Does Mac version work properly for new OSX intel machines? I just d/l the latest mac version and most programs seem to work except "tkmedit", which I can't able to run. Anyone done any freesurfing on a new mac machine?
Moo.
On 2/17/06, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
- Not offhand.
for the others run:
set sdir=$SUBJECTS_DIR/$s/surf mris_curvature -max $sdir/lh.white
this will write a file named lh.white.max (or use the pial if you want). Similarly:
mris_curvature -min will write the min curvature
and
mris_curvature -w will write the Gaussian (to lh.white.K) and mean (to lh.white.H) curvatures.
cheers, Bruce
On Thu, 16 Feb 2006, Roberto Toro wrote:
three more quick questions: (1). do you know of a paper using the folding index successfully? (2). is it possible to access k_max and k_min for every vertex? (3). is it possible to access the mean curvature and the gaussian curvature for every vertex? (... to obtain (2)...)
thanks, roberto
On 15 Feb 2006, at 17:28, Bruce Fischl wrote:
yes. On Wed, 15 Feb 2006, Roberto Toro wrote:
Hi,
I found the reference to D. Van Essen's paper:
Van Essen, D and Drury, H (1997) "Structural and functional analyses of human cerebral cortex using a surface-based atlas" J Neurosci 17(18):7079-7102
and the folding index is defined (from that paper) as "the integral of the product of the maximum principal curvature and the difference between maximum and minimum curvature, divided by 4*pi", ie,
FI= (1/4pi) \int \int |kmax|(|kmax|-|kmin|) dA
is this what freesurfer is using?
thanks,
roberto
On 8 Feb 2006, at 16:39, Bruce Fischl wrote:
the Gaussian and mean curvature are differential geometric measures and you can find them in any standard textbook (e.g. do Carmo). The folding indices come from one of David Van Essen's papers - sorry, I don't have the reference offhand, but it shouldn't be too hard to find. Bruce On Wed, 8 Feb 2006, Goradia, Dhruman D wrote:
Hi, The output of function "mris_anatomical_stats" contains the following measurements: integrated rectified mean curvature, integrated rectified Gaussian curvature, folding index and intrinsic curvature index. Can someone please give me a brief explanation of what these measurements are or suggest some reading material. -Dhruman Dhruman D. Goradia (M.S.) Research Specialist. Western Psychiatric Institute and Clinic. 3811 O'Hara St. Suite 431 Pittsburgh, PA 15213 Phone: 412-586-9017
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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-- Moo Chung http://www.stat.wisc.edu/~mchung Assistant Professor Department of Statistics, Biostatistics & Medical Informatics University of Wisconsin-Madison
Moo,
Sorry, we do not as yet have an Intel Mac to build/test freesurfer. The existing build works only because I think the PowerPC instruction set is being emulated on the Intel Mac's.
I may make a try at building an Intel Mac version (its possible to build Intel code on a PowerPC) but I won't be able to test it, but it might be better than nothing until we get a machine. I'll post something if and when I do this.
Out of curiousity, what does tkmedit do? Crash? Or stream a bunch of X-windows error codes? Also, does tksurfer work?
Nick
On Thu, 2006-05-04 at 13:51 -0500, Moo K. Chung wrote:
Does Mac version work properly for new OSX intel machines? I just d/l the latest mac version and most programs seem to work except "tkmedit", which I can't able to run. Anyone done any freesurfing on a new mac machine?
Moo.
On 2/17/06, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
- Not offhand.
for the others run:
set sdir=$SUBJECTS_DIR/$s/surf mris_curvature -max $sdir/lh.white
this will write a file named lh.white.max (or use the pial if you want). Similarly:
mris_curvature -min will write the min curvature
and
mris_curvature -w will write the Gaussian (to lh.white.K) and mean (to lh.white.H) curvatures.
cheers, Bruce
On Thu, 16 Feb 2006, Roberto Toro wrote:
three more quick questions: (1). do you know of a paper using the folding index successfully? (2). is it possible to access k_max and k_min for every vertex? (3). is it possible to access the mean curvature and the gaussian curvature for every vertex? (... to obtain (2)...)
