That’s correct! --Greg ____________________________________________________________________ Greg Burgess, Ph.D. Staff Scientist, Human Connectome Project Washington University School of Medicine Department of Psychiatry Phone: 314-362-7864 Email: [email protected]
> On Aug 4, 2016, at 9:59 AM, Michael F.W. Dreyfuss <[email protected]> > wrote: > > Thank you for the quick reply. So essentially your recommendation is to use > FEAT for the subject level analyses (levels 1 and 2) and PALM for the group > analyses (level 3). Is that right? > > Unfortunately I will not be able to attend this year, but I look forward to > seeing those examples afterward. > > Thank you, > Michael > From: Burgess, Gregory <[email protected]> > Sent: Thursday, August 4, 2016 10:05:47 AM > To: Michael F.W. Dreyfuss > Cc: [email protected] > Subject: Re: [HCP-Users] PALM for Cifti data > > PALM isn’t intended to replace the level 1 (timeseries) analysis. Permutation > testing doesn’t handle the autocorrelated timeseries appropriately, because > time points are not truly exchangeable. > > > > It should be possible to do a repeated measures analysis in PALM (treating > acitvation estimates from each run as repeated measures). However, the > easiest use would be to use the output of the level 2 analyses as inputs to a > simple group-level random effects analysis. > > > > As an aside, if you’re attending the 2016 HCP Course in Boston > (https://urldefense.proofpoint.com/v2/url?u=https-3A__www.humanconnectome.org_courses_2016_exploring-2Dthe-2Dhuman-2Dconnectome.php&d=DQIGaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=f522JxvwVVfhjK8FuJh8M_y_NVR2c6KtnEBhDXM9mVo&s=rduAtqYT7Im5F6ssw1vH--GekVqzWTKfS7c0ZBo1EOg&e= > ), you will be able to go through a practical session on this! (We hope to > release the practicals to the public after the course, but that will likely > take some time to implement.) > > > > --Greg > > > > ____________________________________________________________________ > > Greg Burgess, Ph.D. > > Staff Scientist, Human Connectome Project > > Washington University School of Medicine > > Department of Psychiatry > > Phone: 314-362-7864 > > Email: [email protected] > > > > > On Aug 4, 2016, at 8:47 AM, Michael F.W. Dreyfuss <[email protected]> > > wrote: > > > > > > 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 > > > _______________________________________________ > > > HCP-Users mailing list > > > [email protected] > > > https://urldefense.proofpoint.com/v2/url?u=http-3A__lists.humanconnectome.org_mailman_listinfo_hcp-2Dusers&d=DQIGaQ&c=lb62iw4YL4RFalcE2hQUQealT9-RXrryqt9KZX2qu2s&r=rPclmYysc_z1plf99IoNsmxWf1JolkKMmL6bXnYFSwg&m=f522JxvwVVfhjK8FuJh8M_y_NVR2c6KtnEBhDXM9mVo&s=8-kM3d9NIuXk4DnyKq-H8gg3iihdinoRpdJHXUfRGU8&e= > > > > > > ________________________________ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. 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