On 3/9/20 5:53 PM, Hengameh Marzbani wrote: > > External Email - Use Caution > > Hello Freesurfer developers, > 1- I want to extract the uncorrected clusters from the uncorrected > significance maps obtained from mri_glmfit for structural data (to illustrate > cluster, size, location, and significance) like abs.sig.cluster.summary > (summary of clusters (text))which is obtained from mri_glmfit-sim. Is there a > way to do this? Set the clusterwise p-value thresh to 1 (--cwp 1) > 2- I don't see any clusters when I use cluster-based correction for multiple > comparisons (for example mri_glmfit-sim \ --glmdir lh.Area.glmdir \ --sim > mc-z 10000 2 mc-z.abs\ --sim-sign abs --cache 4 neg \ --cwp 0.05\ > --2spaces). How much is it significant if I report the uncorrected clusters? Usually, reveiewers won't let you report exclusivly uncorrected results. > 3- Are there new ways of looking at the whole brain together (not left and > right hemisphere separately)by Qdec and FSGD? You can load both hemispheres into freeview, if that is what you mean > 4- How can I do fdr correction in mri_glmfit-sim? what flag should I use? You can't, use mri_fdr. Run with --help to get docs > 5- How can I demean and normalize the covariates when I use FSGD? what flag > should I use? Add these lines in your FSGD file DeMeanFlag 1 ReScaleFlag 1 > > Thanks you in advance! > Best regards, > Hengameh > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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