This is occurring at the subject level, specifically during the second level analysis that combines individual within-subject runs.
And yes I may have initially included null EVs in the f-contrasts, and am now going to try only including existing EVs in within-run f-tests.
Will I then be able to combine contrasts across runs (within-subject), i.e. a contrast in one run that contains a given EV that may not exist in the second run, or vice versa?
Thanks,
Binyam
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Matthew Webster
Sent: Monday, August 13, 2018 5:37 AM
To: [log in to unmask]
Subject: Re: [FSL] modelling null or missing EVs in a feat fsf file
Hello,
Is this problem occurring during the subject-level or higher-level processing? Do any of the f-contrasts at subject-level involve these null EVs?
Kind Regards
Matthew
--------------------------------
Dr Matthew Webster
FMRIB Centre
John Radcliffe Hospital
University of Oxford
On 8 Aug 2018, at 22:09, Binyam Nardos <[log in to unmask]<mailto:[log in to unmask]>> wrote:
Hello,
I am using the HCP pipeline’s task fMRI scripts to process task fMRI data in CIFTI format.
My task is loosely structured as such:
BOLD 1: contains EV1, EV2, EV3
BOLD 2: contains EV1, EV3, EV4
BOLD 3: contains: EV2, EV5, EV6
As you can see, not every EV is present in every run. My initial approach when creating the fsf files was to model existing EVs in a given run using the 3 column file input format, and model EVs that don’t exist in a particular run (e.g. EV6 in BOLD 1) as a null EV using the “Empty (all zeros) option. Using this setup, I am unable to create copes nor conduct ftests. I get an error during level 2 of the task fMRI processing script saying some of the contrasts are not linearly independent (or are a linear sum of other contrasts).
Can you please advise whether all EVs (1 to 6 in the above case) need to be modeled in the design matrix/fsf to enable subsequent second level analyses across runs then subjects etc? If so, what is the appropriate way to model an EV that is not present in a given run?
Thank you.,
Binyam
Binyam Nardos, PhD
Oregon Health and Science University
Postdoctoral Researcher, Fair Neuroimaging Lab
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