Please name your tstat and p-value outputs ending in .func.gii, not simply
.gii .  This will allow you to open them in wb_view directly, allowing you
to do sanity checks with fewer intervening steps.  However, from what you
have said, I am fairly certain they are entirely 0s (you can use wb_command
-file-information to check the range of the maps, and any non-numeric
values, once you have named your outputs ending in .func.gii).  I am not
sure how to check whether PALM was called with meaningful inputs that would
be expected to give significant results.

On a side note, by using -cifti-create-dense-scalar without specifying ROIs
for right and left cortex, you have generated CIFTI files that include the
medial wall, and do not match the 91k grayordinates of HCP data.  I am
guessing that your subcortical labels are in fact the same as the HCP 91k
grayordinate subcortical labels, so I suggest you use
-cifti-create-dense-from-template, which makes it easier to match an
existing specification of grayordinates.

Tim



On Mon, Jul 2, 2018 at 3:17 PM, Gail Rosenbaum <[email protected]>
wrote:

> Hi,
>
> I am trying to run PALM with TFCE on dense timeseries CIFTI files created
> through an HCP-style protocol, and preprocessed using the HCP pipeline
> (version 3.22).  I am running these analyses on an HPC using SLURM.
>
> It seems that I successfully ran PALM (there were no warnings or errors).
> When I use -cifti-create-dense-scalar to merge the subcortical and cortical
> output files, my t-statistic maps look fine in wb_view. However, when I use
> the same code to merge the fwep and uncp maps and open them in wb_view,
> they appear to be completely empty (and the range of values when I turn on
> the color bar is just 0). I have tried using workbench versions 1.2.3 and
> 1.3.0.
>
> For reference, here is the command that I used to successfully merge the
> t-stat files:
>
> wb_command -cifti-create-dense-scalar 
> mbmfGroup${contrast}_results_merged_tfce_tstat.dscalar.nii
> -volume mbmfResults${contrast}_vol_tfce_tstat.nii data_sub_label.nii
> -left-metric mbmfResults${contrast}_SurfL_tfce_tstat.gii -right-metric
> mbmfResults${contrast}_SurfR_tfce_tstat.gii
>
> And here is the command I used for the (seemingly) unsuccessful p-value
> maps:
>
> wb_command -cifti-create-dense-scalar mbmfGroup${contrast}_results_
> merged_tfce_tstat_fwep.dscalar.nii -volume 
> mbmfResults${contrast}_vol_tfce_tstat_fwep.nii
> data_sub_label.nii -left-metric 
> mbmfResults${contrast}_SurfL_tfce_tstat_fwep.gii
> -right-metric mbmfResults${contrast}_SurfR_tfce_tstat_fwep.gii
>
> My first thought was that there were no significant results, but since the
> t-maps seem reasonable and even the uncorrected p-maps are empty
> (presumably if nothing were signifiant, these uncorrected p-values would
> not 0), I think something must have gone wrong.
>
> Any insights into what might be going on would be appreciated! Thank you!
>
> Gail Rosenbaum
>
> --
> Gail Rosenbaum, PhD
> Postdoctoral Fellow | Hartley Lab
> New York University
>
> _______________________________________________
> HCP-Users mailing list
> [email protected]
> http://lists.humanconnectome.org/mailman/listinfo/hcp-users
>

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