[Freesurfer] Gaussian Curvature Calculation
Hi All I wonder could you tell me how Gaussian curvature values are computed at a vertex, i.e. Gauss_Bonnet scheme? Is there any way to vary the neighborhood over which the vertex curvature values are computed? Thanks for your help, Lisa Ronan - - - - - - - - - - Research Associate Brain Mapping Unit Sir William Hardy Building Department of Psychiatry University of Cambridge ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Gaussian Curvature Calculation
Many thanks for that. Am I correct in thinking that the Gauss_Bonnet scheme is given by the "--discrete" option in mris_curvature_stats, while the latter option is given by the "--continuous" flag? L On Fri, Feb 26, 2010 at 1:46 PM, Bruce Fischl wrote: > Hi Lisa, > > we actually provide a discrete estimate using Gauss-Bonnet (Rudolph can > give you the details), and a slightly larger-scale estimate by fitting a > quadratic patch to each neighborhood (5mm on a side I think). The curvature > then comes from the Hessian of the height function of that patch. > > cheers, > Bruce > > > On Fri, 26 Feb 2010, Lisa Ronan wrote: > > Hi All >> >> I wonder could you tell me how Gaussian curvature values are computed at a >> vertex, i.e. Gauss_Bonnet scheme? Is there any way to vary the >> neighborhood >> over which the vertex curvature values are computed? >> >> Thanks for your help, >> >> Lisa Ronan >> >> - - - - - - - - - - >> Research Associate >> Brain Mapping Unit >> Sir William Hardy Building >> Department of Psychiatry >> University of Cambridge >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] (no subject)
Hi All, I am interested in creating a surface label for the temporal lobe. I have tried running the mri_annotation2label calling the aparc.a2005s annotations, then merging the appropriate labels. The process sees to work fine except no label is made for S_temporal_superior. I understand from the --help that "if there are no points in the annotation file for a particular index, no label file is created", but I'm not quite sure what this means. There are stats generated for this region so I'm not sure what's going wrong. I would be grateful for any help on this. Kind regards, Lisa Ronan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] qdoc BadMatch error
Hi All, I am having the same problem as outlined previously by Andrew, namely a problem loading qdec in Ubuntu Feisty Reading /home/freesurfer/lib/tcl/tkUtils.tcl Using /home/freesurfer//lib/tcl/fsgdfPlot.tcl X Error of failed request: BadMatch (invalid parameter attributes) Major opcode of failed request: 66 (X_PolySegment) Serial number of failed request: 5049 Current serial number in output stream: 5052 Any ideas as to how to resolve it? Many thanks in advance, Lisa Ronan Brain Morphometry Lab Beaumont Hospital Dublin 9 Ireland On 8/21/07, Andrew Reid <[EMAIL PROTECTED]> wrote: > > Hi, > > Just installed version 4.0.0 and tried to execute qdec. When I do so I > get the following error. Any ideas what it means and how to remedy it? > > > Reading /home/typically/freesurfer/lib/tcl/tkUtils.tcl > Using /home/typically/freesurfer/lib/tcl/fsgdfPlot.tcl > X Error of failed request: BadMatch (invalid parameter attributes) > Major opcode of failed request: 66 (X_PolySegment) > Serial number of failed request: 4721 > Current serial number in output stream: 4724 > > I am using Ubuntu Fiesty. > > Thanks in advance, > > Andrew Reid > Department of Neurophysiology and Neuroinformatics > UMC St. Radboud > Nijmegen, The Netherlands > ___ > 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
Re: [Freesurfer] LGI error in make_outer_surface at 31
Dear List
I have recently come up agains the same problem as described below, namely
the error when I compute lGI reads
>>reading filled volume...
closing volume...
??? Undefined function or method 'fspecial' for input arguments of
type 'char'.
