 |
 |
Hi, I'm afraid I don't understand the problem. If you're analyzing 10 components then you will need to run 10 separate 2 sample t-tests. I'm also not sure what the Beckmann template is. Cheers, Jeanette On Fri, Sep 28, 2012 at 5:35 AM, Jacobs H (NP) < [log in to unmask]> wrote: > Dear Jeanette, > > Thank you very much for your help. > However, I came across another error: the number of time points in the > merged 4D file does not match my design matrix. > Probably this is because I used the Beckmann template in the dual > regression (providing the components). > So, now I have 40 people x 10 components, which is different from my > design matrix (having 2 groups of 20 people). > > How should I proceed to get separate files for each component? And still > be able to proceed to stage 3 from DR do the 2 sample t-test on the > subtracted images (condition-condition2)? > > Thank you very much! > > Best > Heidi > > ================================================ > Dr. Heidi Jacobs > Postdoc researcher > Faculty of Health, Medicine and Life Sciences > School for Mental Health and Neurosciences > Division Cognitive Neuropsychiatry and Clinical Neurosciences > Alzheimer Center Limburg > [log in to unmask] > www.maastrichtuniversity.nl > www.heidijacobs.nl > > Dr. Tanslaan 12, 6229 ET Maastricht > P.O. Box 616, 6200 MD Maastricht, The Netherlands > T +31 43 38 84 090 F +31 43 38 84 092 > ================================================ > ________________________________________ > Van: FSL - FMRIB's Software Library [[log in to unmask]] namens Jeanette > Mumford [[log in to unmask]] > Verzonden: vrijdag 28 september 2012 1:11 > Aan: [log in to unmask] > Onderwerp: Re: [FSL] Repost: question regarding pre and post comparison > > Hi, > > you need to first create a 4D image and use that as input into randomise > fslmerge -t can be used for this purpose. See the the help for complete > usage. > > Cheers, > Jeanette > > On Thu, Sep 27, 2012 at 3:36 PM, Jacobs H (NP) < > [log in to unmask]<mailto:[log in to unmask]>> > wrote: > Hi, > > I managed to subtract all the pre and post files of all my subjects from > stage 2 from DR (where I used the Beckmann template). Furthermore, I also > made a .mat and .con file for an 2 group unpaired t-test of these files. > I now would like to run the statistics on these ' subtracted' images and > then find out in which components there is a group difference for the > condition1-2. > Should I use randomise for this? I tried it, but it won't work: > > randomise -i A01_subtracted_DR2.nii.gz A02_subtracted_DR2.nii.gz > A03_subtracted_DR2.nii.gz A04_subtracted_DR2.nii.gz > A05_subtracted_DR2.nii.gz A06_subtracted_DR2.nii.gz > A07_subtracted_DR2.nii.gz A08_subtracted_DR2.nii.gz > A09_subtracted_DR2.nii.gz A10_subtracted_DR2.nii.gz > A11_subtracted_DR2.nii.gz A12_subtracted_DR2.nii.gz > A13_subtracted_DR2.nii.gz A14_subtracted_DR2.nii.gz > A15_subtracted_DR2.nii.gz A16_subtracted_DR2.nii.gz > A17_subtracted_DR2.nii.gz A18_subtracted_DR2.nii.gz > A19_subtracted_DR2.nii.gz A20_subtracted_DR2.nii.gz > J01_subtracted_DR2.nii.gz J02_subtracted_DR2.nii.gz > J03_subtracted_DR2.nii.gz J04_subtracted_DR2.nii.gz > J06_subtracted_DR2.nii.gz J07_subtracted_DR2.nii.gz > J08_subtracted_DR2.nii.gz J09_subtracted_DR2.nii.gz > J10_subtracted_DR2.nii.gz J11_subtracted_DR2.nii.gz > J12_subtracted_DR2.nii.gz J13_subtracted_DR2.nii.gz > J14_subtracted_DR2.nii.gz J15_subtracted_DR2.nii.gz > J16_subtracted_DR2.nii.gz J17_subtracted_DR2.nii.gz > J18_subtracted_DR2.nii.gz J19_subtracted_DR2.nii.gz > J20_subtracted_DR2.nii.gz J21_subtracted_DR2.nii.gz -o > Output_DR3_subtraction -d model_subtractedDR2.mat -t > model_subtractedDR2.con -n 5000 > > Could you tell me what I am doing wrong and how I should proceed on this? > Thank you very much! > > Heidi > > > ================================================ > Dr. Heidi Jacobs > Postdoc researcher > Faculty of Health, Medicine and Life Sciences > School for Mental Health and Neurosciences > Division Cognitive Neuropsychiatry and Clinical Neurosciences > Alzheimer Center Limburg > [log in to unmask]<mailto:[log in to unmask]> > www.maastrichtuniversity.nl<http://www.maastrichtuniversity.nl> > www.heidijacobs.nl<http://www.heidijacobs.nl> > > Dr. Tanslaan 12, 6229 ET Maastricht > P.O. Box 616, 6200 MD Maastricht, The Netherlands > T +31 43 38 84 090<tel:%2B31%2043%2038%2084%20090> F +31 43 38 84 > 092<tel:%2B31%2043%2038%2084%20092> > ================================================ > ________________________________________ > Van: