Sure. Right now I would like to extract the corpus callosum, as defined by DTI. After some image arithmetic and thresholding, I have a scalar image of left-right diffusion with values from 0 to 1.2. I would like to pick a voxel in the center of the CC and grow a region around it picking up voxels in the range 0.9 - 1.2, and only if they share at least two (or some other number of) faces. The result will be an extracted single irregular ROI of the CC.
I am more of an EEG person, and have done this with EEG tools like EMSE and Brain Voyager.
Thanks, -Jeff
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request@nmr.mgh.harvard.edu Sent: Tuesday, August 10, 2010 5:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 78, Issue 18
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When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Re: Red Hat vs. CentOs (Paul Raines) 2. Exec format error. Wrong Architecture. (Kristina Fanucci) 3. Re: Red Hat vs. CentOs (Don Hagler) 4. [freesurfer] a puzzling installation error (Glen Lee) 5. region seeding and growing (Eriksen, Jeffrey (Portland)) 6. Re: region seeding and growing (Bruce Fischl) 7. surface-based aal template (Zhangyuanchao) 8. File Format for talairach.m3z (Soon Hock Wei)
----------------------------------------------------------------------
Message: 1 Date: Mon, 9 Aug 2010 15:42:57 -0400 (EDT) From: Paul Raines raines@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Red Hat vs. CentOs To: dahlia@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: Pine.LNX.4.62.1008091542210.9461@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Yes, it should be almost no different.
On Mon, 9 Aug 2010 dahlia@nmr.mgh.harvard.edu wrote:
Hi,
I'd like to make sure that a Dell desktop with pre-installed RHEL
would
work seamlessly with Freesurfer, equivalent to CentOS. Is this
correct?
Thanks, Dahlia. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Jeff,
we autoamtically segment the cc from an anatomical, which would probably be a more accurate measure.
cheers Bruce On Tue, 10 Aug 2010, Eriksen, Jeffrey (Portland) wrote:
Sure. Right now I would like to extract the corpus callosum, as defined by DTI. After some image arithmetic and thresholding, I have a scalar image of left-right diffusion with values from 0 to 1.2. I would like to pick a voxel in the center of the CC and grow a region around it picking up voxels in the range 0.9 - 1.2, and only if they share at least two (or some other number of) faces. The result will be an extracted single irregular ROI of the CC.
I am more of an EEG person, and have done this with EEG tools like EMSE and Brain Voyager.
Thanks, -Jeff
-----Original Message----- From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request@nmr.mgh.harvard.edu Sent: Tuesday, August 10, 2010 5:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 78, Issue 18
Send Freesurfer mailing list submissions to freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request@nmr.mgh.harvard.edu
You can reach the person managing the list at freesurfer-owner@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..."
Today's Topics:
- Re: Red Hat vs. CentOs (Paul Raines)
- Exec format error. Wrong Architecture. (Kristina Fanucci)
- Re: Red Hat vs. CentOs (Don Hagler)
- [freesurfer] a puzzling installation error (Glen Lee)
- region seeding and growing (Eriksen, Jeffrey (Portland))
- Re: region seeding and growing (Bruce Fischl)
- surface-based aal template (Zhangyuanchao)
- File Format for talairach.m3z (Soon Hock Wei)
Message: 1 Date: Mon, 9 Aug 2010 15:42:57 -0400 (EDT) From: Paul Raines raines@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Red Hat vs. CentOs To: dahlia@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu Message-ID: Pine.LNX.4.62.1008091542210.9461@gate.nmr.mgh.harvard.edu Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
Yes, it should be almost no different.
On Mon, 9 Aug 2010 dahlia@nmr.mgh.harvard.edu wrote:
Hi,
I'd like to make sure that a Dell desktop with pre-installed RHEL
would
work seamlessly with Freesurfer, equivalent to CentOS. Is this
correct?
Thanks, Dahlia. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Bruce,
Yes, you are likely correct, but my boss wants to do it this way. Besides, I am going to have other uses for region growing that you might find scientifically acceptable. But the question still stands - does Freesurfer give me access to such a basic tool, or will I have to write my own with Matlab/IDL/C etc.?
Thanks, -Jeff
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, August 11, 2010 2:00 PM To: Eriksen, Jeffrey (Portland) Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 78, Issue 18
Hi Jeff,
we autoamtically segment the cc from an anatomical, which would probably
be a more accurate measure.
cheers Bruce On Tue, 10 Aug 2010, Eriksen, Jeffrey (Portland) wrote:
Sure. Right now I would like to extract the corpus callosum, as
defined
by DTI. After some image arithmetic and thresholding, I have a scalar image of left-right diffusion with values from 0 to 1.2. I would like
to
pick a voxel in the center of the CC and grow a region around it
picking
up voxels in the range 0.9 - 1.2, and only if they share at least two (or some other number of) faces. The result will be an extracted
single
irregular ROI of the CC.
I am more of an EEG person, and have done this with EEG tools like
EMSE
and Brain Voyager.
