your interpretation is correct. Here's the matlab code
cd glmdir/yourcontrast X = load('../Xg.dat'); C = load('C.dat'); y = load('cache.th20.abs.y.ocn.dat'); [beta rvar] = fast_glmfit(y,X); [F pvalues] = fast_fratio(beta,X,rvar,C); pvalues will be an array with the pvalue for each cluster
make sure that $FREESURFER_HOME/fsfast/toolbox in in your matlab path
doug
On 12/10/2013 01:50 AM, Sinead Kelly wrote:
Hi Doug,
thank you for your reply. It is unusual as I also get a significant result in SPSS for a non-significant cluster in mri-glmfit. Just to make sure I am doing things correctly - I am interpreting each column in the xxx.y.ocn.dat file as a cluster in the xxx.sig.cluster.summary file (in numerical order) so the first column in the y.ocn.dat file corresponds to cluster 1 in the sig.cluster.summary file. I do have matlab so if you have the code, that would be great.
Thanks so much again for your help,
Sinead
On 9 December 2013 19:52, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
That is the right file to use, and one would expect to see significant results. Are you sure you are using exactly the same model? If you have matlab, I can give you some code to do the analysis using the exact model that mri_glmfit uses. doug On 12/9/13 10:43 PM, Sinead Kelly wrote:Dear Freesurfer users, I have just ran mri-glmfit on cortical thickness data and corrected for multiple comparisons using Monte Carlo Simulation. I have significant clusters (cwp < .05), however, when I analyse the average thickness measures from the xxx.y.ocn.dat file in SPSS, there are no significant differences between my groups. I'm not sure if I am using the correct approach to extract thickness values for the significant clusters. Thank you for your help, Sinead -- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ 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.-- Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8