FSL - FMRIB's Software Library [[log in to unmask]<mailto: > [log in to unmask]>] namens Stephen Smith [[log in to unmask]<mailto: > [log in to unmask]>] > Verzonden: donderdag 27 september 2012 10:22 > Aan: [log in to unmask]<mailto:[log in to unmask]> > Onderwerp: Re: [FSL] Repost: question regarding pre and post comparison > > HI - yes it's the stage 2 outputs you want. > Cheers. > > > On 27 Sep 2012, at 09:18, Jacobs H (NP) wrote: > > Hi, > > I got fslmaths working! > But should I use the dr_stage2_subject[#SUB].nii.gz from stage 2 dual > regression? Thus: subtract the two measurements for each subject and feed > this stage 3 DR (with the subtracted maps) for doing a 2 sample t-test? > > Thanks > Heidi > ================================================ > Dr. Heidi Jacobs > Postdoc researcher > Faculty of Health, Medicine and Life Sciences > School for Mental Health and Neurosciences > Division Cognitive Neuropsychiatry and Clinical Neurosciences > Alzheimer Center Limburg > [log in to unmask]<mailto:[log in to unmask] > ><mailto:[log in to unmask]<mailto: > [log in to unmask]>> > www.maastrichtuniversity.nl<http://www.maastrichtuniversity.nl> > www.heidijacobs.nl<http://www.heidijacobs.nl> > > Dr. Tanslaan 12, 6229 ET Maastricht > P.O. Box 616, 6200 MD Maastricht, The Netherlands > T +31 43 38 84 090<tel:%2B31%2043%2038%2084%20090> F +31 43 38 84 > 092<tel:%2B31%2043%2038%2084%20092> > ================================================ > ________________________________________ > Van: FSL - FMRIB's Software Library [[log in to unmask]<mailto: > [log in to unmask]>] namens Jeanette Mumford [[log in to unmask] > <mailto:[log in to unmask]>] > Verzonden: maandag 24 september 2012 16:35 > Aan: [log in to unmask]<mailto:[log in to unmask]> > Onderwerp: Re: [FSL] Repost: question regarding pre and post comparison > > Hi, > > Yes, to test how the pre/post differences compare between your two groups, > you would first subtract the pre/post within subject and then enter these > differences into a 2-sample t-test. > > Other within pre or within post difference between your groups would be > run with separate two-sample t-tests. > > Cheers, > Jeanette > > On Mon, Sep 24, 2012 at 3:35 AM, Jacobs H (NP) < > [log in to unmask]<mailto:[log in to unmask] > ><mailto:[log in to unmask]<mailto: > [log in to unmask]>>> wrote: > Dear FSL team, > > I am struggling a bit with the statistics for my resting state analyses. > I have two groups (each 20 subejcts) and a pre and post measurement. I > already ran the ICA and now would like to do the dual regression. > In this regression I would like to investigate the main effect of group, > condition (pre/post) and the interaction (group differences on the > difference between post and pre). > > Should I do a 2by2 anova with 4 EV's (group1 timepoint 1; group 1 > timepoint 2; group 2 timepoint 1; group 2 timepoint 2). > > And then create the following contrast file > > main effect group: 1 1 -1 -1 > main effect time 1 -1 1 -1 > interaction: 1 -1 -1 1 > > However, I read somewhere that I should subtract both conditions for each > individual and then compare the two group on this 'subtracted image'?? > Is this correct? > > Any advice would be greatly appreciated!! > > Thanks! > > Best > Heidi > > > > > > > ================================================ > Dr. Heidi Jacobs > Postdoc researcher > Faculty of Health, Medicine and Life Sciences > School for Mental Health and Neurosciences > Division Cognitive Neuropsychiatry and Clinical Neurosciences > Alzheimer Center Limburg > [log in to unmask]<mailto:[log in to unmask] > ><mailto:[log in to unmask]<mailto: > [log in to unmask]>> > www.maastrichtuniversity.nl<http://www.maastrichtuniversity.nl>< > http://www.maastrichtuniversity.nl> > www.heidijacobs.nl<http://www.heidijacobs.nl><http://www.heidijacobs.nl> > > Dr. Tanslaan 12, 6229 ET Maastricht > P.O. Box 616, 6200 MD Maastricht, The Netherlands > T +31 43 38 84 090<tel:%2B31%2043%2038%2084%20090><tel:%2B31%2043%2038%2084%20090> > F +31 43 38 84 092<tel:%2B31%2043%2038%2084%20092> > ================================================ > > > > --------------------------------------------------------------------------- > Stephen M. Smith, Professor of Biomedical Engineering > Associate Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [log in to unmask]<mailto:[log in to unmask]><mailto: > [log in to unmask]<mailto:[log in to unmask]>> > http://www.fmrib.ox.ac.uk/~steve > --------------------------------------------------------------------------- >