Hi Tilak
I think you need to improve your data if that is an option. I couldn't
see the gray/white boundary in either occipital or perirolandic cortex,
so no parameters are going to help there
cheers
Bruce
On Mon, 25 Apr 2016, Ramtilak Gattu
wrote:
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 degr
ees, 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%2fXh
u5hDy10Q%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=VJ0QiLxUz9fI6GCUofGHq7IAQY6k4uG50U0ic
0zBkHE%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%2b5WB6dN
eC3osudU%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.
>>
>>
>>
>
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