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Hi Virendra,

I don't seem to be able to replicate the issue. Could you show the full
command line and the full output you receive in the screen?

Thanks.

All the best,

Anderson

On 10 August 2017 at 00:33, neuroimage analyst <[log in to unmask]
> wrote:

> Hi, Anderson
>
> I tried running the CCA in PALM using v108 but it complained about line
> saying "Reference to a cleared variable o"
> *M = plm.Pset{p}*plm.Rz{y}{m}{c}{o}*plm.X{y}{m}{c}{o};*
>
> So I modified the line to:
> *M = plm.Pset{p}*cell2mat(plm.Rz{y}{m}{c})*plm.X{y}{m}{c};*
>
> and it is running fine.The reason I had to convert cell 2 mat as cell
> Matlab doesn't support cell multiplication.
>
> The script did not finish running as yet but it has produced *_vox_cca_c1
> and *_vox_cca_c2. These files are identical although c1 = 1 0 0 ... and c2
> = -1 0 0 ...
>
> Is this the expected behaviour? and whether the changes that I did in
> those lines are correct?
>
> Thanks
>
> Regards
>
> Virendra
>
> On Wed, Aug 9, 2017 at 7:04 AM, Anderson M. Winkler <
> [log in to unmask]> wrote:
>
>> Hi Virendra,
>>
>> Just one call. It won't change what you'd like to test: after removing
>> EV2, and the mean-centering that is done internally when CCA is used, the
>> EV1 will be coding group differences. The contrasts should then be:
>>
>> C1: [1 0 0 ...]
>> C2: [-1 0 0 ...]
>>
>> That's it!
>>
>> All the best,
>>
>> Anderson
>>
>>
>> On 9 August 2017 at 10:40, neuroimage analyst <
>> [log in to unmask]> wrote:
>>
>>> 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
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>
>>
>