thanks, roberto
On 15 Feb 2006, at 17:28, Bruce Fischl wrote:
yes. On Wed, 15 Feb 2006, Roberto Toro wrote:
Hi,
I found the reference to D. Van Essen's paper:
Van Essen, D and Drury, H (1997) "Structural and functional analyses of human cerebral cortex using a surface-based atlas" J Neurosci 17(18):7079-7102
and the folding index is defined (from that paper) as "the integral of the product of the maximum principal curvature and the difference between maximum and minimum curvature, divided by 4*pi", ie,
FI= (1/4pi) \int \int |kmax|(|kmax|-|kmin|) dA
is this what freesurfer is using?
thanks,
roberto
On 8 Feb 2006, at 16:39, Bruce Fischl wrote:
the Gaussian and mean curvature are differential geometric measures and you can find them in any standard textbook (e.g. do Carmo). The folding indices come from one of David Van Essen's papers - sorry, I don't have the reference offhand, but it shouldn't be too hard to find. Bruce On Wed, 8 Feb 2006, Goradia, Dhruman D wrote: > Hi, > The output of function "mris_anatomical_stats" contains the following > measurements: integrated rectified mean curvature, integrated rectified > Gaussian curvature, folding index and intrinsic curvature index. Can > someone please give me a brief explanation of what these measurements > are or suggest some reading material. > -Dhruman > Dhruman D. Goradia (M.S.) > Research Specialist. > Western Psychiatric Institute and Clinic. > 3811 O'Hara St. Suite 431 > Pittsburgh, PA 15213 > Phone: 412-586-9017 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
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
-- Moo Chung http://www.stat.wisc.edu/~mchung Assistant Professor Department of Statistics, Biostatistics & Medical Informatics University of Wisconsin-Madison
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Nick - the problem is a bug on MacIntel which means that GLX cannot work when either run remotely on a PPC, displaying on a Mcintel, or running locally under emulation mode. Probably a native build would work. Apple are looking into this bug.
Cheers.
On 4 May 2006, at 21:07, Nick Schmansky wrote:
Moo,
Sorry, we do not as yet have an Intel Mac to build/test freesurfer. The existing build works only because I think the PowerPC instruction set is being emulated on the Intel Mac's.
I may make a try at building an Intel Mac version (its possible to build Intel code on a PowerPC) but I won't be able to test it, but it might be better than nothing until we get a machine. I'll post something if and when I do this.
Out of curiousity, what does tkmedit do? Crash? Or stream a bunch of X-windows error codes? Also, does tksurfer work?
Nick
On Thu, 2006-05-04 at 13:51 -0500, Moo K. Chung wrote:
Does Mac version work properly for new OSX intel machines? I just d/l the latest mac version and most programs seem to work except "tkmedit", which I can't able to run. Anyone done any freesurfing on a new mac machine?
Moo.
On 2/17/06, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
- Not offhand.
for the others run:
set sdir=$SUBJECTS_DIR/$s/surf mris_curvature -max $sdir/lh.white
this will write a file named lh.white.max (or use the pial if you want). Similarly:
mris_curvature -min will write the min curvature
and
mris_curvature -w will write the Gaussian (to lh.white.K) and mean (to lh.white.H) curvatures.
cheers, Bruce
On Thu, 16 Feb 2006, Roberto Toro wrote:
three more quick questions: (1). do you know of a paper using the folding index successfully? (2). is it possible to access k_max and k_min for every vertex? (3). is it possible to access the mean curvature and the gaussian curvature for every vertex? (... to obtain (2)...)
thanks, roberto
On 15 Feb 2006, at 17:28, Bruce Fischl wrote:
yes. On Wed, 15 Feb 2006, Roberto Toro wrote:
Hi,
I found the reference to D. Van Essen's paper:
Van Essen, D and Drury, H (1997) "Structural and functional analyses of human cerebral cortex using a surface-based atlas" J Neurosci 17(18):7079-7102
and the folding index is defined (from that paper) as "the integral of the product of the maximum principal curvature and the difference between maximum and minimum curvature, divided by 4*pi", ie,
FI= (1/4pi) \int \int |kmax|(|kmax|-|kmin|) dA
is this what freesurfer is using?
