Hi, I am trying to adapt palm into my analysis scripts upon your recommendation
and I have a few questions:
1) Does this function essentially like FEAT/film_gls? That is, should I be
running PALM for level 1 (run), level 2 (subject) and level 3 (group) analyses,
or just at one of these levels?
2) Are there any examples available of how I can work palm in place of film_gls
in existing HCP processing scripts? I'm thinking of lines like the following:
#Run film_gls on subcortical volume data
film_gls --rn=${FEATDir}/SubcorticalVolumeStats --sa --ms=5
-in=${FEATDir}/${LevelOnefMRIName}_AtlasSubcortical"$TemporalFilterString""$SmoothingString".nii.gz
--pd="$DesignMatrix" --con=${DesignContrasts} --fcon=${DesignfContrasts}
--thr=1 --mode=volumetric
rm
${FEATDir}/${LevelOnefMRIName}_AtlasSubcortical"$TemporalFilterString""$SmoothingString".nii.gz
3) Can I simply use the same design files produces by feat_model from my fsf
files? Such as done at the line:
feat_model ${FEATDir}/design ${ResultsFolder}/${LevelOnefMRIName}/${Confound}
4) For motion, is it recommended to you detrended regressors on non-detrended
regressors?
Sorry for all the questions but I am finding few examples available of how this
is implemented practically.
Thank you,
Michael Dreyfuss
MD-PhD Student
Weill Cornell Medical College
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