Error in ==> make_outer_surface at 31
Gaussian = fspecial('gaussian',[2 2],1);
ERROR: make_outer_surface did not create output file
I have tried re-running the subject (as recommended below), as well as
looking at any output from the mris_compute_lgi -debug flag directly, but
the error is the same (Note I am trying to process subjects on a linux
computer, and have verified that the same subject runs successfully on a
Mac).
I'd appreciate any suggestions you might have,
Thanks in advance,
Lisa
On Wed, Sep 24, 2008 at 7:18 PM, Martin Kavec wrote:
> Hi Jenifer,
>
> I don't know what the error exactly means, but sometimes just re-running
> the
> analysis helps.
>
> Best,
>
> Martin
>
> On Wednesday 24 September 2008 19:24:40 Juranek, Jenifer wrote:
> > Hi,
> > Encountering some difficulties with LGI on a RHEL4 box (64bit) with
> MATLAB
> > v7.6.0.324 (R2008a) installed. Subject was processed under fsv405.
> Specific
> > error is pasted below:
> >
> > Any suggestions to correct my error?
> >
> > Thanks,
> > Jenifer
> >
> > >> reading filled volume...
> >
> > closing volume...
> > ??? Undefined function or method 'fspecial' for input arguments of type
> > 'char'.
> >
> > Error in ==> make_outer_surface at 31
> > Gaussian = fspecial('gaussian',[2 2],1);
> >
> >
> > ERROR: make_outer_surface did not create output file
> > 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain
> > 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64
> > GNU/Linux
> >
> > recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008
> >
> > [jjuranek@localhost jjuranek_fsv405]$
> >
> >
> > ___
> > 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
>
___
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Re: [Freesurfer] LGI error in make_outer_surface at 31
Dear List
Just to say that the below error turned out to be a problem with my
pathdef.m file.
Very best,
Lisa
On Mon, Apr 4, 2011 at 4:24 PM, Lisa Ronan wrote:
> Dear List
>
> I have recently come up agains the same problem as described below, namely
> the error when I compute lGI reads
>
> >>reading filled volume...
> closing volume...
> ??? Undefined function or method 'fspecial' for input arguments of
> type 'char'.
> Error in ==> make_outer_surface at 31
> Gaussian = fspecial('gaussian',[2 2],1);
>
> ERROR: make_outer_surface did not create output file
>
> I have tried re-running the subject (as recommended below), as well as
> looking at any output from the mris_compute_lgi -debug flag directly, but
> the error is the same (Note I am trying to process subjects on a linux
> computer, and have verified that the same subject runs successfully on a
> Mac).
>
> I'd appreciate any suggestions you might have,
>
> Thanks in advance,
>
> Lisa
>
> On Wed, Sep 24, 2008 at 7:18 PM, Martin Kavec wrote:
>
>> Hi Jenifer,
>>
>> I don't know what the error exactly means, but sometimes just re-running
>> the
>> analysis helps.
>>
>> Best,
>>
>> Martin
>>
>> On Wednesday 24 September 2008 19:24:40 Juranek, Jenifer wrote:
>> > Hi,
>> > Encountering some difficulties with LGI on a RHEL4 box (64bit) with
>> MATLAB
>> > v7.6.0.324 (R2008a) installed. Subject was processed under fsv405.
>> Specific
>> > error is pasted below:
>> >
>> > Any suggestions to correct my error?
>> >
>> > Thanks,
>> > Jenifer
>> >
>> > >> reading filled volume...
>> >
>> > closing volume...
>> > ??? Undefined function or method 'fspecial' for input arguments of type
>> > 'char'.
>> >
>> > Error in ==> make_outer_surface at 31
>> > Gaussian = fspecial('gaussian',[2 2],1);
>> >
>> >
>> > ERROR: make_outer_surface did not create output file
>> > 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux
>> localhost.localdomain
>> > 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64
>> > GNU/Linux
>> >
>> > recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008
>> >
>> > [jjuranek@localhost jjuranek_fsv405]$
>> >
>> >
>> > ___
>> > 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 mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
