Hey Bruce, Following up with the question can I find any documentation to improve the segmentation like what are the parameters that needs to be tweaked. Can we use any seed points to classify and improve the segmentation? How to decide the thresholds in choosing the parameters to improve the segmentation?
Thanks Regards Tilak On Mon, Apr 25, 2016 at 12:17 PM, Ramtilak Gattu < ti...@neurologicstudies.com> wrote: > Hey Bruce, > > These scans are done on 3T Siemens Trio. > > Will send you CNR for some of the cases . Are you looking for any specific > structures in particular. > > Thanks > > Regards > Tilak > > On Mon, Apr 25, 2016 at 12:01 PM, Ramtilak Gattu < > ti...@neurologicstudies.com> wrote: > >> Hello Bruce, >> >> Thanks for the response. I previously mentioned the parameters in the >> earlier discussion for the same topic and you have suggested to decrease >> the TE and increase the voxelsize to 1.2mm for better SNR. For the >> recollection I am again mentioning the complete parameters here- >> >> The parameter in the sequence are TE=4.92 ms, TR=19 ms, Flip angle =20 >> degrees, voxel size 1x1x1, receiving coil is the 12 channel >> >> head coil and the transmitting coil is the body coil and GRAPPA of 2. We are >> using Freesurfer version 5.3. >> >> >> I am including all the recon result files for one case for your review. >> >> >> https://waynestateprod-my.sharepoint.com/personal/ao3080_wayne_edu/_layouts/15/guestaccess.aspx?guestaccesstoken=etz0FRv0sU01dbi%2fRsmwZmSlq5pNMZA5%2fXhu5hDy10Q%3d&docid=1bd7f60d2dc074a12ae531ebbdcb3829b >> >> >> >> Thanks >> >> >> Regards >> >> Tilak >> >> >> On Sun, Apr 24, 2016 at 1:52 PM, Ramtilak Gattu < >> ti...@neurologicstudies.com> wrote: >> >>> Hello Bruce, >>> >>> Attached are the files for two subjects with brain.mgz and lh.white. >>> >>> The values of WM in those regions in brain.mgz are above 90. >>> >>> Thanks >>> >>> Regards >>> Tilak >>> >>> >>> On Sun, Apr 24, 2016 at 1:49 PM, Ramtilak Gattu < >>> ti...@neurologicstudies.com> wrote: >>> >>>> >>>> >>>> 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. 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