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 > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
