Hi Michael,

Please see an example in this page: https://fsl.fmrib.ox.ac.uk/fsl
/fslwiki/PALM/Examples

The Example 9 is for simple statistics on brainordinates (no spatial
statistics) and Example 10 is for TFCE and cluster-level inference.

Thanks to Tim Coalson for the help with the wb_command options.

Hope this helps!

All the best,

Anderson


On 15 September 2016 at 07:21, Anderson M. Winkler <wink...@fmrib.ox.ac.uk>
wrote:

> Hi Michael,
>
> TFCE needs to be run separately for the surface-based and for the
> volume-based parts of the CIFTI file. This means that the input file has to
> be separated using wb_command, then PALM be executed, then the results need
> to be corrected via Bonferroni or Šidák. I will add hopefully today still a
> section in the documentation with the steps and update here.
>
> Also, although it's unrelated to this error, Donna is right: the extension
> for the -t option wasn't supplied correctly.
>
> All the best,
>
> Anderson
>
>
> On 15 September 2016 at 06:22, Michael F.W. Dreyfuss <
> mid2...@med.cornell.edu> wrote:
>
>> Thank you,
>>
>>
>> The $ContrastName is the argument of the -o option, so it is just the
>> name designated for the output. There are no csv files unless you mean the
>> .mat and .con files which are the arguments of -d and -t respectively for
>> the design files and contrast files. Since it is a group average, it
>> actually runs without the contrast file as well.
>>
>>
>> Again, this whole command runs fine and gives reasonable output with the
>> -fdr flag instead of -T, but I would like to be able to run TFCE here. Has
>> the -T option been used with palm on cifti data successfully? Maybe it is
>> not meant is only for use on volumetric data?
>>
>>
>> Thanks a lot,
>>
>> Michael
>> ------------------------------
>> *From:* Dierker, Donna <do...@wustl.edu>
>> *Sent:* Wednesday, September 14, 2016 11:09:04 PM
>> *To:* Michael F.W. Dreyfuss
>> *Cc:* hcp-users@humanconnectome.org
>> *Subject:* Re: [HCP-Users] Palm with TFCE on Cifti data
>>
>> Michael, if $ContrastName is a csv file, make sure its extension is csv.
>> I’ve gotten errors like that before when I named it .con.
>>
>>
>>
>>
>>
>> > On Sep 14, 2016, at 11:29 AM, Michael F.W. Dreyfuss <
>> mid2...@med.cornell.edu> 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
>>
>> > _______________________________________________
>>
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>>
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>>
>>
>>
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