Hi Tim,
Thanks for the clarification.
Here are the calls to palm for the separated subcortical and cortical
files:
palm -i data_sub.nii -d ${StudyFolder}Level3/L3Setup.mat -t
${StudyFolder}Level3/L3Setup.con -o mbmfResults${contrast}_vol -T -logp
palm -i data_L.func.gii -d ${StudyFolder}Level3/L3Setup.mat -t
${StudyFolder}Level3/L3Setup.con -o mbmfResults${contrast}_SurfL -T -tfce2D
-s ${StudyFolder}Level3/mbmfGroup_L.midthick.surf.gii
${StudyFolder}Level3/L_area.func.gii -logp
palm -i data_R.func.gii -d ${StudyFolder}Level3/L3Setup.mat -t
${StudyFolder}Level3/L3Setup.con -o mbmfResults${contrast}_SurfR -T -tfce2D
-s ${StudyFolder}Level3/mbmfGroup_R.midthick.surf.gii
${StudyFolder}Level3/R_area.func.gii -logp
For this analysis, I am simply trying to take the mean of the activation to
see if any clusters are significantly greater than baseline. The design
matrix (L3Setup.mat) is a 36x1 matrix (there are 36 subjects in my current
analysis) and the t- L3Setup.con is just a 1. Maybe I set this up
incorrectly?
Thanks,
Gail
On Mon, Jul 2, 2018 at 5:27 PM, Timothy Coalson <[email protected]> wrote:
> 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_t
>> stat_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
>>
>
>
--
Gail Rosenbaum, PhD
Postdoctoral Fellow | Hartley Lab
New York University
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