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
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 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 listFreesurfer@nmr.mgh.harvard.eduhttps://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.
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
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Douglas Greve -
Douglas N Greve
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Sinead Kelly