Thanks, -Jeff
Hi Jeff,
you are welcome to our source code which has region-growing algorithms in the volume (e.g. for control point detection) and on the surface.
cheers Bruce
On Mon, 16 Aug 2010, Eriksen, Jeffrey (Portland) wrote:
Bruce,
Yes, you are likely correct, but my boss wants to do it this way. Besides, I am going to have other uses for region growing that you might find scientifically acceptable. But the question still stands - does Freesurfer give me access to such a basic tool, or will I have to write my own with Matlab/IDL/C etc.?
Thanks, -Jeff
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, August 11, 2010 2:00 PM To: Eriksen, Jeffrey (Portland) Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 78, Issue 18
Hi Jeff,
we autoamtically segment the cc from an anatomical, which would probably
be a more accurate measure.
cheers Bruce On Tue, 10 Aug 2010, Eriksen, Jeffrey (Portland) wrote:
Sure. Right now I would like to extract the corpus callosum, as
defined
by DTI. After some image arithmetic and thresholding, I have a scalar image of left-right diffusion with values from 0 to 1.2. I would like
to
pick a voxel in the center of the CC and grow a region around it
picking
up voxels in the range 0.9 - 1.2, and only if they share at least two (or some other number of) faces. The result will be an extracted
single
irregular ROI of the CC.
I am more of an EEG person, and have done this with EEG tools like
EMSE
and Brain Voyager.
Thanks, -Jeff
you can also use mri_binarize which has a --dilate option. I think it dilates if it has one or more faces in common. You might also look into fslmaths (you can easily convert from mgz to nifti) if that's an issue
On 8/16/10 8:46 PM, Bruce Fischl wrote:
Hi Jeff,
you are welcome to our source code which has region-growing algorithms in the volume (e.g. for control point detection) and on the surface.
cheers Bruce
On Mon, 16 Aug 2010, Eriksen, Jeffrey (Portland) wrote:
Bruce,
Yes, you are likely correct, but my boss wants to do it this way. Besides, I am going to have other uses for region growing that you might find scientifically acceptable. But the question still stands - does Freesurfer give me access to such a basic tool, or will I have to write my own with Matlab/IDL/C etc.?
Thanks, -Jeff
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, August 11, 2010 2:00 PM To: Eriksen, Jeffrey (Portland) Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 78, Issue 18
Hi Jeff,
we autoamtically segment the cc from an anatomical, which would probably
be a more accurate measure.
cheers Bruce On Tue, 10 Aug 2010, Eriksen, Jeffrey (Portland) wrote:
Sure. Right now I would like to extract the corpus callosum, as
defined
by DTI. After some image arithmetic and thresholding, I have a scalar image of left-right diffusion with values from 0 to 1.2. I would like
to
pick a voxel in the center of the CC and grow a region around it
picking
up voxels in the range 0.9 - 1.2, and only if they share at least two (or some other number of) faces. The result will be an extracted
single
irregular ROI of the CC.
I am more of an EEG person, and have done this with EEG tools like
EMSE
and Brain Voyager.
Thanks, -Jeff
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
and mri_morphology which has a dilation operator in it On Mon, 16 Aug 2010, Douglas Greve wrote:
you can also use mri_binarize which has a --dilate option. I think it dilates if it has one or more faces in common. You might also look into fslmaths (you can easily convert from mgz to nifti) if that's an issue
On 8/16/10 8:46 PM, Bruce Fischl wrote:
Hi Jeff,
you are welcome to our source code which has region-growing algorithms in the volume (e.g. for control point detection) and on the surface.
cheers Bruce
On Mon, 16 Aug 2010, Eriksen, Jeffrey (Portland) wrote:
Bruce,
Yes, you are likely correct, but my boss wants to do it this way. Besides, I am going to have other uses for region growing that you might find scientifically acceptable. But the question still stands - does Freesurfer give me access to such a basic tool, or will I have to write my own with Matlab/IDL/C etc.?
Thanks, -Jeff
-----Original Message----- From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] Sent: Wednesday, August 11, 2010 2:00 PM To: Eriksen, Jeffrey (Portland) Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 78, Issue 18
Hi Jeff,
we autoamtically segment the cc from an anatomical, which would probably
be a more accurate measure.
cheers Bruce On Tue, 10 Aug 2010, Eriksen, Jeffrey (Portland) wrote:
Sure. Right now I would like to extract the corpus callosum, as
defined
by DTI. After some image arithmetic and thresholding, I have a scalar image of left-right diffusion with values from 0 to 1.2. I would like
to
pick a voxel in the center of the CC and grow a region around it
picking
up voxels in the range 0.9 - 1.2, and only if they share at least two (or some other number of) faces. The result will be an extracted
single
irregular ROI of the CC.
I am more of an EEG person, and have done this with EEG tools like
EMSE
and Brain Voyager.
Thanks, -Jeff
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas Greve -
Eriksen, Jeffrey (Portland)