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I have the same error that doesn't resolve with --mgh or mgz.
warning: excluding contrast file
/Volumes/mnu/MRI/XXX/NIFTI/FreeSurfer/rs-fMRI_AROMA/G3V0_Comparison/fc.MDseed.surf.rh/MD/G3V0_PALM.glmdir/group.effect/C.dat
since it has multiple rows
ER
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Hi FreeSurfer community,
I try to ues fspalm to correct multiple comparisons for a surface-based
thickness analysis. Below is the code I use:
python fspalm --glmdir Home/*/lh.group.glmdir --cft 1.3 --cwp .5
--onetail --name palm_onetail_1.3 --iters
You need the patch. See the docs here
https://surfer.nmr.mgh.harvard.edu/fswiki/FsPalm under Setting Up
On 12/16/2020 2:02 PM, Marina Fernández wrote:
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Dear experts,
When I was running permutations with fspalm an error appeared because it
couldn't find the
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Dear experts,
When I was running permutations with fspalm an error appeared because it
couldn't find the --sig2p-max option when using mri_surfcluster
internally. You can find below the terminal output.
How can I fix this error?
Thank you in advance
I think palm itself requires mgh or mgz files. I can't remember why we don't
convert it. You can run mri_glmfit with --mgz or --mgh (or just without
--nii.gz) and it should work.
On 9/9/2019 9:24 AM, Barbour, Tracy,M.D. wrote:
Hello Freesurfer community!
I am trying to run fspalm on surface ba
Hello Freesurfer community!
I am trying to run fspalm on surface based data. I have installed PALM, fspalm,
mri_surfcluster, and mri_volcluster.
This is my fspalm command:
fspalm --glmdir TEPSC.glmdir --cft 1.3 --twotail --name palm-twotail-1.3
--iters 1000 --2spaces --cwp .05
When I run the f
