Dear all, I am interested in measuring mean thickness within ROI in MPRAGEs of children. My mean thickness values tend to be around 3.3 mm, with a standard deviation of about 1mm. I am concerned that these standard deviations are somewhat high. What typical values should I be expecting for standard deviation? Thanks, Sasha
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Hi Sasha,
the standard deviation across the surface isn't a very meaningful number, since the thickness isn't spatially stationary.
cheers, Bruce
On Thu, 24 Aug 2006, Sasha Wolosin wrote:
Dear all, I am interested in measuring mean thickness within ROI in MPRAGEs of children. My mean thickness values tend to be around 3.3 mm, with a standard deviation of about 1mm. I am concerned that these standard deviations are somewhat high. What typical values should I be expecting for standard deviation? Thanks, Sasha
Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I understand that thickness may vary greatly across the entire surface, but shouldn't we expect some stability within smaller regions (e.g. those in the Desikan/Killany atlas)?
Bruce Fischl fischl@nmr.mgh.harvard.edu 8/24/2006 4:40 pm >>>
Hi Sasha,
the standard deviation across the surface isn't a very meaningful number, since the thickness isn't spatially stationary.
cheers, Bruce
On Thu, 24 Aug 2006, Sasha Wolosin wrote:
Dear all, I am interested in measuring mean thickness within ROI in MPRAGEs
of
children. My mean thickness values tend to be around 3.3 mm, with a standard deviation of about 1mm. I am concerned that these standard deviations are somewhat high. What typical values should I be
expecting
for standard deviation? Thanks, Sasha
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
not really, since they contain both gyral and sulcal regions. Better than the whole surface I guess, but spatial standard deviations don't mean a whole lot - it's the cross subject ones you care about
Bruce On Thu, 24 Aug 2006, Sasha Wolosin wrote:
I understand that thickness may vary greatly across the entire surface, but shouldn't we expect some stability within smaller regions (e.g. those in the Desikan/Killany atlas)?
Bruce Fischl fischl@nmr.mgh.harvard.edu 8/24/2006 4:40 pm >>>
Hi Sasha,
the standard deviation across the surface isn't a very meaningful number, since the thickness isn't spatially stationary.
cheers, Bruce
On Thu, 24 Aug 2006, Sasha Wolosin wrote:
Dear all, I am interested in measuring mean thickness within ROI in MPRAGEs
of
children. My mean thickness values tend to be around 3.3 mm, with a standard deviation of about 1mm. I am concerned that these standard deviations are somewhat high. What typical values should I be
expecting
for standard deviation? Thanks, Sasha
Disclaimer: The materials in this e-mail are private and may contain Protected
Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi, I have a few datasets I ran in freesurfer that were originally in 181x217x181 format. As usual, these were converted to 256^3 early in the process. Basically, I'd like to run some comparison stats between the freesurfer volumes and the same subjects run in a couple other programs (that are still 181x217x181), and was wondering what the best way would be to reobtain an exact overlay between the two.
Thanks,
-Aaron-
Which way do you want to go? Convert FS volumes back into the native space or the other way around?
To convert native space vols into FS, run something like:
tkregister2 --s subjectname --mov mri/orig/001.mgz --regheader --reg reg.dat
This will bring up both the conformed and nonconf volumes, and there should be an exact registration. Once you're confidient of that, you can add --noedit in which case it will simply produce reg.dat without bringing up the gui.
Then you can run
mri_vol2vol --mov anynativevolume --fstarg --o anynativevolume.inconformedspace.mgz
The new volume will be in the conformed (orig.mgz) space.
doug
Goldman, Aaron (NIH/NIMH) [C] wrote:
Hi, I have a few datasets I ran in freesurfer that were originally in 181x217x181 format. As usual, these were converted to 256^3 early in the process. Basically, I'd like to run some comparison stats between the freesurfer volumes and the same subjects run in a couple other programs (that are still 181x217x181), and was wondering what the best way would be to reobtain an exact overlay between the two.
Thanks,
-Aaron-
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Could you tell me the transformation vector that is used to convert a e.g.(181x217x181) array to a FS (256^3) array. I would like to backtransform from FS to native space.
Thanks, Fred
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
Which way do you want to go? Convert FS volumes back into the native space or the other way around?
