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
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