Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
Hello Bruce,
Attached are the files for two subjects with brain.mgz and lh.white.
https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/...
The values of WM in those regions in brain.mgz are above 90.
Thanks
Regards Tilak
________________________________________ From: Ramtilak Gattu Sent: Saturday, April 23, 2016 5:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
Hello Bruce,
Thanks a lot for your earlier expert option suggestion in improving the segmentation during the recon process. I am attaching a snap shot where yellow is with expert options and red is with default options. My concern is where I have indicated with blue arrows . Could you please suggest why is it still failing to pick up those areas. Is it because of misregistration with the atlas if so where can I find the results after the non linear registration and would it be possible to improve with any more expert options during the registration and the segmentation subsequently.
Thanks
Regards Tilak
________________________________________ From: Ramtilak Gattu Sent: Wednesday, March 30, 2016 4:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
Thank you for recommending the expert options. I have run this on two subjects (rows) and you can see the post analysis results on the right (column) in the attached image . As you have mentioned it didnt work well in the cerebellum any other ways to improve in the inferior regions?
Thanks
Regards Tilak ________________________________________ From: Ramtilak Gattu Sent: Monday, March 28, 2016 5:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
Thank you,
Attached is the scripts folder for one subject .
Thanks
Regards Tilak ________________________________________ From: Ramtilak Gattu Sent: Monday, March 28, 2016 4:11 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
Sorry, Actually just found out that the receiving coil is the 12 channel head coil and the transmitting coil is the body coil. I am attaching a snapshot showing the sag orientation of the three cases that I previously mentioned and uploaded for your review.
From these figures do you really think there is not enough contrast, just wondering
1) why it worked in the bottom image and it failed in the upper two (T1_sag_comparison.jpg) 2) it failed in the left image and did good in the right image (T1_sag_comparison_2.jpg).
We have similar data in 25 of the subjects. Is there a way to salvage the existing data and improve our results we will certainly follow your input in changing the existing protocol and collect some data and run the analysis to see if it improves the results.
One more thought is if is there any other way around to increase the contrast by taking help from T2 image and run recon-all. Do you think it will help?
Thanks for you help .
Regards Tilak
________________________________________ From: Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Monday, March 28, 2016 11:22 AM To: Ramtilak Gattu Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
what was the transmit coil? I think I would either reduce the voxel sizes a bit or not use grappa. Probably go to 1.2 mm or so, which would be a 70% increase in SNR. That won't help the transmit bias field though if you have one. The 8 channel can also sometimes be a problem. The 32 channel coils work much better
On Mon, 28 Mar 2016, Ramtilak Gattu wrote:
Hey Bruce,
The scans are done on 3T Siemens TRIO and 8 coil head channel with a GRAPPA of 2.
Here is the screen shot of protocol used.
https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/...
Thanks
Regards Tilak
From: Ramtilak Gattu Sent: Sunday, March 27, 2016 3:23 PM To: Bruce Fischl Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
Hey Bruce,
I have uploaded the files in
https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/...
I have also included the 001.mgz in there.
Thanks
Regards Tilak
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Saturday, March 26, 2016 8:35 PM To: Ramtilak Gattu Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
can you send me the rawavg.mgz from the subjects's mri file instead of these dicoms (which I can't read) On Sat, 26 Mar 2016, Ramtilak Gattu wrote:
Hey Bruce,
Thanks for the quick reply.
I have uploaded the cases in
https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/... xWlpwBQnNAhG8%3d&docid=0a72431d82b4d4b9b924cccbdfb7f34f8
The voxel dimensions are 1x1x1 mm.
Thanks
Regards
Tilak
From: Ramtilak Gattu Sent: Friday, March 25, 2016 9:59 PM To: freesurfer@nmr.mgh.harvard.edu Cc: tilakgattu@hotmail.com Subject: improving white/grey segmentation in recon -all for better volume estmation
Hello all,
We have run recon -all on some healthy control subjects T1 images but we found out that the gray-white segmentation on half our subjects is bad and it leads to increased white matter volumes and decreased gray matter volumes. I have included a snap shot showing the difference in segmentation from bad to good for 3 cases
https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/... WPDE1klUw%3d&docid=0dd4546a8004f46578b7a2177b192806a
. The parameter in the sequence are TE=4.92 ms, TR=19 ms, Flip angle =20 degrees. and use a snapshot one slice to show the good CNR. We are using Freesurfer version 5.3.
Thanks
Regards
Tilak.
