That "2" is a voxel-wise threshold used to form the cluster. The cwp is a cluster-wise threshold used to eliminate non-significant clusters from the output.
Bruce Fischl wrote: > 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 -- 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
