Hello,
I have a question regarding performing Monte Carlo simulations when a custom design matrix is being used. The wiki says that "For both MC simulations, you must supply the smoothness of your data as Full-Width/Half-Max (FWHM) of the residual. This can be obtained from the ResidualFWHM value in y.fsgd in the glm output directory." If I understand correctly, this means that the --fwhm flag should be specified when running mri_glmfit to generate CSD's... However, when running a custom design matrix, the y.fsgd file is not generated (since the --fsgd flag cannot be specified at the same time as --X). So, my question is: how do I get the required FWHM value?
Thanks, - Jerry
there should be a fwhm.dat file in the output.
doug
Jerry Yeou-Wei Chen wrote:
Hello,
I have a question regarding performing Monte Carlo simulations when a custom design matrix is being used. The wiki says that "For both MC simulations, you must supply the smoothness of your data as Full-Width/Half-Max (FWHM) of the residual. This can be obtained from the ResidualFWHM value in y.fsgd in the glm output directory." If I understand correctly, this means that the --fwhm flag should be specified when running mri_glmfit to generate CSD's... However, when running a custom design matrix, the y.fsgd file is not generated (since the --fsgd flag cannot be specified at the same time as --X). So, my question is: how do I get the required FWHM value?
Thanks,
- Jerry
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
How did I miss that??? Thanks! - Jerry
On Thu, Apr 17, 2008 at 3:01 PM, Doug Greve greve@nmr.mgh.harvard.edu wrote:
there should be a fwhm.dat file in the output.
doug
Jerry Yeou-Wei Chen wrote:
Hello,
I have a question regarding performing Monte Carlo simulations when a custom design matrix is being used. The wiki says that "For both MC simulations, you must supply the smoothness of your data as Full-Width/Half-Max (FWHM) of the residual. This can be obtained from the ResidualFWHM value in y.fsgd in the glm output directory." If I understand correctly, this means that the --fwhm flag should be specified when running mri_glmfit to generate CSD's... However, when running a custom design matrix, the y.fsgd file is not generated (since the --fsgd flag cannot be specified at the same time as --X). So, my question is: how do I get the required FWHM value?
Thanks,
- Jerry
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@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
Jerry,
can you post your command lines and log file? there should be fwhm.dat along with the y.fsgd.
How did I miss that??? Thanks!
- Jerry
On Thu, Apr 17, 2008 at 3:01 PM, Doug Greve greve@nmr.mgh.harvard.edu wrote:
there should be a fwhm.dat file in the output.
doug
Jerry Yeou-Wei Chen wrote:
Hello,
I have a question regarding performing Monte Carlo simulations when a custom design matrix is being used. The wiki says that "For both MC simulations, you must supply the smoothness of your data as Full-Width/Half-Max (FWHM) of the residual. This can be obtained from the ResidualFWHM value in y.fsgd in the glm output directory." If I understand correctly, this means that the --fwhm flag should be specified when running mri_glmfit to generate CSD's... However, when running a custom design matrix, the y.fsgd file is not generated (since the --fsgd flag cannot be specified at the same time as --X). So, my question is: how do I get the required FWHM value?
Thanks,
- Jerry
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@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
Actually, I do have the fwhm.dat file... I was just commenting on how obvious that should have been to me! Thanks, though! - Jerry
On Fri, Apr 18, 2008 at 10:56 AM, Pratap Kunwar pkunwar@nmr.mgh.harvard.edu wrote:
Jerry,
can you post your command lines and log file? there should be fwhm.dat along with the y.fsgd.
How did I miss that??? Thanks!
- Jerry
On Thu, Apr 17, 2008 at 3:01 PM, Doug Greve greve@nmr.mgh.harvard.edu wrote:
there should be a fwhm.dat file in the output.
doug
Jerry Yeou-Wei Chen wrote:
Hello,
I have a question regarding performing Monte Carlo simulations when a custom design matrix is being used. The wiki says that "For both MC simulations, you must supply the smoothness of your data as Full-Width/Half-Max (FWHM) of the residual. This can be obtained from the ResidualFWHM value in y.fsgd in the glm output directory." If I understand correctly, this means that the --fwhm flag should be specified when running mri_glmfit to generate CSD's... However, when running a custom design matrix, the y.fsgd file is not generated (since the --fsgd flag cannot be specified at the same time as --X). So, my question is: how do I get the required FWHM value?
Thanks,
- Jerry
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://
mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Centergreve@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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Jerry Yeou-Wei Chen -
Pratap Kunwar