I'm not sure what is going on there. Can you send me the cluster.summary file? doug
On 02/18/2015 02:47 PM, Hirsch, Gabriella wrote: > > Yes – sorry this is probably easier with images. > > The files I’m visualizing are the sig.mgh (uncorrected) and > cache.th13.abs.sig.ocn. mgh (cluster corrected) respectively, > overlayed on an fsaverage brain. I am visualizing using tksurfer. > > When I run mri_glmfit, I get the “example_sig” output (see attached), > which was expected. However, after I run the clusterwise correction > (mri_glmfit-sim), my clusters come out in a different color (in this > case red, every time, for every cluster; see “example_cluster”). > > The tutorial indicates the cluster color scale is arbitrary, however, > ALL of my clusters post-correction are always the same color, and > always different from the pre-corrected clusters. I found this a > little confusing since red is a color from the heat map, which may be > interpreted as an inverse of the original uncorrected output – but it > seems this color is in fact arbitrary. Is this correct? > > Gabriella > > *From:*freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas > Greve > *Sent:* Wednesday, February 18, 2015 2:16 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] cluster colors > > > I don't think I understand. What files are you visualizing? What is > your command to visualize? > > On 2/18/15 3:42 PM, Hirsch, Gabriella wrote: > > Hi FS experts, > > I had a quick question I was hoping someone could help me with; I > used the group analysis tutorial > > (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis_tktools) > to analyse two groups of subjects. > > I ran the mri_glmfit command, as well as the clusterwise > correction (mri_glmfit-sim) on the same data; however upon > visualization, the two outputs present clusters in different > colors (before correction all clusters are blue and after > post-correction all clusters are red - this is consistent across > conditions). According to the tutorial, I should disregard the red > color since it is arbitrary (and not, in fact, an inversion of > what I see from the uncorrected data). Note that I have NOT > changed the contrast or any other setting. > > Am I understanding this correctly? > > Thank you. > Gabriella > > > > > _______________________________________________ > > 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 > 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.