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 Tilak
can you tell us a bit more about your acquisition? It is *very* noisy and low contrast. I expect some of what you are seeing is the result of big topological defects caused by segmentation inaccuracies. I can't tell for users with only the brain.mgz/lh.white/001.mgz
cheers Bruce
On Sun, 24 Apr 2016, Ramtilak Gattu wrote:
Hello Bruce,
Attached are the files for two subjects with brain.mgz and lh.white.
https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/...
The values of WM in those regions in brain.mgz are above 90.
Thanks
Regards Tilak
From: Ramtilak Gattu Sent: Saturday, April 23, 2016 5:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
Hello Bruce,
Thanks a lot for your earlier expert option suggestion in improving the segmentation during the recon process. I am attaching a snap shot where yellow is with expert options and red is with default options. My concern is where I have indicated with blue arrows . Could you please suggest why is it still failing to pick up those areas. Is it because of misregistration with the atlas if so where can I find the results after the non linear registration and would it be possible to improve with any more expert options during the registration and the segmentation subsequently.
Thanks
Regards Tilak
From: Ramtilak Gattu Sent: Wednesday, March 30, 2016 4:26 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
Thank you for recommending the expert options. I have run this on two subjects (rows) and you can see the post analysis results on the right (column) in the attached image . As you have mentioned it didnt work well in the cerebellum any other ways to improve in the inferior regions?
Thanks
Regards Tilak ________________________________________ From: Ramtilak Gattu Sent: Monday, March 28, 2016 5:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
Thank you,
Attached is the scripts folder for one subject .
Thanks
Regards Tilak ________________________________________ From: Ramtilak Gattu Sent: Monday, March 28, 2016 4:11 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
Sorry, Actually just found out that the receiving coil is the 12 channel head coil and the transmitting coil is the body coil. I am attaching a snapshot showing the sag orientation of the three cases that I previously mentioned and uploaded for your review.
From these figures do you really think there is not enough contrast, just wondering
- why it worked in the bottom image and it failed in the upper two (T1_sag_comparison.jpg)
- it failed in the left image and did good in the right image (T1_sag_comparison_2.jpg).
We have similar data in 25 of the subjects. Is there a way to salvage the existing data and improve our results we will certainly follow your input in changing the existing protocol and collect some data and run the analysis to see if it improves the results.
One more thought is if is there any other way around to increase the contrast by taking help from T2 image and run recon-all. Do you think it will help?
Thanks for you help .
Regards Tilak
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Monday, March 28, 2016 11:22 AM To: Ramtilak Gattu Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
what was the transmit coil? I think I would either reduce the voxel sizes a bit or not use grappa. Probably go to 1.2 mm or so, which would be a 70% increase in SNR. That won't help the transmit bias field though if you have one. The 8 channel can also sometimes be a problem. The 32 channel coils work much better
On Mon, 28 Mar 2016, Ramtilak Gattu wrote:
Hey Bruce,
The scans are done on 3T Siemens TRIO and 8 coil head channel with a GRAPPA of 2.
Here is the screen shot of protocol used.
https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/...
Thanks
Regards Tilak
From: Ramtilak Gattu Sent: Sunday, March 27, 2016 3:23 PM To: Bruce Fischl Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
Hey Bruce,
I have uploaded the files in
https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/...
I have also included the 001.mgz in there.
Thanks
Regards Tilak
From: Bruce Fischl fischl@nmr.mgh.harvard.edu Sent: Saturday, March 26, 2016 8:35 PM To: Ramtilak Gattu Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for better volume estmation
can you send me the rawavg.mgz from the subjects's mri file instead of these dicoms (which I can't read) On Sat, 26 Mar 2016, Ramtilak Gattu wrote:
Hey Bruce,
Thanks for the quick reply.
I have uploaded the cases in
https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/... xWlpwBQnNAhG8%3d&docid=0a72431d82b4d4b9b924cccbdfb7f34f8
The voxel dimensions are 1x1x1 mm.
Thanks
Regards
Tilak
From: Ramtilak Gattu Sent: Friday, March 25, 2016 9:59 PM To: freesurfer@nmr.mgh.harvard.edu Cc: tilakgattu@hotmail.com Subject: improving white/grey segmentation in recon -all for better volume estmation
Hello all,
We have run recon -all on some healthy control subjects T1 images but we found out that the gray-white segmentation on half our subjects is bad and it leads to increased white matter volumes and decreased gray matter volumes. I have included a snap shot showing the difference in segmentation from bad to good for 3 cases
https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/... WPDE1klUw%3d&docid=0dd4546a8004f46578b7a2177b192806a
. The parameter in the sequence are TE=4.92 ms, TR=19 ms, Flip angle =20 degrees. and use a snapshot one slice to show the good CNR. We are using Freesurfer version 5.3.
Thanks
Regards
Tilak.
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.
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