Hi Tilak
this one (attached) worked pretty well on one of the datasets you sent me.
Run recon-all with -expert xopts.txt and the usual other args. I would be
very cautious about interpreting results though. For example there is very
little gray/white contrast in multiple regions such as perirolandic cortex,
and any apparent difference/correlation in thicknesss may just be subject
motion. Similarly, I can't distinguish gray from white in the cerebellum,
but hippocampus and amygdala/basal ganglia might be ok
cheers
Bruce
On Mon, 28 Mar 2016, Ramtilak Gattu wrote:
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.
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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
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