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/15/guestaccess.aspx?guestaccesstoken=jgsnvwnZQjIfytimmwD7%2ffzAPxvQUAO9CG0t8s11A6Q%3d&docid=1b9c854cfa76a467086454f2ed39311ef > > 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 <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 . 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 mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
