The first 5 will be the condition betas averaged across all runs. The other 28 are 4 skips * 4 runs = 16 3 polyfit (0,1,2) * 4 runs = 12
On 11/24/2023 11:14 AM, Deyan Mitev wrote:
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Hello Freesurfer Developers,
I want to extract the beta values for an fMRI dataset that I analyzed with FSFAST, so that I get one beta map (in the ras space) per condition/regressor. The dataset has 5 conditions/regressors specified in the paradigm file and each participant has 4 runs. I used the following commands when running FSFAST (example for left hemisphere):
mkanalysis-sess -analysis localiser.sm5.lh -surface fsaverage lh -fwhm 5 -paradigm parbench.par -event-related -spmhrf 0 -refeventdur 4 -polyfit 2 -nskip 4 -TR 2 -nconditions 5 -per-run -fsd bold
mkcontrast-sess -analysis localiser.sm5.lh -contrast right-vs-left -c 3 -c 5 -a 2 -a 4
selxavg3-sess -sf sessid -analysis localiser.sm5.lh
From the output when I navigate to PARTICIPANT_FOLDER/bold/localiser.sm5.lh and examine the beta file with mri_info, I get: mri_info beta.nii.gz --dim 163842 1 1 33
My understanding is that the first number is the actual beta values for a given regressor in ras space and the last number (33) is the different betas. From an archived post I found that the first N betas represent the first N conditions. Is that per run, or collapsed over runs? Or is it that the first five betas are the five conditions for run 1, the second five for run 2, etc until 20? What are the other nuisance regressors used to make the rest of the betas then?
Kind Regards, Deyan
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