On Sat, Apr 23, 2016 at 7:47 PM, Ramtilak Gattu <ti...@neurologicstudies.com > wrote:
> 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 > > a) misregistration with the atlas > (i) if so where can I find the results after the non linear > registration and > (ii) would it be possible to improve with any more expert options > during the registration and the segmentation subsequently. > > b) or is it should be just changing the lower limit values for the WM and > higher limit values for the GM. I am not sure which way to tune the values > should I go low on WM values and go high on GM values. These are the actual > values > > mri_segment -wlo 87.7 -ghi 103.3 > mris_make_surfaces -min_gray_at_white_border 79.4 -max_border_white 109.3 > -min_border_white 90 -max_csf 68.7 -max_gray 98.7 > -max_gray_at_csf_border 84.7 -min_gray_at_csf_border 58.1 > > For example Should these be changed to > > mri_segment -wlo 80 -ghi 110 > > Thanks for your help in advance. > > Regards > Tilak > > > 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 <fis...@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/15/guestaccess.aspx?guestaccesstoken=VJ0QiLxUz9fI6GCUofGHq7IAQY6k4uG50U0ic0zBkHE%3d&docid=034b186e0a218401590414fc271f3cf5f > > > > 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/15/guestaccess.aspx?guestaccesstoken=0MdoYLvWY2ZYOdi983YqZtMFGMns%2b5WB6dNeC3osudU%3d&docid=000b5dcba90f2419e9bdf4ce77dfd7a5e > > > > I have also included the 001.mgz in there. > > > > Thanks > > > > Regards > > Tilak > > > > ________________________________________ > > From: Bruce Fischl <fis...@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/15/guestaccess.aspx?guestaccesstoken=%2bkyhy0gR4k7Q3AechqG%2bjqb89ALB94 > >> 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: tilakga...@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/15/guestaccess.aspx?guestaccesstoken=ajPIRobFq548RyhRJWPQ9q70vAXUGIJ9h5 > >> 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 . 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