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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