Another question: I've noticed that when loading the cluster .annot file, tksurfer also loads the desikan parcellation color table. How can I load the clusters by themselves? And also, I know that loading the cluster overlay allows you to see which clusters are significant by looking at their level of transparency, but is there a way to load ONLY the clusters that are significant? Thanks again,
Nathan
On 8/12/09 3:49 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
The QDEC script runs mri_glmfit-sim, which automatically finds and uses the FWHM, so you should not have to do anything. Recently (about a month ago), I found a bug in some of the simulation software, so you should upgrade to the latest FS version.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Doug,
Sorry, I'm still a bit unclear on how/when I need to pass along the fwhm. I have been generating my scripts for the cluster correction through the qdec GUI. Where along the line do I need to pass it the fwhm? Do I need to go into the script itself and add it somewhere?
On 8/12/09 2:02 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
If you are running an MC simulation (not perm) directly from mri_glmfit (and not mri_glmfit-sim) then you must pass it a fwhm or the results will be wrong. The smoothing level is measured by QDEC (mri_glmfit) as part of the analysis. You can't run the simulation from QDEC, so specifying the smoothing level for the simulation from QDEC is not an issue.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Doug,
Thanks for the info. One quick follow-up question: Let's say for example the smoothing before I run the simulation is 2.75. When you say I need to match the smoothing, do I achieve that by adding 2.75mm of smoothness to the data before running the cluster simulation? In the qdec GUI it only allows you to smooth in increments of 5. Is there a command line flag that would allow me to choose my own level?
On 8/11/09 5:48 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
- The smoother the data, the more likely a cluster will be found by
chance. When the data are created, they start with some smoothness level. When you smooth them you add more. So you need to match the total level of smoothing when you do the simulations, otherwise your clusters will be way too significant. mri_glmfit creates a fwhm.dat file with an estimate of the total smoothness.
- Just if they are nearest neighbors. There is no option to tinker with
this.
- Vertices in the maps created by the simulation are thresholded at the
level you pass. This is what defines the cluster.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all,
I have a couple of questions regarding the way the cluster correction simulation in freesurfer works. I've read the wiki pages on the subject, but if I've missed something and any of this is answered elsewhere please let me know. My technical knowledge of these things is not great so I am just trying to get some background. First of all, how does smoothing the data prior to running the simulation affect the results? I've run corrections on the same data smoothed with a 10mm FWHM, and also on completely unsmoothed data, and the cluster results were different. Secondly, what determines whether vertices are neighbors or not? Is there an option to tinker with this or is it predetermined? Lastly, how do the p values of individual vertices factor into the simulation? Are they taken into account when the determination of the max cluster size under the null hypothesis is performed? Thanks in advance,
Nate
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
-- 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
-- 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
It should not be doing that. The color table is embedded in the annot. Can you describe it further? There's not a good way to load only the significant clusters, but you can load the cluster significance file as an overlay and set the threshold to whatever you want.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Another question: I've noticed that when loading the cluster .annot file, tksurfer also loads the desikan parcellation color table. How can I load the clusters by themselves? And also, I know that loading the cluster overlay allows you to see which clusters are significant by looking at their level of transparency, but is there a way to load ONLY the clusters that are significant? Thanks again,
Nathan
On 8/12/09 3:49 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
The QDEC script runs mri_glmfit-sim, which automatically finds and uses the FWHM, so you should not have to do anything. Recently (about a month ago), I found a bug in some of the simulation software, so you should upgrade to the latest FS version.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Doug,
Sorry, I'm still a bit unclear on how/when I need to pass along the fwhm. I have been generating my scripts for the cluster correction through the qdec GUI. Where along the line do I need to pass it the fwhm? Do I need to go into the script itself and add it somewhere?
On 8/12/09 2:02 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
If you are running an MC simulation (not perm) directly from mri_glmfit (and not mri_glmfit-sim) then you must pass it a fwhm or the results will be wrong. The smoothing level is measured by QDEC (mri_glmfit) as part of the analysis. You can't run the simulation from QDEC, so specifying the smoothing level for the simulation from QDEC is not an issue.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Doug,
Thanks for the info. One quick follow-up question: Let's say for example the smoothing before I run the simulation is 2.75. When you say I need to match the smoothing, do I achieve that by adding 2.75mm of smoothness to the data before running the cluster simulation? In the qdec GUI it only allows you to smooth in increments of 5. Is there a command line flag that would allow me to choose my own level?
On 8/11/09 5:48 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
- The smoother the data, the more likely a cluster will be found by
chance. When the data are created, they start with some smoothness level. When you smooth them you add more. So you need to match the total level of smoothing when you do the simulations, otherwise your clusters will be way too significant. mri_glmfit creates a fwhm.dat file with an estimate of the total smoothness.
- Just if they are nearest neighbors. There is no option to tinker with
this.
- Vertices in the maps created by the simulation are thresholded at the
level you pass. This is what defines the cluster.
doug
Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all,
I have a couple of questions regarding the way the cluster correction simulation in freesurfer works. I've read the wiki pages on the subject, but if I've missed something and any of this is answered elsewhere please let me know. My technical knowledge of these things is not great so I am just trying to get some background. First of all, how does smoothing the data prior to running the simulation affect the results? I've run corrections on the same data smoothed with a 10mm FWHM, and also on completely unsmoothed data, and the cluster results were different. Secondly, what determines whether vertices are neighbors or not? Is there an option to tinker with this or is it predetermined? Lastly, how do the p values of individual vertices factor into the simulation? Are they taken into account when the determination of the max cluster size under the null hypothesis is performed? Thanks in advance,
Nate
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
-- 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
-- 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@nmr.mgh.harvard.edu
-
Dankner, Nathan (NIH/NIMH) [F] -
Douglas N Greve