Antonella Kis wrote: > Dear Doug, > > Thank you very much for your valuable reply. > > I still have few questions on which I would like to ask your advise: > > QUESTION 1: > > While running the recall-all for all my subjects I also used the > -qcache option. I am not sure how this data is further used for my GLM > analysis. > > I will appreciate if you can confirm if in this case in order to do a > thickness-age correlation group study I need to complete the > following steps: > > STEP 1: Uncached Data: resamples each subjects data to fsaveragea > (into a common space), and Concatenating all the subjects' into a > single file by running > > mris_preproc --fsgd AGE_fsgd.fsgd \ > --target fsaverage --hemi lh \ > --meas thickness \ > --out lh.AGE.thickness.00.mgh > > STEP 2: The independent variable is the thickness smoothed at various > FWHM (full-width/half-max), usually 0, 5, 10, 10, 20, and 25mm so run: > > mris_preproc --fsgd AGE_fsgd.fsgd \ > --cache-in thickness.fwhm10.fsaverage \ > --target fsaverage --hemi lh \ > --out lh.AGE.thickness.10.mgh > > STEP 3: If I run the next step (I know is optional) where I can use > this data lh.AGE.thickness.10B.mgh? Is this a better data to be use > for my further steps? You would use it in the same place that you would use lh.AGE.thickness.10.mgh. It is just a different way to compute it if you did not qcache. > > OPTIONAL: THIS WILL TAKE ABOUT 5 MINUTES > > mri_surf2surf --hemi lh \ > --s fsaverage \ > --sval lh.AGE.thickness.00.mgh \ > --fwhm 10 \ > --cortex \ > --tval lh.AGE.thickness.10B.mgh > > STEP 4: GLM Analysis (mri_glmfit) > > mri_glmfit \ > --y lh.AGE.thickness.10.mgh \ > --fsgd AGE_fsgd.fsgd dods\ > --C lh-Avg-thickness-age-Cor.mtx \ > --surf fsaverage lh \ > --cortex \ > --glmdir lh.AGE.glmdir > > STEP 5: View the uncorrected significance map with tksurfer: > > tksurfer fsaverage lh inflated \ > -annot aparc.annot -fthresh 2 \ > -overlay lh.AGE.glmdir/lh-Avg-thickness-age-Cor/sig.mgh > > > STEP 6: Viewing the medial surface, change the overlay threshold to > something very, very low (say, .01), View --> Configure --> Overlay, > set "Min" .01 > > STEP 7: CSD (Cluster Simulation Data)- Run the Simulation > > mri_glmfit-sim \ > --glmdir lh.AGE.glmdir \ > --sim mc-z 5 4 mc-z.negative \ > --sim-sign neg \ > --overwrite > > QUESTION 2: You mentioned that I should use the --cache option to > mri_glmfit-sim. How I should do this? Do I need to change STEP 7? Yes, use mri_glmfit-sim \ --glmdir lh.AGE.glmdir \ --cache 4 neg \ --overwrite
> > QUESTION 3: How I can check my data to make sure that I have actual > activation above the voxel-wise threshold and how I can change my > threshold? Based on what I need to change my threshold? Do I change my > treshold until I find some activation? Run tksurfer to view the sig.mgh file. Set the threshold to the one you used in mri_glmfit-sim using the view->configure->overlay. There are no hard and fast rules to setting thresholds, but people usually use p<.05 or p<.01. doug > > > Thank you very much for your valuable help. > Antonella > > > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu> > *To:* Antonella Kis <ator...@yahoo.com> > *Cc:* "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > *Sent:* Tuesday, August 16, 2011 12:04 PM > *Subject:* Re: [Freesurfer] thickness-age correlation > > > > Antonella Kis wrote: > > Dear Freesurfer experts, > > > > I am doing a thickness-age correlation group difference study > (patients versus controls. I would like to know if: > > > > 1) my contrast vector defined as 0 0 0.5 0.5 is correct in order to > test the change in thickness with age > > > Yes. > > 2)what is the best iteration number for the simulation? Should be > 5000 or 1000 or greater? > > > 10,000 -- note that if you're doing a whole-hemisphere correction with > the monte-carlo simulation then you should use the pre-computed > results (use the --cache option to mri_glmfit-sim) > > 3)why when I run the simulation for 5 iterations I've got zero clusters? > > > You should look at your data to make sure that you have actual > activation above the voxel-wise threshold you have set. Also, only 5 > clusters would not be enough to get a significant cluster anyway. > > 4)can I derive the thickness from the significant clusters of glm > analysis? Do I need to run QDEC after GLM? > > > If you mean that you want the average thickness from each subject for > a given cluster, then this information is generated with > mri_glmfit-sim in the csdbase.y.ocn.dat file. > > doug > > Thanks for any enlightenment. > > Antonella > > > > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > > > 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. > > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