To convert native space vols into FS, run something like:
tkregister2 --s subjectname --mov mri/orig/001.mgz --regheader --reg reg.dat
This will bring up both the conformed and nonconf volumes, and there should be an exact registration. Once you're confidient of that, you can add --noedit in which case it will simply produce reg.dat without bringing up the gui.
Then you can run
mri_vol2vol --mov anynativevolume --fstarg --o anynativevolume.inconformedspace.mgz
The new volume will be in the conformed (orig.mgz) space.
doug
Goldman, Aaron (NIH/NIMH) [C] wrote:
Hi, I have a few datasets I ran in freesurfer that
were originally in
181x217x181 format. As usual, these were converted
to 256^3 early in the
process. Basically, I'd like to run some comparison
stats between the
freesurfer volumes and the same subjects run in a
couple other programs
(that are still 181x217x181), and was wondering
what the best way would
be to reobtain an exact overlay between the two.
Thanks,
-Aaron-
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Hi Frederick,
mri_info will give you the various transformations back to native (i.e. scanner) RAS coords.
cheers, Bruce On Tue, 29 Aug 2006, Frederick Klauschen wrote:
Could you tell me the transformation vector that is used to convert a e.g.(181x217x181) array to a FS (256^3) array. I would like to backtransform from FS to native space.
Thanks, Fred
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
Which way do you want to go? Convert FS volumes back into the native space or the other way around?
To convert native space vols into FS, run something like:
tkregister2 --s subjectname --mov mri/orig/001.mgz --regheader --reg reg.dat
This will bring up both the conformed and nonconf volumes, and there should be an exact registration. Once you're confidient of that, you can add --noedit in which case it will simply produce reg.dat without bringing up the gui.
Then you can run
mri_vol2vol --mov anynativevolume --fstarg --o anynativevolume.inconformedspace.mgz
The new volume will be in the conformed (orig.mgz) space.
doug
Goldman, Aaron (NIH/NIMH) [C] wrote:
Hi, I have a few datasets I ran in freesurfer that
were originally in
181x217x181 format. As usual, these were converted
to 256^3 early in the
process. Basically, I'd like to run some comparison
stats between the
freesurfer volumes and the same subjects run in a
couple other programs
(that are still 181x217x181), and was wondering
what the best way would
be to reobtain an exact overlay between the two.
Thanks,
-Aaron-
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Do you mean the matrix? You can get a freesurfer matrix with this:
cd subject/mri tkregister2 --mov orig/001.mgz --s subject --regheader --reg reg.dat --noedit
this will produce reg.dat which will be a text file with a registration matrix. Interpreting the matrix is another story. If you want to map to/from the native space, look at mri_vol2vol (which will use reg.dat). If you want to map to/from the surface, see mri_vol2surf.
doug
Frederick Klauschen wrote:
Could you tell me the transformation vector that is used to convert a e.g.(181x217x181) array to a FS (256^3) array. I would like to backtransform from FS to native space.
Thanks, Fred
--- Doug Greve greve@nmr.mgh.harvard.edu wrote:
Which way do you want to go? Convert FS volumes back into the native space or the other way around?
To convert native space vols into FS, run something like:
tkregister2 --s subjectname --mov mri/orig/001.mgz --regheader --reg reg.dat
This will bring up both the conformed and nonconf volumes, and there should be an exact registration. Once you're confidient of that, you can add --noedit in which case it will simply produce reg.dat without bringing up the gui.
Then you can run
mri_vol2vol --mov anynativevolume --fstarg --o anynativevolume.inconformedspace.mgz
The new volume will be in the conformed (orig.mgz) space.
doug
Goldman, Aaron (NIH/NIMH) [C] wrote:
Hi, I have a few datasets I ran in freesurfer that
were originally in
181x217x181 format. As usual, these were converted
to 256^3 early in the
process. Basically, I'd like to run some comparison
stats between the
freesurfer volumes and the same subjects run in a
couple other programs
(that are still 181x217x181), and was wondering
what the best way would
be to reobtain an exact overlay between the two.
Thanks,
-Aaron-
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Doug Greve -
Frederick Klauschen -
Goldman, Aaron (NIH/NIMH) [C] -
Sasha Wolosin