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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
>>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>