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Thanks so much! -Pete > Hi Peter, > >> I've collected resting-state fmri data from a patient group and a >> control >> group. After processing the data using the pre-stats tab in FEAT and >> subsequently running MELODIC, I merged the subjects' melodic outputs >> together and reran MELODIC. From the resulting output, I've >> indentified a >> number of components of interest that I'd like to compare between >> the two >> groups. > >> My understanding of what I should do is the following: >> >> 1) Create a mask representing the combined thresh_zstat maps for >> both groups. > > nothing wrong with this, but you won't need it later > >> 2) Concatenate all the thresh_zstat maps of a particular component >> for all >> subjects, with all the subjects in one group first, followed by all >> the >> subjects in the second. >> > > No, you wouldn't want to run any model based higher-level analysis on > thresholded lower-level stats images - simply use the associated > unthresholded maps instead. > > >> 3) Create design.mat and design.con files using the GLM Setup utility, >> where my design looks like the following: >> group EV1 EV2 >> groupA groupB Title EV1 EV2 >> s1 1 1 0 | C1 groupA mean 1 0 >> s2 1 1 0 | C2 groupB mean 0 1 >> s3 1 1 0 | C3 A > B 1 -1 >> s4 1 1 0 | C4 B > A -1 1 >> s5 2 0 1 | >> s6 2 0 1 | >> s7 2 0 1 | >> s8 2 0 1 | >> > > That sounds OK > >> 4) run a Two-Sample Unpaired T-test using RANDOMISE with the following >> command: >> >> randomise -i <4D_input> -o <output> -d design.mat -t design.con -c >> 0.99 >> > > nope, the argument to the -c (or -C) option is in units of the raw t- > stats (not z) that is being formed within randomise, i.e. if you want > a cluster forming threshold of t>2.3 use that number here. The output > file contains the p-values, i.e. you can threshold that one at 0.99, > say after having obtained it from randomise. > hope this helps > christian > > > >> Here are my questions: >> Does it appear I am setting up the design correctly? >> Is using the option "-c 0.99" the equivalent of looking for >> significance >> at p<0.01? >> Do you have any other suggestions or recommendations for carrying >> this out? >> >> You help is greatly appreciated. Thanks in advance. >> >> Cheers, >> >> Pete >> >> Center for Magnetic Resonance Research >> University of Minnesota > > ____ > Christian F. Beckmann > University Research Lecturer > Oxford University Centre for Functional MRI of the Brain (FMRIB) > John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK. > [log in to unmask] http://www.fmrib.ox.ac.uk/~beckmann > tel: +44 1865 222551 fax: +44 1865 222717 >