could do the conversion?
Thank you in advance!
All the best
Tina Jeon
PhD Candidate
UT Southwestern Medical Center '14
UT Southwestern Medical Center
The future of medicine, today.
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To: Tina Jeon
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] conversion from ascii to surface
Hi Tina
try mris_convert
cheers
Bruce
On Thu, 16 May 2013, Tina Jeon wrote:
Dear Doug, Nick, and all,
I am trying to convert a surface from Amira to freesurfer in order
I created the ascii file directly from amira, which from what I understand is 0
based.
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 9:15 AM
To: Tina Jeon
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] conversion from
Great! I subtracted the vertices by one and now it works. Appreciate your help
and fast responses.
Tina
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 9:37 AM
To: Tina Jeon
Cc: Freesurfer@nmr.mgh.harvard.edu
Subject: RE
the offset though.
Bruce
On Thu, 23 May 2013, Tina Jeon wrote:
Hello Freesurfers,
I have created labeling files from a subject using the area file (previously
named base). The label file corresponds to the freesurfer generated
cortical label, ctx-rh-bankssts, which I have attached
Doug can you answer this?
The vertex indices can be fixed with matlab but more importantly I need to know
why there is a slight offset in vertex coordinates.
Thank you!
Tina Jeon
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, May 23, 2013
Yes same result as with freeview.
Sent from my iPhone
On May 29, 2013, at 7:46 PM, Bruce Fischl
fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote:
Hi Tina
Did you try visualizing it in tksurfer?
Bruce
On May 29, 2013, at 7:22 PM, Tina Jeon
tina.j
...@nmr.mgh.harvard.edu]
Sent: Wednesday, May 29, 2013 8:41 PM
To: Tina Jeon
Subject: Re: [Freesurfer] mris_divide_parcellation color table error
Sure
On May 29, 2013, at 9:36 PM, Tina Jeon tina.j...@utsouthwestern.edu wrote:
The colors are visually different by a shade then loop every 4 or so colors.
I
Yes it worked. Thank you that is exactly what I needed.
Tina
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thursday, May 30, 2013 12:36 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Tina Jeon
Subject: Re: [Freesurfer] mris_divide_parcellation color table
Dear freesurfer experts,
I am new to the freeview interface. How do I go about drawing a ROI on the
surfaces to create my own label? Both the voxel edit and ROI edit buttons are
not useful in this case.
Thank you in advance,
Tina Jeon
PhD Candidate
Advanced Imaging Research Center
UT
nifti --out
./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh
I open the newly created surface with tkmedit and I get a display error (see
below). Does anyone have any suggestions on how to absolve the issue?
Thanks all help appreciated,
Tina Jeon
Graduate Student
nifti --out
./3t2234/label/15yr_lh_A1C_new.nii.gz --regheader 3t2234 --projfrac 1 --hemi lh
I open the newly created surface with tkmedit and I get a display error (see
below). Does anyone have any suggestions on how to absolve the issue?
Thanks all help appreciated,
Tina Jeon
Graduate Student
I am still getting the same display error with using an mgh file.
mri_vol2surf --src ./3t2234/label/15yr_lh_A1C_new.mgh --out_type mgh --out
./3t2234/label/15yr_lh_A1C_new2.mgh --regheader 3t2234 --projfrac-max 0 1 .1
--hemi lh
Any suggestions?
Thank you,
Tina Jeon
Graduate Student
Advanced
Using tkmedit
-Original Message-
From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Monday, March 12, 2012 1:01 PM
To: Tina Jeon
Cc: Douglas N Greve; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] mri_vol2surf
how are you trying to display it?
On Mon, 12 Mar 2012
convert the .label file to .mgz, however, I am still
getting the same display error and the command is not recognizing the flag
--projfrac-max
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, March 12, 2012 1:35 PM
To: Tina Jeon
Cc: Bruce Fischl
a linux centos.
I can send you my files if need be. Basically I would like my manual roi edits
to project to the entire cortical ribbon.
Thanks,
Tina
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, March 12, 2012 4:12 PM
To: Tina Jeon
Cc
for your help,
Tina
Graduate student
Advanced Imaging Research Center
UT Southwestern Medical Center
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, March 12, 2012 5:01 PM
To: Tina Jeon
Cc: Bruce Fischl; freesurfer@nmr.mgh.harvard.edu
Subject: Re
version FSv5.0.0 on Centos4_x86_64 bit.
Many thanks,
Tina Jeon
Biomedical Engineering Graduate Student
Advanced Imaging Research Center
UT Southwestern Medical Center
P: (214) 645-2892
F: (214) 645-2885
UT Southwestern Medical Center
The future of medicine
#/surf/*h.base.asc
Thank you,
Tina Jeon
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, April 02, 2012 12:50 PM
To: Tina Jeon; Freesurfer@nmr.mgh.harvard.edu
Subject: Re: Freesurfer base file question
Hi Tina, sorry no one got to your first
/*h.base.mgh --outdir
junk mris_convert -c *h.base.mgh #/surf/*h.white #/surf/*h.base.asc
Thank you,
Tina Jeon
-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Monday, April 02, 2012 12:50 PM
To: Tina Jeon; Freesurfer@nmr.mgh.harvard.edu
Subject: Re: Freesurfer
Hello freesurfer team,
I am trying to run tkregister2 and I come up with this error message :
No glx extension!
register: ### tkoInitWindow(name) failed
Any idea on what this could be from? Previously this command had worked.
Thanks,
Tina Jeon
in the ascii files for the surfaces we
found -120 in the coordinates but native space is [0,240] (i.e., without
negatives).
Is using tkregister2 the solution? Or using an affine registration matrix to
transform the coordinates?
Thanks in advance. Your help would be greatly appreciated.
Tina Jeon
Hello all!
After creating some labeling files from aparc.a2005s.annot, I noticed that my
sulci and gyri volumes generated from the .label files (i.e., after running
mri_annotation2label and mri_label2vol) were only representing the outer layer
of the white surface. Is there any way to generate
to generate .label files that include
the entire cortical ribbon?
Thanks, any help would be appreciated.
Tina Jeon
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The information
by registering the
freesurfer conformed structural space to diffusion space.
Ultimately I want to align the gyri and sulci volumes to the diffusion images I
have. Is this a viable solution?
Thanks in advance,
Tina Jeon
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Hello all,
Can freesurfer be run on diffusion weighted images and/or B0 images? I am
trying to obtain segmentation of the gray/white surfaces.
Thanks,
Tina Jeon
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suggest a way that I can open the text file
using a different graphical interface?
Thank you in advance,
Tina Jeon
Graduate Student
Advanced Imaging Research Center
UT Southwestern Medical Center
UT Southwestern Medical Center
The future of medicine, today
system. The left and right surfaces must have been translated somewhere in the
inflation process. How do I put them back into the correct coordinate space
that the pial and white surfaces are? Thank you.
Tina Jeon, M.S.
Project Supervisor
UT Southwestern Medical Center
Advanced Imaging
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