It should be the sig.mgh file in your contrast directory. doug ps. Please post to the list and not me directly. thanks!
On 07/18/2012 11:56 AM, Antonella Kis wrote: > Hi Doug, > > Many thanks for your prompt response and your help. I have one more > question please. I searched for mri_surfcluster command and I am not > sure what should be my input file. > > Can you please clarify this for me? Should this be L-frontal.fsgd > since I have more subjects? > > > Thank you. > Antonella > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <gr...@nmr.mgh.harvard.edu> > *To:* freesurfer@nmr.mgh.harvard.edu > *Sent:* Wednesday, July 18, 2012 11:39 AM > *Subject:* Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option > > Hi Antonella, first of all, FDR and clusterwise correction are doing > different things. Technically, you don't get clusters from FDR. FDR will > choose a voxel-wise threshold for you, and any voxel above threshold can > be interpreted as surviving FDR (but you should know how to interpret it > -- see Tom Nichols' paper). Of course, many of the voxels may appear as > clusters. In your case, FDR found a voxel-wise threshold of 3.8 > (meaning p<1.5849e-04). The fastest way to get the values you want is > to go outside of QDEC. First, run mri_surfcluster using a threshold of > 3.8 (--thmin 3.8). Specify an output cluster number map (--ocn ocn.mgh) > and a summary file (--sum sum.dat). This will produce a lot of > "clusters", two of which should be the ones below (you can prune the > list by specifying that the clusters need to be a certain size > (--minarea). Once you have the ocn file, you can run mri_segstats, > something like > mri_segstats --seg ocn.mgh --i y.mgh --avgwf avgwf.dat --excludeid 0 > y.mgh is the glmfit input file created by qdec. This will produce > avgwf.dat which will have a column for each cluster, the order will be > the same as that in sum.dat. > > douig > > On 07/18/2012 11:25 AM, Antonella Kis wrote: > > Dear FS team, > > > > > > > > I am doing a cortical thickness study using QDEC. I used FDR and got > > the following clusters: > > > > Generating cluster stats using min threshold of 3.8... > > Found 2 clusters > > Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69 > > ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation > > --------- --- ------ --------- ---- ---- ---- ----- ---------- > > 1 -3.8743 18231 4.55 -39.8 1.5 14.1 14 precentral > > 2 -3.8065 47386 2.66 -8.2 33.1 33.9 4 > superiorfrontal > > ============================================================ > > I need to get the cortical thickness values from each subject within > > this clusters so I am trying to use > > mri_glmfit-sim with --cache option and I wonder what value should I > > choose in this case for cache (2, 3.3 or 4) > > and what --cwpvalthresh 0.05 or .025 to get the same results as FDR's > > results. > > > > I tried: > > mri_glmfit-sim \ > > --glmdir lh.L_frontal.glmdir \ > > --cache 3 neg \ > > --cwpvalthresh .05 \ > > --overwrite > > > > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP > > CWPLow CWPHi NVtxs Annot > > 1 -3.874 18231 320.36 -39.8 1.5 14.1 0.02610 > > 0.02410 0.02820 949 precentral > > 2 -3.807 47386 700.61 -8.2 33.1 33.9 0.00020 > > 0.00000 0.00040 1053 superiorfrontal > > > > so as you can see the clusters are the same but their Size and NVtxs > > is so different. What is wrong? > > > > Thank you for your time and help. > > 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 > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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
