for the cache, the simulation has already been done (using 10,000). This makes it much faster:). doug
Antonella Kis wrote: > Dear Doug, > > Thank you very much! I am ready to start doing my analysis but before > I start you were mentioning that for the simulation 10,000 is a good > number. You also suggested me to run: > > mri_glmfit-sim \ > --glmdir lh.AGE.glmdir \ > --cache 4 neg \ > --overwrite > > but what is the number of the iteration if I run this part? Do I need > to add this and do I need to mention the threshold in the above coding? > > THANKS! > 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:* Wednesday, August 17, 2011 1:10 PM > *Subject:* Re: [Freesurfer] mri_glmfit-sim > > > > Antonella Kis wrote: > > Hi Doug, > > > > > > Thanks again for your help. There are few more things not very clear > > for me and I will be very graetful if you can advise me: > > > > 1). Did you mean that if I did not qcache my data while I was doing > > pre-processing running the recon-all I should use then > > lh.AGE.thickness.10B.mgh? > yes > > > > 2) Are then the mentioned steps the right one to be followed? > yes > > > > 3) I saw on one tutorial about the mri_glm to perform estimations. > > What are this estimations? Do I need to run: > Where did you see reference to mris_glm? This is an old program that we > should not even distribute. > > > > # For the left hemisphere > > mris_glm --surfmeas thickness \ > > --hemi lh \ > > --trgsubj average \ > > --fsgd ./my_gender_age_fsgd.txt doss \ > > --beta ./beta_doss-thickness-100lh.mgz\ > > --var ./var_doss-thickness-100lh.mgz \ > > --y ./y_doss-thickness-100lh_000.mgz \ > > --nsmooth 100 > > # For the right hemisphere > > mris_glm --surfmeas thickness \ > > --hemi rh \ > > --trgsubj average \ > > --fsgd ./my_gender_age_fsgd.txt doss \ > > --beta ./beta_doss-thickness-100rh.mgz \ > > --var ./var_doss-thickness-100rh.mgz \ > > --y ./y_doss-thickness-100rh_000.mgz \ > > --nsmooth 100 > > 4) If I have less than 80 subjects do I need to run the full MC > > simulation and I must supply the smoothest of my data as fwhm from the > > y.fsgd file? Also I would need to mention the threshold like in the > > following example? > Yes. You are better off using mri_glmfit-sim rather than the command > line below. mri_glmfit-sim will run that program giving it the > appropriate fwhm. > > > > mri_glmfit --y lh.gender_age.thickness.10.mgh \ > > --glmdir lh.gender_age.glmdir \ > > --fsgd gender_age.txt doss \ > > --surf fsaverage lh \ > > --fwhm 14.517 --C age.mat \ > > --sim mc-full 10000 2 lh.gender_age.glmdir/csd1 > > > > Do I add the --cache 4 neg \ > > --overwrite > > > > at the end? > > > > 5) When I run tksurfer to view the sig.mgh file and I set the > > threshold to 2, meaning vertices with p<.01, I have just few vertices > > coloured in blue. Does this mean a low activation? If yes, what I have > > to do? > Yes. You can try lowering it to 1.3 (p<.05). If the effect is too > subtle, you will need to add more subjects (assuming there is an effect > at all). > doug > > > > > > Thank you very much! > > Antonella > > > > ------------------------------------------------------------------------ > > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu>> > > *To:* Antonella Kis <ator...@yahoo.com <mailto:ator...@yahoo.com>> > > *Cc:* "freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>" > <freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>> > > *Sent:* Wednesday, August 17, 2011 11:53 AM > > *Subject:* Re: [Freesurfer] mri_glmfit-sim > > > > > > > > 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 > <mailto:gr...@nmr.mgh.harvard.edu> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>>> > > > *To:* Antonella Kis <ator...@yahoo.com <mailto:ator...@yahoo.com> > <mailto:ator...@yahoo.com <mailto:ator...@yahoo.com>>> > > > *Cc:* "freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu>>" > > <freesurfer@nmr.mgh.harvard.edu > <mailto:freesurfer@nmr.mgh.harvard.edu> > <mailto:freesurfer@nmr.mgh.harvard.edu > <mailto: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> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto: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> > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> > > <mailto:gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu> > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > <mailto: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 > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto: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 > > _______________________________________________ > 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 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
