Hi Anderson
I have already uploaded the data. Hope you can help us to deal with the
error.
Best
Paul
2016-09-06 14:52 GMT+08:00 Anderson M. Winkler <[log in to unmask]>:
> Hi Paul,
>
> Thanks for sending. Design and contrasts look fine. Perhaps it's an odd
> combination of values in the data (and perhaps with TFCE). If you could
> upload your data I would be happy to have a look. You should have just
> received an automated OxFile link for the upload. Please also include the
> statistic.fts file (i.e., the F-test).
>
> In any case, for this design and these options, except for the "-accel
> tail" (which where the error is arising), this analysis can be done in
> randomise, so maybe consider using it regardless of what the problem might
> be or when we will be able to figure it out. Thanks.
>
> All the best,
>
> Anderson
>
> PS: sorry for the typo in your name, I just noticed after having sent the
> link.
>
>
> On 5 September 2016 at 08:29, KUN HSIEN CHOU <[log in to unmask]>
> wrote:
>
>> Dear Anderson
>>
>> The following attached files are contrast and design file for the current
>> study. Due to the large sample size of the current study, it is very slow
>> when we try to paste the design into GLM gui, so we use text editor to
>> creat these two file (Maybe there are some error usage when we create these
>> two files).
>>
>> PS: For the statistic.mat. The first three colume are group lable (we
>> have three study groups in this study). The last two colume are demean age
>> and sex.
>>
>> Thanks very much.
>>
>>
>>
>> 2016-09-05 14:53 GMT+08:00 Anderson M. Winkler <[log in to unmask]>:
>>
>>> Hi Paul, hi Niels,
>>>
>>> PALM removes the NaN and Infs before starting so this shouldn't be the
>>> issue. However, depending on the values in the data, design and/or
>>> contrasts, new NaNs or Infs can be created during the analysis, leading to
>>> that error. One possibility is that the test is assessing whether the group
>>> mean is different than zero, which is always the case for GM volume,
>>> leading to statistics that approach infinity, then the error.
>>>
>>> Paul: could you show your design and contrasts? Thanks.
>>>
>>> All the best,
>>>
>>> Anderson
>>>
>>>
>>> On 5 September 2016 at 03:13, KUN HSIEN CHOU <[log in to unmask]>
>>> wrote:
>>>
>>>> For s2_GM_1197.nii : 0.000000 2.378755
>>>> For mask.nii: 0.000000 1.000000
>>>>
>>>> Best
>>>>
>>>> Paul
>>>>
>>>> 2016-09-05 6:37 GMT+08:00 Niels Bergsland <[log in to unmask]>:
>>>>
>>>>> What do you get if you run fslstats -R on your input image and mask?
>>>>>
>>>>>
>>>>> On Monday, September 5, 2016, KUN HSIEN CHOU <[log in to unmask]>
>>>>> wrote:
>>>>>
>>>>>> Hi
>>>>>>
>>>>>> The input data file and the corresponded mask file were also run
>>>>>> through fslmaths with the -nan option before entering into the PALM
>>>>>> software , but the error still occured.
>>>>>>
>>>>>> Best
>>>>>>
>>>>>> Paul
>>>>>>
>>>>>> 2016-09-05 1:05 GMT+08:00 Niels Bergsland <[log in to unmask]>:
>>>>>>
>>>>>>> Hi. I haven't had this issue myself but it sounds like you might
>>>>>>> need to run your input image through fslmaths with the -nan option.
>>>>>>>
>>>>>>> On Sun, Sep 4, 2016 at 4:57 PM, Paul Chou <[log in to unmask]>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Dear PALM developers
>>>>>>>>
>>>>>>>> I tried to perform permutation test for our VBM dataset (we use SPM
>>>>>>>> for VBM preprocessing) using PALM software. After running permutation test,
>>>>>>>> the error message comes out in the MATLAB command window. Could you help me
>>>>>>>> to deal with this error message ? In addtion, although the error message
>>>>>>>> occured, PALM still produced s2_ILAS_1197_vox_tstat.nii for each
>>>>>>>> statistical contrast.
>>>>>>>>
>>>>>>>> I use the following command for PALM analysis (We use the latest
>>>>>>>> version of PALM and Matlab R2012a.). The s2_GM_1197.nii contains 1197
>>>>>>>> subjects VBM preprocessed dataset.
>>>>>>>>
>>>>>>>> palm -i /mnt/HD2T/PLAM_statistic/S2_GM_1197/s2_GM_1197.nii -m
>>>>>>>> dartel4_mask.nii -d statistic.mat -t statistic.con -f statistic.fts -T -C
>>>>>>>> 2.58 -n 1500 -fdr -save1-p -accel tail -o /mnt/HD2T/PLAM_statistic/S2_GM
>>>>>>>> _1197/s2_ILAS_1197
>>>>>>>>
>>>>>>>> The following message is error message :
>>>>>>>> =======================================================
>>>>>>>> Computing p-values.
>>>>>>>> Error using griddedInterpolant
>>>>>>>> The coordinates of the input points must be finite values; Inf and
>>>>>>>> NaN are not permitted.
>>>>>>>>
>>>>>>>> Error in interp1>Interp1D (line 335)
>>>>>>>> F = griddedInterpolant(X,V(:,1),method);
>>>>>>>>
>>>>>>>> Error in interp1 (line 220)
>>>>>>>> Vq = Interp1D(X,V,Xq,method);
>>>>>>>>
>>>>>>>> Error in palm_pareto>andersondarling (line 195)
>>>>>>>> i2 = interp1(i1,ptable,A2,'linear','extrap');
>>>>>>>>
>>>>>>>> Error in palm_pareto (line 127)
>>>>>>>> A2pval = andersondarling(gpdpvals(ytail,apar,kpar),kpar);
>>>>>>>>
>>>>>>>> Error in palm_saveall (line 77)
>>>>>>>> plm.Gpperm{y}{m}{c}(1,t) =
>>>>>>>> palm_pareto(plm.G{y}{m}{c}(1,t
>>>>>>>> ),plm.Gperms{y}{m}{c}(:,t),false,opts.accel.tail_thr,opts.ac
>>>>>>>> cel.G1out);
>>>>>>>>
>>>>>>>> Error in palm_core (line 2476)
>>>>>>>> palm_saveall(plm,opts);
>>>>>>>>
>>>>>>>> Error in palm (line 81)
>>>>>>>> palm_core(varargin{:});
>>>>>>>> ==================================
>>>>>>>>
>>>>>>>> Thank you
>>>>>>>>
>>>>>>>> Paul
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> Niels Bergsland
>>>>>>> Integration Director
>>>>>>> Buffalo Neuroimaging Analysis Center
>>>>>>> 100 High St. Buffalo NY 14203
>>>>>>> [log in to unmask]
>>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>> --
>>>>> Niels Bergsland
>>>>> Integration Director
>>>>> Buffalo Neuroimaging Analysis Center
>>>>> 100 High St. Buffalo NY 14203
>>>>> [log in to unmask]
>>>>>
>>>>
>>>>
>>>
>>
>
