Group Level Analysis Across Different Numbers of Runs

Hi,

I posted this to the FSL forum but haven’t gotten any replies yet: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;eb9b924d.2001

We have a fMRI task that has two runs of a task. Some subjects have a lot of head motion in one run of the task so we exclude those runs.

What we want to know is when running our higher level analysis with 3d cope images as the input, should we be concerned about mixing images where some were derived from analysis of one run (Lv. 1 analyses) and others derived from two runs (Lv. 2 analyses)?

For example my list of inputs looks like:
data/sub-001_L1_task-trust_model-01_type-act_run-02.feat/stats/cope1.nii.gz
data/sub-002_L2_task-trust_model-01_type-act.gfeat/cope1.feat/stats/cope1.nii.gz
data/sub-003_L1_task-trust_model-01_type-act_run-01.feat/stats/cope1.nii.gz
data/sub-012_L2_task-trust_model-01_type-act.gfeat/cope1.feat/stats/cope1.nii.gz
data/sub-004_L2_task-trust_model-01_type-act.gfeat/cope1.feat/stats/cope1.nii.gz
data/sub-005_L2_task-trust_model-01_type-act.gfeat/cope1.feat/stats/cope1.nii.gz
data/sub-006_L2_task-trust_model-01_type-act.gfeat/cope1.feat/stats/cope1.nii.gz
data/sub-007_L2_task-trust_model-01_type-act.gfeat/cope1.feat/stats/cope1.nii.gz
data/sub-008_L2_task-trust_model-01_type-act.gfeat/cope1.feat/stats/cope1.nii.gz
data/sub-009_L2_task-trust_model-01_type-act.gfeat/cope1.feat/stats/cope1.nii.gz
data/sub-010_L2_task-trust_model-01_type-act.gfeat/cope1.feat/stats/cope1.nii.gz
data/sub-011_L2_task-trust_model-01_type-act.gfeat/cope1.feat/stats/cope1.nii.gz
data/sub-012_L2_task-trust_model-01_type-act.gfeat/cope1.feat/stats/cope1.nii.gz

We were looking through Jeannette Mumford’s guide on calculating percent change and wondering if there could be a similar issue with respect to scaling of the betas?

Thanks everyone!

Best,
Caleb

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