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

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