Thank you Anderson So, should I then run CCA for the 2 groups separately in 2 different call to palm? How to set the contrast for 2 groups? Thanks Regards Virendra On Aug 9, 2017 6:23 AM, "Anderson M. Winkler" <[log in to unmask]> wrote: > Hi Virendra, > > Thanks for sending the files and for the patience. > > This error can be fixed by replacing, in line 2047 of palm_core.m, where > it reads: > > *for t = find(yselq),* > > > for the following: > > *for t = find(yselq)',* > > > That is, an apostrophe was missing, which caused the variable t being not > a row but a column, which on its turn changes the behaviour of the for-loop. > > In looking into this, it seems that there was also an issue with the > intersection mask across modalities, which not being produced; this has now > been fixed elsewhere in the code (it wouldn't affect your analysis, but > could crash with different data). This has now been fixed too, in alpha108. > > A separate comment on your data: the design has one column for each of the > two groups. This is generally fine, except for CCA, where we mean-center > all columns, and then the design becomes rank deficient. To get around it, > and avoid warning messages, just remove the 2nd column of your design > matrix and also the corresponding bits of the contrasts. > > Hope this solves the problem. If not, please let me know. Thanks! > > All the best, > > Anderson > > > On 6 August 2017 at 22:30, neuroimage analyst < > [log in to unmask]> wrote: > >> Hi, Anderson. >> >> Thank you for looking into this. You should have received a dropbox link >> with all the relevant files in it. Please let me know if anything else is >> needed from me. I really appreciate your time and help. >> >> Regards >> >> Virendra >> >> On Sun, Aug 6, 2017 at 4:03 PM, Anderson M. Winkler < >> [log in to unmask]> wrote: >> >>> Hi Virendra, >>> >>> Could you send me your inputs, design files, etc? You can put in some >>> online service like Dropbox and send me the link off-list then. >>> >>> Thanks, and apologies for the persistent bug... >>> >>> All the best, >>> >>> Anderson >>> >>> >>> On 6 August 2017 at 11:28, neuroimage analyst < >>> [log in to unmask]> wrote: >>> >>>> Thanks, Anderson. >>>> >>>> However, it throws the following error now. >>>> >>>> *Undefined function 'qr' for input arguments of type 'double' and >>>> attributes* >>>> *'full 3d real'.* >>>> >>>> *Error in palm_core>cca (line 3197)* >>>> *[Qy,~] = qr(Y,0);* >>>> >>>> *Error in palm_core (line 2048)* >>>> * Q{m}{c}(t) =* >>>> * >>>> cca(plm.Yq{m}{c}(:,:,t),M,opts.ccaparm);* >>>> >>>> *Error in palm (line 81)* >>>> *palm_core(varargin{:});* >>>> >>>> I would greatly appreciate your response. >>>> >>>> Thanks >>>> >>>> Regards >>>> >>>> V >>>> >>>> On Sun, Aug 6, 2017 at 5:01 AM, Anderson M. Winkler < >>>> [log in to unmask]> wrote: >>>> >>>>> Hi Virendra, >>>>> >>>>> Thanks for letting me know. This should now be fixed in version >>>>> alpha107. If the problem persists (or some other appears!) please feel free >>>>> to ask again. >>>>> >>>>> All the best, >>>>> >>>>> Anderson >>>>> >>>>> >>>>> On 5 August 2017 at 01:43, neuroimage analyst < >>>>> [log in to unmask]> wrote: >>>>> >>>>>> Hi, Anderson >>>>>> >>>>>> I am trying to run PALM CCA for 3 modalities with the following line: >>>>>> >>>>>> *palm -i mod1.nii.gz -i mod2.nii.gz -i mod3.nii.gz -m mask.nii -d >>>>>> design.mat -t contrast.con -o results -npcmod -npccon -mv CCA -T -logp >>>>>> -accel tail -quiet -noniiclass -nouncorrected -savedof -saveparametric >>>>>> -Tnpc -demean -n 100* >>>>>> >>>>>> However, it throws an error: >>>>>> *Undefined operator '*' for input argument of type 'cell'* >>>>>> *Error in palm_core (line 2044)* >>>>>> *M=plm.Pset(p)*plm.Rz{m}{c}*plm.X{m}{c}* >>>>>> *Error in palm (line 81)* >>>>>> *palm_core(varargin(:))* >>>>>> >>>>>> I would greatly appreciate if you could please help me resolve this >>>>>> error. >>>>>> >>>>>> Thanks >>>>>> >>>>>> Regards >>>>>> >>>>>> Virendra >>>>>> >>>>> >>>>> >>>> >>> >> >