I'll leave that for Doug On Thu, 25 Aug 2011, Antonella Kis wrote:
Hi Bruce, Thank you very much for your prompt and helpful answer. I have one more question, please: I do not understand what's the role of adding the threshold value while running the mri_glmfit-sim with --cache since after adding the threshold 2, I still get clusters with cwp>.01. This is what I was running: mri_glmfit-sim \ --glmdir rh.age.glmdir \ --cache 2 neg \ --cwpvalthresh .025 \ --overwrite And this is my output: # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -6.24 104279 2004.41 6.4 -83.6 34.4 0.0001 0 0 3539 cuneus 2 -5.71 56656 2923.03 24.4 25.4 37.1 0.0001 0 0 5020 superiorfrontal 3 -4.89 156133 1826.82 5.1 -29.7 38.6 0.0001 0 0 4324 posteriorcingulate 4 -4.57 117278 1917.42 43.2 43.4 -8.2 0.0001 0 0 3393 parsorbitalis 5 -4.32 134603 910.13 10.5 45.7 -9.2 0.0009 0 0 1597 medialorbitofrontal 6 -4.01 47845 1018.06 38.9 -73.9 34.6 0.0003 0 0 1802 inferiorparietal 7 -3.97 12268 580.81 14.2 -51 63.3 0.0132 0.01 0.01 1415 superiorparietal 8 -3.78 54798 871.02 53 -39.7 -5.1 0.0010 0 0 1969 bankssts 9 -3.78 21941 555.51 45.8 -28.2 6.4 0.0175 0.02 0.02 1369 superiortemporal 10 -2.91 86118 884.25 10.1 -98.9 11.7 0.0010 0 0 1089 lateraloccipital 11 -2.86 13271 674.26 21.5 -65.4 -6.1 0.0056 0 0.01 722 lingual Is this right? Also, by adding for the lh --cwpvalthresh .025 what exactly means or how the corrections are made for both hemispheres. I know --cwpvalthresh .025 shows only clusters p<.025 but then what means cluster significance values not corrected for 2 spaces? Please advise. Thank you. 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 23, 2011 4:33 PM Subject: Re: [Freesurfer] correction for multiple comparisons Yes, that is correct, you should use .025 if you are correcting for both hemispheres. doug Antonella Kis wrote: > > Hi Doug, > > I would like to run the correction for multiple comparisons. I know > glmfit-sim corrects for multiple comparisons. My question is: > > the corrections for multiple comparisons will be done while running > > mri_glmfit-sim \ > --glmdir rh.age.glmdir \ > --cache 2 neg \ > --overwrite > > or I need to add --cwpvalthresh .025 before --overwrite. I found > on-line that setting a treshold = 2 means p < 0.05 but adding > --cwpvalthresh .025 will do the correction across 2 spaces: lh and rh: > .025 = .05/2 > Bonferroni Correction and will show only the clusters with p<.025. > > Is this right? So to run for multiple corrections in fact I will need > to run: > > mri_glmfit-sim \ > --glmdir rh.age.glmdir \ > --cache 2 neg \ > --cwpvalthresh .025 > --overwrite > > Please advise me. > > Thank you for your time and 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:* Monday, August 22, 2011 2:28 PM > *Subject:* Re: [Freesurfer] GLM or Qdec ? > > > > Antonella Kis wrote: > > Dear FS experts, > > > > I finished running the GLM and I wonder what is the best way to > > further analyse my data in order to see if there is any relation > > between age (at seizure onset) and cortical thickness for my patients > > versus control group. > > > > > > 1). Why when I overlay the sig.mgh in tksurfer lh inflated, I get > > more clusters than the number of clusters obtained from mri_glmfit-sim? > When you look at it in tksurfer, you are looking at uncorrected data. > glmfit-sim corrects for multiple comparisons. Some of the clusters don't > survive. > > > > 2). What sig.mgh represents? > -log10(p) > > > > 3) What's the real significance of a cluster (how a cluster is formed)? > It is based on the likelihood of getting a cluster of that size by > chance given the search space (cortical surface area), smoothness > (FWHM), and cluster-forming threshold (eg, p<.05). > > > > 4). Why my thickness value in clusters (eg cluster no. 1 which > > coresponds to the posteriorcingulate) for subject no.1 is different > > that the thickness value obtained for the same region in the > > lh.aparc.stats while running recon-all? > > > > 5). After running the GLM should I use visualizing and plotting method > > to further analyse my data and load FSGD file > > lh.gender_age.glmdir/y.fsgd? > > > > 6). Should my ROI's be defined or be the same with my clusters? > I don't know what you mean by that. > > > > 7). What is the difference between GLM and Qdec? What method is the > > best to analyse the relation between age and cortical thickness for > > my patients versus control group? > They are the same statistically. They are just different ways to provide > information about your design and contrasts. QDEC is graphical (point > and click). mri_glmfit you create FSGD files and run it from the > command-line. QDEC actually creates FSGD files and contrast files and > runs mri_glmfit. > > > > 8). Why when analysing with Qdec I get more clusters? Are this > > defining or representing the sig.mgh as in GLM? > They should give identical results when run in the same way. My guess is > that you have created two different designs and so are getting different > answers. > > > > 9). When using Qdec were I can find as an output of results the > > number of clusters and the cortical thickness value? > You'll have to run the correction for multiple comparisons (interface on > the results page). This simply runs mri_glmfit-sim. > > doug > > > > > > Thank you and have a great day! > > 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto: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. > > > -- 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
_______________________________________________ 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.
