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Hi Experts,
After completing long_mris_slopes to get the rate of change and then concatenating them into one.mgh file for group analysis (mris_preproc). I am finally getting to mris_glmfit. Got a couple of questions along the way. 1). if I conducted long_mris_slopes, and got for example, lh.long.thickness-rate.fwhm10.fsaverage.mgh. Do I need to do a surface smoothing again (mri_surf2surf) before mris_glmfit? 2). I construct covariates in FSGD besides the group contrast that I am interested in. How do I add covariates into the glmfit model to control for the covariates as I contrast groups in terms of the rate of changing (CV vs. NCV groups) . Do I add them into --C as (1, -1, 0(age), 0(gender), 0(race)). mri_glmfit --y {$hemi}.{$meas}-rate.{$smoothness}.mgh --fsgd FSGD/{$study}.fsgd doss --C Contrasts/CV-NCV.mtx (1, -1) --C Contrasts/NCV-CV.mtx (-1, 1) --surf fsaverage {$hemi} --cortex --glmdir {$hemi}.{$meas}-rate.{$study}.{$smoothness}.glmdir
Best, Zeno
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Hi Freesurfer Experts,
Just a follow-up on the questions I asked last week and tested if the questions get through to the list. Thanks for your help in advance!
Best, Zeno
On Fri, Oct 29, 2021 at 10:39 PM Zeng, Qi qi.zeng@icahn.mssm.edu wrote:
Hi Experts,
After completing long_mris_slopes to get the rate of change and then concatenating them into one.mgh file for group analysis (mris_preproc). I am finally getting to mris_glmfit. Got a couple of questions along the way. 1). if I conducted long_mris_slopes, and got for example, lh.long.thickness-rate.fwhm10.fsaverage.mgh. Do I need to do a surface smoothing again (mri_surf2surf) before mris_glmfit? 2). I construct covariates in FSGD besides the group contrast that I am interested in. How do I add covariates into the glmfit model to control for the covariates as I contrast groups in terms of the rate of changing (CV vs. NCV groups) . Do I add them into --C as (1, -1, 0(age), 0(gender), 0(race)). mri_glmfit --y {$hemi}.{$meas}-rate.{$smoothness}.mgh --fsgd FSGD/{$study}.fsgd doss --C Contrasts/CV-NCV.mtx (1, -1) --C Contrasts/NCV-CV.mtx (-1, 1) --surf fsaverage {$hemi} --cortex --glmdir {$hemi}.{$meas}-rate.{$study}.{$smoothness}.glmdir
Best, Zeno
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On 10/29/2021 10:39 PM, Zeng, Qi wrote:
External Email - Use Caution
Hi Experts,
After completing long_mris_slopes to get the rate of change and then concatenating them into one.mgh file for group analysis (mris_preproc). I am finally getting to mris_glmfit. Got a couple of questions along the way. 1). if I conducted long_mris_slopes, and got for example, lh.long.thickness-rate.fwhm10.fsaverage.mgh. Do I need to do a surface smoothing again (mri_surf2surf) before mris_glmfit?
No
2). I construct covariates in FSGD besides the group contrast that I am interested in. How do I add covariates into the glmfit model to control for the covariates as I contrast groups in terms of the rate of changing (CV vs. NCV groups) . Do I add them into --C as (1, -1, 0(age), 0(gender), 0(race)). mri_glmfit --y {$hemi}.{$meas}-rate.{$smoothness}.mgh --fsgd FSGD/{$study}.fsgd doss --C Contrasts/CV-NCV.mtx (1, -1) --C Contrasts/NCV-CV.mtx (-1, 1) --surf fsaverage {$hemi} --cortex --glmdir {$hemi}.{$meas}-rate.{$study}.{$smoothness}.glmdir
Not sure what you mean here. Your FSGD file will translate into a design matrix. Each column in the design matrix means something (eg, group membership, covariate of a group). You need to create a contrast matrix that embodies your hypothesis. There needs to be an item in the contrast matrix for each column in the design matrix. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples for more info
Best, Zeno
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Zeng, Qi