Hmm, that is strange! Anyways, I will create a local copy of palm_core for this particular project. Second question: Are the values inside every voxel of *_cca1.nii.gz can be treated as effect size? Looks like no voxel passes FWE. I want to see if there is any effect of these 3 modalities. Thanks -Virendra On Thu, Aug 10, 2017 at 10:43 AM, Anderson M. Winkler < [log in to unmask]> wrote: > Hi Virendra, > > I cannot reproduce that error you received, even using same data and > options. In any case, please don't use cell2mat. It may have worked in this > case because of the specific inputs you have (that cell array has just one > element, which is indeed a matrix) but that isn't a general solution. That > error shouldn't appear anyway (it doesn't happen for me). > > All the best, > > Anderson > > > On 10 August 2017 at 12:09, neuroimage analyst < > [log in to unmask]> wrote: > >> Thanks I will do that and let you know how it goes. >> >> And my edits of dropping {o} and adding cell2mat to the lines in >> palm_core were fine? >> >> Thanks >> >> Regards >> >> Virendra >> >> On Aug 10, 2017 7:59 AM, "Anderson M. Winkler" <[log in to unmask]> >> wrote: >> >>> Hi Virendra, >>> >>> In palm_core.m, line 1144, where it reads: >>> >>> *if opts.MV* >>> >>> >>> please replace for: >>> >>> *if opts.MV || opts.CCA* >>> >>> >>> That should be it. The next release will have that fixed. Thanks! >>> >>> Also, you can drop C2. CCA will always rotate the axes to find the best >>> (positive) correlation, so that can go away. >>> >>> All the best, >>> >>> Anderson >>> >>> >>> On 10 August 2017 at 11:00, neuroimage analyst < >>> [log in to unmask]> wrote: >>> >>>> Hi,Anderson >>>> >>>> Here is the log. >>>> >>>> It goes through till here only after I do the above mentioned change , >>>> meaning cell2mat and removing the {o} >>>> >>>> >> palm -i gm.nii.gz -i wm.nii.gz -i non_pv_corrected.nii.gz -m >>>> MNI152_mask.nii -d PALM_CCA/Non_PV_Corrected/design.mat -t >>>> PALM_CCA/Non_PV_Corrected/contrast.con -n 100 -mv CCA -corrmod >>>> -corrcon -logp -demean -accel tail -noniiclass >>>> -nouncorrected.............................................. >>>> ......................... >>>> ======================================================================= >>>> ___ ___ ___ >>>> / /\ / /\ /__/\ >>>> / /::\ / /::\ | |::\ >>>> / /:/\:\ / /:/\:\ ___ ___ | |:|:\ >>>> / /:/~/:/ / /:/~/::\ /__/\ / /\ __|__|:|\:\ >>>> /__/:/ /:/ /__/:/ /:/\:\ \ \:\ / /:/ /__/::::| \:\ >>>> \ \:\/:/ \ \:\/:/__\/ \ \:\ /:/ \ \:\~~\__\/ >>>> \ \::/ \ \::/ \ \:\/:/ \ \:\ >>>> \ \:\ \ \:\ \ \::/ \ \:\ >>>> \ \:\ \ \:\ \__\/ \ \:\ >>>> \__\/ \__\/ \__\/ >>>> >>>> ======================================================================= >>>> Permutation Analysis of Linear Models >>>> ======================================================================= >>>> Running PALM alpha108 using MATLAB 9.1.0.441655 (R2016b) with the >>>> following options: >>>> -i gm.nii.gz >>>> -i wm.nii.gz >>>> -i non_pv_corrected.nii.gz >>>> -m MNI152_mask.nii >>>> -d PALM_CCA/Non_PV_Corrected/design.mat >>>> -t PALM_CCA/Non_PV_Corrected/contrast.con >>>> -n 100 >>>> -mv CCA >>>> -corrmod >>>> -corrcon >>>> -logp >>>> -demean >>>> -accel tail >>>> -noniiclass >>>> -nouncorrected >>>> -savedof >>>> -saveglm >>>> -o PALM_CCA/Non_PV_Corrected/results >>>> Reading input 1/3: gm.nii.gz >>>> Reading input 2/3: wm.nii.gz >>>> Reading input 3/3: non_pv_corrected.nii.gz >>>> Reading design matrix and contrasts. >>>> Elapsed time parsing inputs: ~ 49.4836 seconds. >>>> Number of possible permutations is 1.08209e+27. >>>> Generating 100 shufflings (permutations only). >>>> Building null distribution. >>>> Number of possible permutations is 1.08209e+27. >>>> Generating 100 shufflings (permutations only). >>>> Building null distribution. >>>> Elapsed time with permutations: ~ 25120.2 seconds. >>>> Computing p-values. >>>> Saving p-values (uncorrected, and corrected within modality and within >>>> contrast). >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_fwep_m1_c1 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_fwep_m1_c2 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_fwep_m2_c1 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_fwep_m2_c2 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_fwep_m3_c1 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_fwep_m3_c2 >>>> Saving p-values (corrected across modalities). >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_mfwep_m1_c1 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_mfwep_m2_c1 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_mfwep_m3_c1 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_mfwep_m1_c2 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_mfwep_m2_c2 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_mfwep_m3_c2 >>>> Saving p-values (corrected across contrasts). >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_cfwep_m1_c1 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_cfwep_m1_c2 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_cfwep_m2_c1 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_cfwep_m2_c2 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_cfwep_m3_c1 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_cfwep_m3_c2 >>>> Saving p-values (corrected across modalities and contrasts). >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_mcfwep_m1_c1 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_mcfwep_m1_c2 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_mcfwep_m2_c1 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_mcfwep_m2_c2 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_mcfwep_m3_c1 >>>> Saving file: PALM_CCA/Non_PV_Corrected/resu >>>> lts_vox_tstat_mcfwep_m3_c2 >>>> Saving p-values for classical multivariate (uncorrected and corrected >>>> within contrast). >>>> Index exceeds matrix dimensions. >>>> >>>> Error in palm_competitive (line 113) >>>> unsrtR(:,c) = single(srtR(rev(:,c),c)); % original order as the data >>>> >>>> >>>> Error in palm_pareto (line 90) >>>> [~,Gdist,Gcdf] = palm_competitive(Gdist,'ascend',true); >>>> >>>> >>>> Error in palm_saveall (line 1349) >>>> Ptosave = >>>> palm_pareto(plm.Q{m}{c},plm.Qm >>>> ax{m}{c},plm.mvrev{m}{c},opts.accel.tail_thr,opts.accel.G1out); >>>> >>>> >>>> Error in palm_core (line 2484) >>>> palm_saveall(plm,opts); >>>> >>>> >>>> Error in palm (line 81) >>>> palm_core(varargin{:}); >>>> >>>> Looking forward to your reply. >>>> >>>> Thanks >>>> Regards >>>> Virendra >>>> >>>> >>>> On Thu, Aug 10, 2017 at 6:26 AM, Anderson M. Winkler < >>>> [log in to unmask]> wrote: >>>> >>>>> 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, >>>>>>>>> >>>>>>>>> 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 >>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>> >>>>>>>>>>>>>> >>>>>>>>>>>>> >>>>>>>>>>> >>>>>>>>>> >>>>>>>>> >>> >