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Ah - I've just noticed that you have *commas* instead of decimal points!! On 31 Jul 2012, at 16:01, sandra petris wrote: > I get this: > > > [fsl@localhost stats]$ fslinfo all_FA_skeletonised > data_type FLOAT32 > dim1 182 > dim2 218 > dim3 182 > dim4 15 > datatype 16 > pixdim1 1.0000000000 > pixdim2 1.0000000000 > pixdim3 1.0000000000 > pixdim4 1.0000000000 > cal_max 0.0000 > cal_min 0.0000 > file_type NIFTI-1+ > > > 2012/7/31 Stephen Smith <[log in to unmask]> > I think you may need spaces not tabs….I'm not sure. > > What do you get from > fslinfo all_FA_skeletonised > > > Cheers > > > On 31 Jul 2012, at 15:55, sandra petris wrote: > >> yes I have but I used tabs to separate the columns... >> >> 2012/7/31 Stephen Smith <[log in to unmask]> >> Do you have spaces between the 0 and -1 entries in your design.con ? You need that. >> >> >> On 31 Jul 2012, at 15:51, sandra petris wrote: >> >>> Hi Steve sorry to disturb you again >>> >>> now my matrices are the following: >>> >>> /NumWaves 5 >>> /NumPoints 15 >>> /PPheights 1 1 1 1 1 >>> /Matrix >>> 1 1,0434 1,1634 1,9836 -4,7333 >>> 1 0,3511 0,6998 0,6660 -6,7333 >>> 1 0,3733 0,1620 1,3627 4,2667 >>> 1 -0,7298 1,1634 0,9047 -3,7333 >>> 1 -0,3459 -0,1429 0,6176 -1,7333 >>> 1 -0,0511 0,1898 -0,1555 -3,7333 >>> 1 -0,0954 -2,1662 0,0961 -4,7333 >>> 1 -0,7031 -1,0768 -0,6896 -5,7333 >>> 1 0,3342 0,4163 -0,7304 9,2667 >>> 1 0,8755 -0,1218 -0,4432 -2,7333 >>> 1 -1,3132 -1,0332 0,5826 6,2667 >>> 1 0,4781 -0,9344 0,2008 -0,7333 >>> 1 -0,0692 0,1785 -1,1205 18,2667 >>> 1 0,6799 1,1634 -1,0984 1,2667 >>> 1 -0,8272 0,3381 -2,1765 -4,7333 >>> >>> >>> >>> /NumWaves 5 >>> /NumContrasts 6 >>> /PPheights 1 1 1 1 1 >>> /Matrix >>> 0 1 0 0 0 >>> 0-1 0 0 0 >>> 0 0 1 0 0 >>> 0 0-1 0 0 >>> 0 0 0 1 0 >>> 0 0 0-1 0 >>> >>> >>> >>> I run the randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design_nico.mat -t design_nico.con -n 10000 --T2 -V (without -D) >>> >>> >>> and I got the following error message :( >>> >>> Loading Data: >>> Data loaded >>> ERROR: Program failed >>> >>> An exception has been thrown >>> Runtime error:- detected by Newmat: process fails to converge >>> >>> MatrixType = Rect # Rows = 15; # Cols = 4 >>> Trace: SVD; pinv. >>> >>> >>> >>> >>> >>> 2012/7/31 Stephen Smith <[log in to unmask]> >>> No - I meant you don't need BOTH - you need one or the other. >>> Cheers. >>> >>> >>> >>> On 31 Jul 2012, at 15:36, sandra petris wrote: >>> >>>> ah thanks a lot Steve! I'm gonna delete the -D option and the 1st colums, let'see what happens >>>> >>>> ciao! Sandra >>>> >>>> 2012/7/31 Stephen Smith <[log in to unmask]> >>>> Hi - the answer is clearly in the error message :-) >>>> You don't need the -D option *and* the EV full of 1s. >>>> Steve. >>>> >>>> >>>> On 31 Jul 2012, at 12:34, sandra petris wrote: >>>> >>>>> Hi Stephen, >>>>> >>>>> when I run randomise -i all_FA_skeletonised -o tbss -m mean_FA_skeleton_mask -d design_nico.mat -t design_nico.con -n 10000 -D --T2 -V I got the following error message: >>>>> >>>>> Loading Data: >>>>> Data loaded >>>>> Warning: You have demeaned your data, but at least one design column has non-zero mean >>>>> ERROR: Program failed >>>>> >>>>> An exception has been thrown >>>>> Runtime error:- detected by Newmat: process fails to converge >>>>> >>>>> MatrixType = Rect # Rows = 15; # Cols = 4 >>>>> Trace: SVD; pinv. >>>>> >>>>> >>>>> thanks