finally, how smooth is the inflated surface expected to be in a 'correct' case? Should a small amount of spikes be allowed, as long as they are not 'too severe'?
I can upload more images if needed, thanks in advance!
Kind regards Nikolas
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.
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Nikolas Borrel-Jensen