Ty Doug, Kind regards, Egil ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N Greve <gr...@nmr.mgh.harvard.edu> Sent: 23 March 2015 17:45 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Question regarding Qdec vs mri_glmfit outputs
Use the result from mri_glmfit. doug On 03/20/2015 10:20 AM, Egil Nygaard wrote: > > Dear Freesurfer support, > > I find the qdec to be very pedagogic in its outlay, and would love to > use it. However, I find several discrepancies as compared to results > from the mri_glmfit analyses, and wonder why (see description below). > > 1) One discrepancy is the placement of the clusters; X, Y, Z's. Should > I use: > > * > the figures from the result summary from mri_glmfit, > * > the result summary from Qdec (which is almost the same as from the > results summary from mri_glmfit), > * > or from the “Find clusters and goto max” function in the display > window of Qdec (which shows very different placements than the two > others)? > > 2) Which size should I use? The sizes of the clusters from qdec are > 1-2% smaller than what are reported from the mri_glmfit analyses. > > I expect that the reason for the discrepancies is that I probably do > something different in the mri_glmfit analyses than the standard Qdec > analyses, but I can not figure out what it is. > > > > Below is information about which analyses I have done and some more > information about the Qdec output. > ** > > *Overview analyses:* > > We investigate difference between two groups. We have two sets of > data, one with skewed age and gender distribution between groups (n = > 89) (older participants and more girls in the risk group), and one > with 33 extra control participants (n = 122) making the risk and > control group having similar age and gender distribution. > > The vertex based analyses are done with mri_glmfit in Freesurfer > version 5.3. I have analyzed the data both with DOSS and DODS. Both > without covariates, controlling for age (demeaned continuous variable) > or controlling for gender, or controlling for both age and gender. We > have used smoothing fwhm 10. The results were controlled for multiple > comparisons with the standard mri_glmfit-sim method in Freesurfer with > cache 1.3 abs and 2spaces (did not use 2spaces when comparing > mri_glmfit results with Qdec results). > > We have used tksurfer (DOSS and DODS) and qdec (DODS) to visualize the > results, but mainly used results from > cache.th13.abs.sig.cluster.summary files to compare with the analyses > from SPSS. > > The contrast in the full DODS model in the mri_glmfit is 1 1 -1 -1 0 0 > 0 0, with the fsgd file being: > > GroupDescriptorFile 1 > Title n89-33 > Class group1risk_gender1girl > Class group1risk_gender2boy > Class group2control_gender1girl > Class group2control_gender2boy > Variables age > Input UN001 group1control_gender2boy -1.0172131148 > Etc > > Preproc was done with: > > mris_preproc --target fsaverage --hemi lh --meas area --fsgd > $glm/demographicn122.fsgd --out $preproc > > Smoothing was done with: > mri_surf2surf --hemi lh --s fsaverage --sval $preproc --fwhm 10 > --cortex --tval $smoothing10 > > GLM was done with: > > mri_glmfit --glmdir $contrast --y $smoothing10 --fsgd > $glm/demographicn122.fsgd --C $glm$contrast_kjal.mat --surf fsaverage > lh --cortex > > Correction for multiple comparisons was done with: > > mri_glmfit-sim --glmdir $contrast --cache 1.3 abs > > *Qdec:* > There are discrepancies between results from qdec and mri_glmfit. I am > unsure why. I notice for example that there are small discrepancies in > the fwhm.dat files from Qdec and mri_glmfit. The most important for my > use is that when I compare the clusters in the file: > cache.th13.abs.sig.cluster.summary from the mri_glmfit, and the > clusters from the file: mc-z.abs.th13.sig.cluster.summary from qdec, I > find the same four clusters of group differences in cortex areas with > the same Max number and Vtxmax. However, the sizes are marginally > different, with the sizes from qdec being 1-2% smaller. Most > importantly for me are the differences in the placement of the > clusters. The MNIX, Y and Z from mri_glmfit are not similar to the > TalX, Y and Z from Qdec. The differences are not big, but still > significant for us. I also note that the TalX, Y and Z's from the > result file from Qdec is very different from the TalX, Y and Z's from > the output one get from Qdec when one use the button “Find clusters > and got max” in the visual Display window in Qdec. It seems the output > from Qdec's “Find clusters and got max” shows the mean cluster > placement (all Max figures are 4), whereas the output from mri_glmfit > and from the resultsfile from Qdec shows the placement of masked > clusters (the Max figures vary)? > > Kind regards, > > Egil Nygaard > > > > _______________________________________________ > 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 . 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