in advance for any help >>>>> >>>>> Sandra >>>>> >>>>> >>>>> 2012/7/31 Stephen Smith <[log in to unmask]> >>>>> Hi - these look - what was the error message? >>>>> >>>>> >>>>> On 30 Jul 2012, at 16:14, Sandra Petris wrote: >>>>> >>>>>> Dear fsl experts, >>>>>> >>>>>> >>>>>> I have a question regarding TBSS analysis. I would like to compute the correlation (or regression) between FA and behavioral scores. >>>>>> I have one group of subjects (15 subjects) and behavioral scores (BS) taken from 3 tasks plus 1 regressors of no interest, age that I have demeaned (is it correct?) >>>>>> I assume that the design matrix should look like this: >>>>>> >>>>>> >>>>>> >>>>>> /NumWaves 5 >>>>>> /NumPoints 15 >>>>>> /PPheights 1 1 1 1 1 >>>>>> /Matrix >>>>>> 1 1,0434 1,1634 1,9836 -4,7333 >>>>>> 1 0,3511 0,6998 0,6660 -6,7333 >>>>>> 1 0,3733 0,1620 1,3627 4,2667 >>>>>> 1 -0,7298 1,1634 0,9047 -3,7333 >>>>>> 1 -0,3459 -0,1429 0,6176 -1,7333 >>>>>> 1 -0,0511 0,1898 -0,1555 -3,7333 >>>>>> 1 -0,0954 -2,1662 0,0961 -4,7333 >>>>>> 1 -0,7031 -1,0768 -0,6896 -5,7333 >>>>>> 1 0,3342 0,4163 -0,7304 9,2667 >>>>>> 1 0,8755 -0,1218 -0,4432 -2,7333 >>>>>> 1 -1,3132 -1,0332 0,5826 6,2667 >>>>>> 1 0,4781 -0,9344 0,2008 -0,7333 >>>>>> 1 -0,0692 0,1785 -1,1205 18,2667 >>>>>> 1 0,6799 1,1634 -1,0984 1,2667 >>>>>> 1 -0,8272 0,3381 -2,1765 -4,7333 >>>>>> >>>>>> >>>>>> Is the following contrast matrix correct? >>>>>> >>>>>> >>>>>> /NumWaves 5 >>>>>> /NumContrasts 6 >>>>>> /PPheights 1 1 1 1 1 >>>>>> /Matrix >>>>>> 0 1 0 0 0 >>>>>> 0 -1 0 0 0 >>>>>> 0 0 1 0 0 >>>>>> 0 0 -1 0 0 >>>>>> 0 0 0 1 0 >>>>>> 0 0 0 -1 0 >>>>>> >>>>>> >>>>>> When I run the randomize command I receive an error message.....are the NumWaves/NumConntrast an PPWheights correct? >>>>>> >>>>>> Any help will be greatly appreciated >>>>>> >>>>>> >>>>>> Best, Sandra >>>>>> >>>>> >>>>> >>>>> --------------------------------------------------------------------------- >>>>> 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] http://www.fmrib.ox.ac.uk/~steve >>>>> --------------------------------------------------------------------------- >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> --------------------------------------------------------------------------- >>>> 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] http://www.fmrib.ox.ac.uk/~steve >>>> --------------------------------------------------------------------------- >>>> >>>> >>>> >>>> >>> >>> >>> --------------------------------------------------------------------------- >>> 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] http://www.fmrib.ox.ac.uk/~steve >>> --------------------------------------------------------------------------- >>> >>> >>> >>> >> >> >> --------------------------------------------------------------------------- >> 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] http://www.fmrib.ox.ac.uk/~steve >> --------------------------------------------------------------------------- >> >> >> >> > > > --------------------------------------------------------------------------- > 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] http://www.fmrib.ox.ac.uk/~steve > --------------------------------------------------------------------------- > > > > --------------------------------------------------------------------------- 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] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------