Are you setting the cwp to .01? The cwp controls the threshold for cluster significance. The number after "--cache" controls the cluster-forming threshold
Antonella Kis wrote: > Hi Doug, > > Since running mri_glmfit-sim will do a correction by multiple > comparison (I suppose is doing a Monte Carlo to remove areas that are > not statically significant) I wonder why I still get clusters with > p>0.01? Do I need to apply FDR before -sim? > > Thank you for your time and help. > Antonella > > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu> > *To:* Bruce Fischl <fis...@nmr.mgh.harvard.edu> > *Cc:* Antonella Kis <ator...@yahoo.com>; > "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> > *Sent:* Thursday, August 25, 2011 12:23 PM > *Subject:* Re: [Freesurfer] Fw: fsaverage > > 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 > <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: 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 > <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:* 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> > >> <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>> > >> > 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 > >> > > >> > > >> > 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> > >> 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 > >> > >> > >> > >> > >> > >> > > ------------------------------------------------------------------------ > > > > _______________________________________________ > > 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 > > > -- 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
