...@wustl.edu
From: on behalf of Gail Rosenbaum
Date: Monday, July 2, 2018 at 4:42 PM
To: NEUROSCIENCE tim
Cc: hcp-users
Subject: Re: [HCP-Users] Blank p-value maps after running PALM on CIFTI files
Hi Tim,
Thanks for the clarification.
Here are the calls to palm for the separated subcortical
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
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,
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
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
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
