For completeness since the same question was cross-posted here, there are
now two examples in the wiki about CIFTI: https://fsl.fmrib.ox.ac.uk/
fsl/fslwiki/PALM/Examples
Example 9 is for simple statistics on brainordinates (no spatial
statistics) and Example 10 is for TFCE and cluster-level inference.
On 15 September 2016 at 07:21, Anderson M. Winkler <[log in to unmask]>
wrote:
> I've just replied to this in the HCP list (and will update here too when
> the documentation is ready).
>
> On 14 September 2016 at 18:28, Michael F.W. Dreyfuss <
> [log in to unmask]> wrote:
>
>> Hello, I am trying to run palm on cifti data with TFCE to find mean
>> activation across a group. When I use the -T flag, the program crashed with
>> the error:
>>
>> Command:
>> palm -i ${ContrastName}.dtseries.nii -transposedata -d
>> $LevelThreeFEATDir/design.mat -o $ContrastName -t
>> /tmp/CtxFGNG/CtxFGNG_Level3_Analysis/desion -T -ise
>>
>> Error:
>> 0.01% [Design 1/1, Contrast 1/1, Shuffling 1/10000, Modality 1/1]
>> Saving file: FoodNogo_dat_tstat
>> Index exceeds matrix dimensions.
>>
>> Error in palm_tfce (line 77)
>> elseif plm.Yisvtx(y) || plm.Yisfac(y),
>>
>> Error in palm_core (line 1680)
>> Gtfce{y}{m}{c} =
>> tfcefunc(G{y}{m}{c},y,opts,plm);
>>
>> Error in palm (line 81)
>> palm_core(varargin{:});
>>
>>
>> Alternatively, if I use the same command, but replace -T with -fdr, the
>> program runs smoothly, so I do not think the problem is with my design
>> files or data unless they need to be generated in a special way for TFCE
>> using palm. Are there any recommendation or previous examples of how I can
>> use TFCE on cifti data using palm?
>>
>> Any help on this is very appreciated.
>>
>> Thank you,
>> Michael
>>
>
>
