Hi Erik, I don't entirely follow what you are doing. It is not appropriate to run mri_glmfit-sim on an fdr corrected map. Why not analyze your functional data on fsaverage5?
On 11/15/2016 12:59 AM, ERIK JAHNER wrote: > Dear free surfer experts, > > > I was wondering if someone could give me some general guidance on > controlling for multiple comparisons using clustering and FDR. This > the situation. I completed an analysis of functional data by first > dividing the cortex into parcellations using the icosahedron 5 file > then exported the values to matlab. I now have a correlation and > significance value for all 10242 parcelations. My uncorrected results > made theoretical sense, topologically. However, I attempted to use an > FDR procedure on all these parcellations setting the FDR at .05 and > no parcellations remained (all values were above the .05 threshold). > Because my parcelationas are likely topologically correlated with the > nearest neighboring clusters, it is my understanding that it makes > more sense to use a clustering method to first identify clusters and > then run a correction using FDR as cited in Chumbley, & Friston 2009. > > > To complete clustering prior to FDR, I have projected the significance > values from the parcellations back onto the surface vertices and then > run the clustering approach described in the group analysis tutorial > (mri_glmfit.sim). I have projected these group results onto the > associated vertices on the fsaverage5 surface. However, when I > run mri_glmfit.sim, no clusters remain. I believe that I am running > into this problem because I am trying to get clusters of vertices when > the data was actually analyzed using 10242 ROIs. Please note, I have > placed the correlation and significance values (from my analysis in > matlab) in a slope directory under GLM prior to running the analysis > on the significance values associated with each vertex. > > > By replacing the significance file generated from a thickness study > with the significance file that I created, does freesurfer conduct the > same analysis without reference to the type of data; does it only > matter that I am using significance values or should I be replacing > another file in the directory (I am using a different methodology to > obtain my correlation and significance values)? The fsgd file that is > in the folder still represents the groups correctly even though the > neural data has been changed external to free surfer. > > > Any suggestions or appropriate literature on how to correct for > multiple comparisons using clusters of ROIs on surface would be > appreciated? > > > Thank you, > > Erik Jahner > > > > _______________________________________________ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 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 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.
