External Email - Use Caution Also, when I run the lme_mass_fit_EMinit, lme_mass_RgGrow, lme_mass_fit_Rgw,
I get a warning: Matrix is close to singular or badle scaled. Results may be inaccurate. RCOND=3e-21/ In parallel_function>make_general_channel/channel_general (line 914) In remoteParallelFunction (line 38). What could cause this warning? I am afraid my results will not be correct. Swati ____________________________________________ Swati Rane Levendovszky, PhD Interim Director, Diagnostic Imaging Sciences Center Assistant Professor, Integrated Brain Imaging Center Radiology University of Washington Box 357115 | AA035 HSB | Seattle, WA 98195 srle...@uw.edu<mailto:srle...@uw.edu> | Ph: 206 543 6159 Web: https://sites.google.com/site/uwswatirane/ ____________________________________________ From: Swati Rane <srle...@uw.edu> Date: Thursday, March 12, 2020 at 10:18 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] longitudinal FreeSurfer help Hi Kersten, Thanks for the reply. I think I am trying to understand the steps that follow. Do I have to check whether my model with 2 random effects (intercept and time) is better than that with one (intercept)? For the contrast I am interested in group wise longitudinal cortical thinning. And also, if the longitudinal thinning is different between groups. Given that my X=[intercept time grp1 time*grp1 grp2 time*grp2 grp3 time*grp3 age@timepoint1 gender] How do I set up CM? Do I need to run the lme_mass_F multiple time per contrast I provide? Will my CM be For Longitudinal thinning in grp 1: [1 0 0 1 0 0 0 0 0 0] For Longitudinal thinning in grp 2: [1 0 0 0 0 1 0 0 0 0] For Longitudinal thinning in grp 3: [1 0 0 0 0 0 0 1 0 0] For Longitudinal thinning difference grp 2 – grp 1: [1 0 0 -1 0 1 0 0 0 0]? Can you explain the CM set-up described in the tutorial? Thank you. Swati From: <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of "Diers, Kersten /DZNE" <kersten.di...@dzne.de> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Date: Thursday, March 12, 2020 at 5:19 AM To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] longitudinal FreeSurfer help External Email - Use Caution Hello Swati, your points 1-4 look fine, as far as I can see. Regarding 5, the recommended spatiotemporal mass-univariate approach consists of calling three functions: lme_mass_fit_EMinit, lme_mass_RgGrow, lme_mass_fit_Rgw in that order. If that does not work, it is in my eyes possible to use the more simple mass-univariate approach using lme_mass_fit_vw as an alternative. Regarding 6, which specific questions do you have? Best regards, Kersten On Do, 2020-03-12 at 05:58 +0000, Swati Rane wrote: External Email - Use Caution Dear FreeSurfer experts, I simply do not understand the LME setup for longitudinal analyses. Here is what I have: 3 groups each with variable longitudinal data (in terms of umber of time points and interval between timepoints). I am interested in detecting if the rates of longitudinal atrophy in each of the 3 groups and whether it is significantly different between the 3 groups. 1. My Qdec file contains: fsid, fsid_base, time, age, group, gender 2. I read in the relevant files with (output of surf2surf, lh.cortex, lh.sphere) 3. I read the Qdec file removed the first column, obtained the subject IDs, keep numerical data and get a sorted ‘M’ matrix 4. X=[intercept time grp1 time*grp1 grp2 time*grp2 grp3 time*grp3 age@timepoint1 gender] 5. After that, should I use voxel wise mass-univariate model or spatiotemporal mass-univariate model lme_mass_fit_vw or lme_mass_fit_EMinit? 6. After that I don’t understand the subsequent steps. Can you help me understand? Any help is appreciated. Thanks! Swati _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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