thanks,
roberto
On 8 Feb 2006, at 16:39, Bruce Fischl wrote:
> the Gaussian and mean curvature are differential geometric > measures and > you can find them in any standard textbook (e.g. do Carmo). > The folding > indices come from one of David Van Essen's papers - sorry, I > don't have > the reference offhand, but it shouldn't be too hard to find. > Bruce > On Wed, 8 Feb 2006, Goradia, Dhruman D wrote: >> Hi, >> The output of function "mris_anatomical_stats" contains the >> following >> measurements: integrated rectified mean curvature, >> integrated rectified >> Gaussian curvature, folding index and intrinsic curvature >> index. Can >> someone please give me a brief explanation of what these >> measurements >> are or suggest some reading material. >> -Dhruman >> Dhruman D. Goradia (M.S.) >> Research Specialist. >> Western Psychiatric Institute and Clinic. >> 3811 O'Hara St. Suite 431 >> Pittsburgh, PA 15213 >> Phone: 412-586-9017 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
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
-- Moo Chung http://www.stat.wisc.edu/~mchung Assistant Professor Department of Statistics, Biostatistics & Medical Informatics University of Wisconsin-Madison
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
------------------------------------------------------------------------ --- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) steve@fmrib.ox.ac.uk http://www.fmrib.ox.ac.uk/~steve ------------------------------------------------------------------------ ---
not yet, sorry. We don't have any. On Thu, 4 May 2006, Moo K. Chung wrote:
Does Mac version work properly for new OSX intel machines? I just d/l the latest mac version and most programs seem to work except "tkmedit", which I can't able to run. Anyone done any freesurfing on a new mac machine?
Moo.
On 2/17/06, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
- Not offhand.
for the others run:
set sdir=$SUBJECTS_DIR/$s/surf mris_curvature -max $sdir/lh.white
this will write a file named lh.white.max (or use the pial if you want). Similarly:
mris_curvature -min will write the min curvature
and
mris_curvature -w will write the Gaussian (to lh.white.K) and mean (to lh.white.H) curvatures.
cheers, Bruce
On Thu, 16 Feb 2006, Roberto Toro wrote:
three more quick questions: (1). do you know of a paper using the folding index successfully? (2). is it possible to access k_max and k_min for every vertex? (3). is it possible to access the mean curvature and the gaussian
curvature
for every vertex? (... to obtain (2)...)
thanks, roberto
On 15 Feb 2006, at 17:28, Bruce Fischl wrote:
yes. On Wed, 15 Feb 2006, Roberto Toro wrote:
Hi,
I found the reference to D. Van Essen's paper:
Van Essen, D and Drury, H (1997) "Structural and functional analyses of human cerebral cortex using a surface-based atlas" J Neurosci 17(18):7079-7102
and the folding index is defined (from that paper) as "the integral of
the
product of the maximum principal curvature and the difference between maximum and minimum curvature, divided by 4*pi", ie,
FI= (1/4pi) \int \int |kmax|(|kmax|-|kmin|) dA
is this what freesurfer is using?
thanks,
roberto
On 8 Feb 2006, at 16:39, Bruce Fischl wrote:
the Gaussian and mean curvature are differential geometric measures
and
you can find them in any standard textbook (e.g. do Carmo). The
folding
indices come from one of David Van Essen's papers - sorry, I don't
have
the reference offhand, but it shouldn't be too hard to find. Bruce On Wed, 8 Feb 2006, Goradia, Dhruman D wrote: > Hi, > The output of function "mris_anatomical_stats" contains the following > measurements: integrated rectified mean curvature, integrated
rectified
> Gaussian curvature, folding index and intrinsic curvature index. Can > someone please give me a brief explanation of what these measurements > are or suggest some reading material. > -Dhruman > Dhruman D. Goradia (M.S.) > Research Specialist. > Western Psychiatric Institute and Clinic. > 3811 O'Hara St. Suite 431 > Pittsburgh, PA 15213 > Phone: 412-586-9017 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This message has been checked for viruses but the contents of an attachment may still contain software viruses, which could damage your computer system: you are advised to perform your own checks. Email communications with
the
University of Nottingham may be monitored as permitted by UK
legislation.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
This message has been checked for viruses but the contents of an
attachment
may still contain software viruses, which could damage your computer
system:
you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.
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
-- Moo Chung http://www.stat.wisc.edu/~mchung Assistant Professor Department of Statistics, Biostatistics & Medical Informatics University of Wisconsin-Madison
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Moo K. Chung -
Nick Schmansky -
Steve Smith