Hi:
I am having troubles in preparing a picture showing MR image segmentation in the coronal, axial and sagittal planes.
Any light on that?
Thanks, --francesca
Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, May 31, 2005 1:50 PM To: Wan Park Cc: free surfer Subject: [Freesurfer] Re: Gray Volume question
Hi Wan,
they haven't been normalized. Typically you would normalize by the total intracranial volume, which can be a bit tricky to get from only a T1. If you normalize by total brain volume, that should be a bit more conservative, as it would normalize out total atrophy.
cheers, Bruce
On Tue, 31 May 2005, Wan Park wrote:
Hi, I have a question. I am getting the gray volume for a standard area (G_subcallosal) in different brains (male and female) with different conditions.
If I want to compare these volumes, should I normalize them with the total
brain (or hemisphere) volume or can I use these results directly? I understand that the FS fills the volume from a particular brain into a standard brain. So, are the volumes already normalized? Thanks,
Wan
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
can you describe the problem in more detail?
On Tue, 31 May 2005, Bagnato, Francesca (NIH/NINDS) wrote:
Hi:
I am having troubles in preparing a picture showing MR image segmentation in the coronal, axial and sagittal planes.
Any light on that?
Thanks, --francesca
Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Tuesday, May 31, 2005 1:50 PM To: Wan Park Cc: free surfer Subject: [Freesurfer] Re: Gray Volume question
Hi Wan,
they haven't been normalized. Typically you would normalize by the total intracranial volume, which can be a bit tricky to get from only a T1. If you normalize by total brain volume, that should be a bit more conservative, as it would normalize out total atrophy.
cheers, Bruce
On Tue, 31 May 2005, Wan Park wrote:
Hi, I have a question. I am getting the gray volume for a standard area (G_subcallosal) in different brains (male and female) with different conditions.
If I want to compare these volumes, should I normalize them with the total
brain (or hemisphere) volume or can I use these results directly? I understand that the FS fills the volume from a particular brain into a standard brain. So, are the volumes already normalized? Thanks,
Wan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Goodmorning:
My problem is related to the fact that I would like to save an image in whatever format suitable for a presentation (from my free-surfer subject). I am not sure which is the volume I should download to begin with and what I should load on it - afterwards - to show the cortical GM segmentation in the three planes.
Thanks,
--francesca
_____
From: Bruce Fischl Sent: Tue 5/31/2005 6:36 PM To: Bagnato, Francesca (NIH/NINDS) Cc: free surfer Subject: Re: [Freesurfer] pictures of MRI image segmentation
can you describe the problem in more detail?
On Tue, 31 May 2005, Bagnato, Francesca (NIH/NINDS) wrote:
Hi:
I am having troubles in preparing a picture showing MR image segmentation
in
the coronal, axial and sagittal planes.
Any light on that?
Thanks, --francesca
Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu ]
Sent: Tuesday, May 31, 2005 1:50 PM To: Wan Park Cc: free surfer Subject: [Freesurfer] Re: Gray Volume question
Hi Wan,
they haven't been normalized. Typically you would normalize by the total intracranial volume, which can be a bit tricky to get from only a T1. If you normalize by total brain volume, that should be a bit more conservative, as it would normalize out total atrophy.
cheers, Bruce
On Tue, 31 May 2005, Wan Park wrote:
Hi, I have a question. I am getting the gray volume for a standard area (G_subcallosal) in different brains (male and female) with different conditions.
If I want to compare these volumes, should I normalize them with the
total
brain (or hemisphere) volume or can I use these results directly? I understand that the FS fills the volume from a particular brain into a standard brain. So, are the volumes already normalized? Thanks,
Wan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Francesca,
I would load the surfaces over the T1 volume and take snapshots of that. You can also do tools->configure->surface and make the lines thicker, as they are hard to see if they are only 1 pixel wide.
cheers, Bruce
On Wed, 1 Jun 2005, Bagnato, Francesca (NIH/NINDS) wrote:
Goodmorning:
My problem is related to the fact that I would like to save an image in whatever format suitable for a presentation (from my free-surfer subject). I am not sure which is the volume I should download to begin with and what I should load on it - afterwards - to show the cortical GM segmentation in the three planes.
Thanks,
--francesca
From: Bruce Fischl Sent: Tue 5/31/2005 6:36 PM To: Bagnato, Francesca (NIH/NINDS) Cc: free surfer Subject: Re: [Freesurfer] pictures of MRI image segmentation
can you describe the problem in more detail?
On Tue, 31 May 2005, Bagnato, Francesca (NIH/NINDS) wrote:
Hi:
I am having troubles in preparing a picture showing MR image segmentation
in
the coronal, axial and sagittal planes.
Any light on that?
Thanks, --francesca
Francesca Bagnato, MD NIB-NINDS-NIH 10 Center Drive Building 10, Room 5B16 Bethesda, MD, 20892 USA ph #: 001-301-402.6391 fax #: 001-301-402.0373
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu ]
Sent: Tuesday, May 31, 2005 1:50 PM To: Wan Park Cc: free surfer Subject: [Freesurfer] Re: Gray Volume question
Hi Wan,
they haven't been normalized. Typically you would normalize by the total intracranial volume, which can be a bit tricky to get from only a T1. If you normalize by total brain volume, that should be a bit more conservative, as it would normalize out total atrophy.
cheers, Bruce
On Tue, 31 May 2005, Wan Park wrote:
Hi, I have a question. I am getting the gray volume for a standard area (G_subcallosal) in different brains (male and female) with different conditions.
If I want to compare these volumes, should I normalize them with the
total
brain (or hemisphere) volume or can I use these results directly? I understand that the FS fills the volume from a particular brain into a standard brain. So, are the volumes already normalized? Thanks,
Wan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, During running recon-all, I get this line INFO: Volume /tmp/mritotal_5659/nu_8_dxyz.mnc cannot be found. I looked in my /tmp folder and I have a mritotal_7563 folder but no mritotal_5659 folder. Will this affect my recon-all processing? This error also appears in my orig.euler files. I am running the line recon-all-nmr -stage3 -stage4a -stage4b -subjid t217c, my subjects directory is /space/troy/2/users/garysdata, and i am running this on the computer troy. Thanks, Margaret
Hi Margaret,
no, that shouldn't matter.
Bruce
On Wed, 1 Jun 2005, Margaret Duff wrote:
Hi, During running recon-all, I get this line INFO: Volume /tmp/mritotal_5659/nu_8_dxyz.mnc cannot be found. I looked in my /tmp folder and I have a mritotal_7563 folder but no mritotal_5659 folder. Will this affect my recon-all processing? This error also appears in my orig.euler files. I am running the line recon-all-nmr -stage3 -stage4a -stage4b -subjid t217c, my subjects directory is /space/troy/2/users/garysdata, and i am running this on the computer troy. Thanks, Margaret _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bagnato, Francesca (NIH/NINDS) -
Bruce Fischl -
Margaret Duff