Hi Doug, we are eager to try the FSL randomise program on a FS data set we have. However, we have one (stupid, maybe) question: is the file design.con something that we make manually, or is it generated by some of the previous processes?
If we are going to make it ourselves, how should it be? In our GLM, we have two classes (males, females) and two variables (memory score, hippocampal volume), and we want to assess the relationship between the memory score and thickness when gender and hippocampal volume is regressed out), e.g. DOSS: 0 0 1 0 Thanks, - Anders > > FYI, FSL has a nice site documenting the randomise program :) > > http://www.fmrib.ox.ac.uk/fsl/randomise/index.html > > > Doug Greve wrote: > >> >> mris_glm does not correct for multiple comparisons itself. However, >> you can use fdr inside of tksurfer, or ... >> >> Steve Smith and I just worked out how to use the FSL randomise program >> to compute the vertex-wise threshold. Randomise implements permutation >> testing, which is much less conservative than FDR or GRF. >> >> When you run mris_glm, make sure to specify the --y output (something >> like --y y-lh.mgh). then run mri_surf2surf to convert it to nifit, >> something like: >> >> mri_surf2surf --srcsubject average7 --trgsubject average7 \ >> --srcsurfval y-lh.mgh --src_type mgh \ >> --trg_type nii --trgsurfval y-lh.nii --hemi lh >> >> You will also need to convert the design matrix produced by mris_glm >> (something like y.X.mat) into ascii. This can be done in matlab with >> something like: >> >> load y.X.mat >> save('X.asc','X','-ascii') >> >> Then run: >> >> randomise -i y-lh -o y-lh \ >> -d X.asc -t design.con -n 5000 -V >> >> Where design.con has your contrasts >> >> The output will be something like: y-lh_max_tstat1.mgh, which you can >> view with tksurfer with something like: >> >> tksurfer average7 lh inflated -overlay y-lh_max_tstat1.mgh >> >> We're still working out the details on this (obviously:), you may have >> to play with this a little to get the command lines exactly correct. >> >> Note that randomise program cannot do cluster-based thresholding >> because it is not aware that these values are really on the surface >> (not in a volume), but the max stat will work. >> >> doug >> >> >> Antao Du wrote: >> >>> Hi, >>> >>> I am running mris_glm to compare the cortical thickness between two >>> groups. >>> I have a question, which method is used for correcting multiple >>> comparison >>> in the analysis? Thanks, >>> >>> Antao >>> >>> _______________________________________________ >>> 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 > [EMAIL PROTECTED] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > _______________________________________________ > 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
