improving white/grey segmentation in recon -all for better volume estmation - Freesurfer

23 Apr 2016

      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/...
...
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.
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