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 <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/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 <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/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: 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/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.
>>
>>
>>
>
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