As you have found, the outputs from PALM contain only 0s, therefore using a different wb_command operation to convert them will not help with your current issue.
If you can post the PALM call you used, it might help others who know PALM figure out what your problem might be. Tim On Mon, Jul 2, 2018 at 4:12 PM, Gail Rosenbaum <[email protected]> wrote: > Hi Tim, > > Thank you for your quick reply. > > I renamed the maps and confirmed that there are no values in the maps (I > pasted the output of wb_command -file-information for the left hemisphere > output below in case that is useful). > > Regarding -cifti-create-dense-from-template: I used this command in the > first iteration of my analyses and had the same issue. I switched to > -cifti-create-dense-scalar to see if it would work (and because this is the > suggested command and usage in the "HCP Practical 11: Task fMRI Analyses" > pdf) and again did not have any luck. That being said, I'm new to CIFTI > files so I appreciate the usage suggestions, and I will try > -cifti-create-dense-scalar and specify ROIs, but I am not sure this will > help this issue because using a full template produced the same issue. > > Thanks, > Gail > > Output of wb_command -file-information: > > Name: mbmfResultsAllRPE3_SurfL_dpv_tstat_uncp.func.gii > Type: Metric > Structure: CortexLeft > Data Size: 129.97 Kilobytes > Maps to Surface: true > Maps to Volume: false > Maps with LabelTable: false > Maps with Palette: true > All Map Palettes Equal: true > Map Interval Units: NIFTI_UNITS_UNKNOWN > Number of Maps: 1 > > Number of Vertices: 32492 > Map Minimum Maximum Mean Sample Dev % Positive % Negative > Inf/NaN Map Name > 1 0.000 0.000 0.000 0.000 0.000 0.000 > 0 #1 > > On Mon, Jul 2, 2018 at 4:45 PM, Timothy Coalson <[email protected]> wrote: > >> 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${contrast}_results_m >>> erged_tfce_tstat_fwep.dscalar.nii -volume >>> mbmfResults${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 >>> >> >> > > > -- > Gail Rosenbaum, PhD > Postdoctoral Fellow | Hartley Lab > New York University > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
