nope, but in occipital and perirolandic cortex I couldn't see the
gray/white boundary in your data, so make sure your scans have contrast
there
On Mon, 25 Apr 2016,
Ramtilak Gattu 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 chan
nel
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=VJ0QiLxUz9fI6G
CUofGHq7IAQY6k4uG50U0ic0zBkHE%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=0MdoYLvWY2ZYOd
i983YqZtMFGMns%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=%2bkyhy0gR4k7Q
3AechqG%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=ajPIRobFq548Ry
hRJWPQ9q70vAXUGIJ9h5
>> 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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