Hi - I suspect that one of the FEAT settings may not be quite right for this dataset. The best thing to do would be to create a tarfile of the feat directory and email it to me (directly, not to the list) and we will take a look: tar cvf send.tar <yourdirectoryname>.feat gzip -9 send.tar then email to me! Thanks, Steve. On Thu, 17 Oct 2002, tulu wrote: > Hi Smith and FSL experts, > I setup the model and use the parameter according to your suggestion. I > set the thresholding as uncorrected voxel P in 0.1 ( it is very large). > Then I run the FEAT. No voxel is above the threshold. It is very strange > that if I use the SPM to perform the same study, I can set the p value > in 0.05 or below and get a reasonable result. Is there anything wrong ? > Besides, if I have the variance for each image, such as the cognitive > score in controls and patients, how to input the variance ? > Thank for your help > JLH > > -----Original Message----- > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On > Behalf Of Stephen Smith > Sent: Thursday, October 17, 2002 6:27 PM > To: [log in to unmask] > Subject: Re: [FSL] parameter about the group analysis by FEAT > > Hi - so it seems like you have only one image per subject, and I will > assume that they are all registered together (if not - you need to do > this). It also seems like you DON'T have variance images for the > subjects. > > Therefore there is not too much advantage in using FLAME (the advanced > estimation for group-stats in FEAT) over ordinary-least-squares (ie what > you get if you turned off FILM for first-level anllayses or turn off > FLAME > for higher-level analyses). The only time where you MIGHT get an > improvement with using FLAME is if your two groups have very different > variances. (Note for other people - if you do all your analysis at > first- > and second-level using FEAT then of course, FEAT will pass up parameter > estimates AND variances to the second-level, so FLAME is definitely of > value). > > So - in order to input your data into FEAT you probably may as well run > a > "first-level" analysis, according to Joe's suggestions. Start by > concatenating the two 4D files into one by: > avwmerge -t allsubjects.hdr controls.hdr patients.hdr > > And then do a first-level analysis with a single EV of 1's and -1's. In > your case you want TR=1 skip=0 OFF=43 ON=7 phase=0 conv=NO > temporalfiltering=NO temporalderivative=NO > > contrast 1 (patients-controls) = [1] > contrast 2 (controls-patients) = [-1] > > hope this works ok! > > Steve. > > > > On Thu, 17 Oct 2002, tulu wrote: > > > Dear FSL experts, > > Thanks Joe and Smith for your help. I only have the normalized raw > data > > from controls and disease. So I think I don't have first level time > > series PET data. Dr. Joe, you understand correctly. However I still > have > > the problem in the stats portion. What is the basic shape I should > > choice ? I choice the square and I did not know how to setup the skip, > > off, on, phase and stop after. My data is a 4d analyze format which > 1-43 > > subject is controls and 44-50 is diseases. Besides, if I need to enter > > the covariance data, how should I do ? > > Thanks your help > > JLH > > > > -----Original Message----- > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On > > Behalf Of Joe Devlin > > Sent: Wednesday, October 16, 2002 11:11 PM > > To: [log in to unmask] > > Subject: Re: [FSL] parameter about the group analysis by FEAT > > > > >Thank for your reply. I only have the experience of " compare > > >populations: 1scan/subject" ( that is a two sample t test) in SPM. > Now > > I > > >have the 2 groups subjects in 4d analyze format. I like to try the > > >"simple" analysis (compared population) and I don't know how to do > it. > > >Please give me any suggestion. Thanks > > > > If I understand correctly, basically you want to compute a two-tailed > > t-test comparing > > patients to controls across the voxels in the brain. I don't see any > a > > priori reason why > > you couldn't do this in Feat but I don't think you want any of the > fancy > > options. > > > > It sounds like you want something like: > > - Put all scans (1 per subject) into a single 4d file containing first > > the > > normals and then the patients. > > > > - You need all of your scans registered into standard space (which you > > can > > do with McFlirt > > if you haven't already done this). Probably, though, it would be best > > to > > do this before using > > Feat because Feat assumes that a single time series comes from a > single > > individual. In this > > case you will enter one time series from many subjects. > > > > - Misc: DOn't change anything here. > > - Data: TR = 1, delete volumes = 0, & you don't want high pass > > filtering. > > - Pre-stats: Turn off temporal filtering here and set the spatial > > smoothing > > to whatever you want (typically 8-16mm in PET). > > Definitely don't want motion correction or slice timing correction. > > May > > not want brain extraction depending on how much > > skull shows up in your PET images. Probably do want some form of > > intensity normalisation but this is slightly tricky (see > > previous email). > > - Stats: Turn off pre-whitening. Select full model setup and create a > > single ev. It should be a set of 1s -- one for each > > normal. Patients will be implicitly modeled. Turn off > convolution, > > temporal filtering and temporal derivatives. The final > > model should look like a column of 1s -- 1 per control followed by > > zeros > > -- 1 per patient. Presumably you want two > > contrasts: Controls > patients (1) and Patients > controls (-1). > > - Post stats: Pick a statistical threshold for accepting significant > > results. > > - Registration: None. Best to do this before creating the 4d data set > > for > > analysis because of the assumptions Feat > > makes -- namely that you're analysing fMRI data rather than pet. > > > > Good luck. > > Joe > > > > > > >JLH > > > > > >-----Original Message----- > > >From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On > > >Behalf Of Stephen Smith > > >Sent: Wednesday, October 16, 2002 5:18 PM > > >To: [log in to unmask] > > >Subject: Re: [FSL] parameter about the group analysis by FEAT > > > > > >Hi - I'm a little confused by this - are you saying that you have > > >already > > >carried out the first-level analyses from each subject and want to > pass > > >the relevant stats up to second level? Or are you wanting to carry > out > > >the > > >first-level AND the second-level anlaysis inside FEAT? > > > > > >Thanks, Steve. > > > > > > > > > > > > > > >On Wed, 16 Oct 2002, tulu wrote: > > > > > > > Hello Smith and FSL experts, > > > > I try to setup the study. I have one group of controls (N=43) in > 4d > > > > analyze format and another groups of disease (N=7). I use the > first > > > > level analysis and number of analysis is 2 ( 2 groups of patients > > ?). > > > > The TR=3, High pass filter cutoff=100. Turn off the FILM > > prewhitening > > > > and turn on the intensity norm. Then the FSL ask to setup model > > >contrast > > > > details after I push the go. Is there any thing should change ? > > Thanks > > > > JLH > > > > > > > > -----Original Message----- > > > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] > On > > > > Behalf Of Stephen Smith > > > > Sent: Tuesday, October 15, 2002 10:30 PM > > > > To: [log in to unmask] > > > > Subject: Re: [FSL] parameter about the group analysis by FEAT > > > > > > > > Well - for the first-level analyses the things that spring to mind > > >are: > > > > > > > > Set TR to whatever it effectively was. > > > > > > > > Turn ON intensity norm? > > > > > > > > Highpass - if you set TR "right" then choose A+B length etc? > > > > > > > > Stats - turn off FILM prewhitening and also turn off convolutions > > and > > > > derivatives? > > > > > > > > Let us know how you get on...thanks, Steve. > > > > > > > > > > > > > > > > On Tue, 15 Oct 2002, tulu wrote: > > > > > > > > > Hello, Smith and FSL expert, > > > > > Thank for your reply. Since I am not familiar with the fmri > > setting, > > > > can > > > > > you tell me the detail setting about this particular case ? Such > > as > > > > the > > > > > TR, high pass filter cutoff and the setting in stats ? I will > > share > > > > the > > > > > result if it can work. Thanks > > > > > JLH > > > > > > > > > > -----Original Message----- > > > > > From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] > > On > > > > > Behalf Of Stephen Smith > > > > > Sent: Tuesday, October 15, 2002 7:00 PM > > > > > To: [log in to unmask] > > > > > Subject: Re: [FSL] parameter about the group analysis by FEAT > > > > > > > > > > A scary can of worms - does FEAT work on PET/SPECT? Well - we > > >haven't > > > > > tested it ONCE on PET data, so seems risky to make any > > > > promises.....but > > > > > in > > > > > theory.....should be ok..... > > > > > > > > > > There are bound to be practical issues that come up - will be > very > > > > > interested to see how you get on. The new FEAT5 group stats > stuff > > > > > (FLAME) > > > > > should add value to group stats with PET just like with FMRI, > but > > as > > >I > > > > > said, we've not tested it at all. Your particular case > (N=7/N=43) > > > > could > > > > > well be a good example of when FLAME is better than simple OLS > > > > > (ordinary-least-squares, ie dumb "random effects"). > > > > > > > > > > Thanks, Steve. > > > > > > > > > > > > > > > On Tue, 15 Oct 2002, Jung Lung Hsu wrote: > > > > > > > > > > > Dear FSL experts, > > > > > > I have a simple question about the FSL. I have 2 groups of > > >patients > > > > by > > > > > PET > > > > > > study. One is disease (N = 7)and another is control (N = 43). > I > > >like > > > > > to > > > > > > know the difference between the disease group and control. Is > it > > > > > possible > > > > > > to use the FEAT to do group analysis ? If so, what is the > detail > > > > > parameter > > > > > > I should enter in the FEAT program ? Thanks > > > > > > JLH > > > > > > > > > > > > > > > > Stephen M. Smith > > > > > Head of Image Analysis, FMRIB > > > > > > > > > > Oxford University Centre for Functional MRI of the Brain > > > > > John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK > > > > > +44 (0) 1865 222726 (fax 222717) > > > > > > > > > > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > > > > > > > > > > > > > Stephen M. Smith > > > > Head of Image Analysis, FMRIB > > > > > > > > Oxford University Centre for Functional MRI of the Brain > > > > John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK > > > > +44 (0) 1865 222726 (fax 222717) > > > > > > > > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > > > > > > > > > > Stephen M. Smith > > > Head of Image Analysis, FMRIB > > > > > > Oxford University Centre for Functional MRI of the Brain > > > John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK > > > +44 (0) 1865 222726 (fax 222717) > > > > > > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > > > > Joe > > > > Stephen M. Smith > Head of Image Analysis, FMRIB > > Oxford University Centre for Functional MRI of the Brain > John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve > Stephen M. Smith Head of Image Analysis, FMRIB Oxford University Centre for Functional MRI of the Brain John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask] http://www.fmrib.ox.ac.uk/~steve