The residual FWHM is measured from the data itself. You apply a certain amount of smoothing, but there is already some smoothness to the data, so the final fwhm is a combination of what is already there and what you apply. A fwhm of 47 is huge and may indicate that something is wrong. What is the input? cortical thickness? Are you using your own mask or is this a whole hemisphere analysis?
doug
On 6/2/13 10:29 PM, Joshua deSouza wrote:
Hello Doug,
Thank you for your quick replies to my queries. Really appreciate it.
I have found the files containing the cortical thickness values. Thank you. I assume that the order in which they follow are based on the fsgd file and the cluster annotation numbers.
I was just slightly confused about the residual fwhm. I have already done a smoothing of 15 on the file and have recieved a residual value of 47, which I assume is extremely large. Since I'm finding out values for the entire cortex I cannot do a glmfit-sim as there are no fwhm cache values of 47. Could you please tell me what the residual values mean? What do you recommend I do? Is there anything I can read up on to find out more about this? (Please pardon my questions if they seem a little trivial)
Thank you
Joshua
On Sun, Jun 2, 2013 at 11:33 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
This file is always created by mri_glmfit-sim. It might be named something different depending on your parameters (should always end in y.ocn.dat) doug On 6/2/13 3:57 AM, Joshua deSouza wrote:Hi Doug, This file that your saying, will be created after glmfit-sim is done using the cache function and a threshold of 1.3 and absolute ,with y being the fsgd file? Am I understanding this correctly? Thank you Joshua On Sat, Jun 1, 2013 at 12:14 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: There should be a file called something like cache.th13.abs.y.ocn.dat. This will have a column for each cluster and a row for each subject. The value in the row will be the input for each subject. doug On 05/30/2013 11:21 PM, Joshua deSouza wrote: > Hello everyone, > > Please pardon my rather simple question > > I have done a GLM fit anlysis and have obtained a file sig.mgh alonf > with a few others after the analysis.As I know, I do not have to > create ROIs in order to do this. I also understand that doing a > multiple comparison analysis just compares the regions of importance > and evaluates them giving the most resilient cluster depending on the > threshold. So, this does not give a thickness estimate. I would like > to know how do I get the cortical thickness values from the results? > If so, can I do it after glmfit? > > And thanks Doug for your help in the other questions that I had prior > to this! > > Thank you > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto: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.