External Email - Use Caution I meant the latter. Thank you very much for responding to my questions.
I have one more question: Can we do non-parametric approaches by Freesurfer? On Sat, Mar 14, 2020 at 2:13 AM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > Are you asking how to do subcortical analysis or are you asking how to > account for subcortical analysis during correction for multiple > corrections? For the latter, use --3spaces > > On 3/12/2020 2:03 PM, Hengameh Marzbani wrote: > > External Email - Use Caution > thank you for your detailed and helpful explanation. > > question 3: I mean just left and right. But what should I do if I want to > consider subcortical as well as left and right? > > Best Regards > Hengameh > > On Thu, Mar 12, 2020 at 12:07 AM Douglas N. Greve <dgr...@mgh.harvard.edu> > wrote: > >> >> >> On 3/11/2020 4:21 PM, Hengameh Marzbani wrote: >> >> External Email - Use Caution >> >> Thank you for the quick response. >> >> question 1: I need the results of mri-glmfit (before doing mri-glmfit-sim). >> I can see the clusters by tksurfer. But, Can I have a text file included all >> clusters? >> >> You can, the easiest way is to run mri_glmfit-sim and it will give you a >> list of clusters in a text file. If you set the cwp to 1, then it will give >> you all the clusters. See the help. >> >> question 3: I want to do the analyse by considering the whole brain. Is >> correct to use --2spaces? and also I I want to visualize the results in both >> hemisphere simultaneously. is it possible by freeview? >> >> Whole brain meaning left, right, and subcort or just left and right? If >> just left and right, then use --2spaces >> >> question 5: I can't understand what is the reason of using demean and >> normalize. Would you mind explaining to me? And when is it necessary to use >> them? >> >> Demeaning makes the design matrix better conditioned. But also if you are >> looking at the difference in average thickness between two groups >> regressing out, eg, age, then simply using age as a regressor will reduce >> the efficiency of the estimation because the age itself will have a >> non-zero mean, so the regression is left trying to figure out what part of >> the thickness average is due to the group and what part is due to age. >> >> Thank you so much. >> >> Hengameh >> >> >> On Tue, Mar 10, 2020 at 2:03 AM Douglas N. Greve <dgr...@mgh.harvard.edu> >> wrote: >> >>> >>> >>> 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 >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> Freesurfer mailing >> listfreesur...@nmr.mgh.harvard.eduhttps://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 > > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 -- *Sincerely* *Hengameh Marzbani* *PhD candidate of Biomedical Engineering, Amirkabir University of Technology (AUT) - Tehran Polytechnic* *Medical Image Processing and Brain Stimulation Specialist at National Brain Mapping Laboratory (NBML), Tehran, Iran*
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