External Email - Use Caution
Hello,
The following command
trac-all -c dmrirc.example -bedp
always exits with the following error.
{
WARN: Running bedbostx locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_mgh -n 2 -model 1
/home/
External Email - Use Caution
Hi,
Could I please get the pass code for FS_7_2_0_ubuntu_18_04_06.ova
Thanks
Regards
Tilak
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesu
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Hello all,
We built a CC mask with 3 segments ( Genu, body and Splenium) and made it a
part of the existing ASEG.mgz in "fsaverage" folder.
Would like to incorporate this shown Corpus Callosum (CC) mask into aseg
calculations replacing the existing
nt subject we process
from here on.
Would it be possible to replace certain existing labels with our own custom
roi's and do the final volume calculations?
If so how?
Thanks
Regards
Tilak
From: Ramtilak Gattu
Sent: Sunday, May 15, 2022 5:01 PM
External Email - Use Caution
Hi,
We are interested in replacing a couple of labels in aseg atlas with our own
roi's already in the same space as of "aseg.mgz" atlas in the fsaverage folder.
What would be the best way to do this? Could someone help or guide me if anyone
has done
: Ramtilak Gattu
Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error
Maybe you could let us know if the system integrity protection feature is
turned on the Mac (which is the default). The following command will report if
it is enabled or disabled, e.g., when enabled
00:59:59 EDT 2021
For more details, see the log file
/Users/tilak/Desktop/Work/CNS_cases/Hipps/Amy_Damboise/scripts/hippocampal-subfields-T1.log
tilak@tilak Hipps %
From: fsbuild
Sent: Tuesday, March 23, 2021 11:00 PM
To: freesurfer@nmr.mgh.harvard.edu
External Email - Use Caution
Hi,
I am also encountering the same issue as WON JONG CHWA on my macbook pro (16gb
ram) and I even tried the same on imac (8gb ram). I ran recon-all successfully
on both systems. Here are my system details
Hardware Overview:
Model Name: MacBook
glxgears shows up a screen with three gear wheels in blue, pink and green and
frame information rate being printed out on the command window.
From: Ramtilak Gattu
Sent: Tuesday, June 28, 2016 2:55:32 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview
Regards
Tilak
From: Ramtilak Gattu
Sent: Tuesday, June 28, 2016 2:01:00 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem
Hey Ruopeng,
I still couldnt figure out whats going on the freeview display. I updated the
Nvidia drivers but still
Hey Ruopeng,
I still couldnt figure out whats going on the freeview display. I updated the
Nvidia drivers but still its not displaying in gray scale.
please help.
thanks
Regards
Tilak
From: Ramtilak Gattu
Sent: Friday, June 24, 2016 12:25:50 PM
To
That is all . No error messages at all.
From: Ramtilak Gattu
Sent: Friday, June 24, 2016 10:25:42 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem
I tried updating my Nvidia drivers. but now whenever I try to open freeview it
says
I tried updating my Nvidia drivers. but now whenever I try to open freeview it
says " aborted ( core dumped).
please help.
Thanks
Regards
Tilak
From: Ramtilak Gattu
Sent: Thursday, June 23, 2016 5:27:12 PM
To: freesurfer@nmr.mgh.harvard.edu
Subjec
May be thats the problem. I'll try to give it a shot to see if it fixes the
problem.
Thanks.
From: Ramtilak Gattu
Sent: Thursday, June 23, 2016 4:10:28 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem
This issue is only
This issue is only with freesurfer , images on fslview doesnt have this problem.
From: Ramtilak Gattu
Sent: Thursday, June 23, 2016 3:31:41 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: freeview display problem
That is just one layer the yellow contrast
That is just one layer the yellow contrast is from when we tune the contrast up
or down.
From: Ramtilak Gattu
Sent: Thursday, June 23, 2016 2:37:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: freeview display problem
Hello ,
I am having strange freeview
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 i
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,
>
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 w
lues of WM in those regions in brain.mgz are above 90.
Thanks
Regards
Tilak
From: Ramtilak Gattu
Sent: Saturday, April 23, 2016 5:26 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] improving white/grey segmentation in recon -all for
be
On Sat, Apr 23, 2016 at 7:47 PM, Ramtilak Gattu 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 opti
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
&docid=034b186e0a218401590414fc271f3cf5f
Thanks
Regards
Tilak
From: Ramtilak Gattu
Sent: Saturday, March 26, 2016 6:59 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: improving white/grey segmentation in recon -all for better volume
estmation
Hey B
oxel 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
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
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