Hi
> (1) nuisance regression (WM, CSF)
>
> 1-a). With the WM, we can do:
>
> flirt -in WM_mask_in_highres_space \
> -applyxfm \
> -init rest.feat/reg/highres2example_func.mat\
> -ref example_func.nii.gz \
> -out WM_in_func_space
>
> fslmaths WM_in_func_space –bin WM_mask_in_func_space
>
> fslmeants -i filtered_func_data.nii.gz -m WM_mask_in_func_space -o WM_in_func_bin_timeseries
>
2 comments: first, there is no necessity to binarise the WM mask per se. If you start with the pve map for WM thenthe relative proportions reflect the confidence at each voxel of it being WM and you might want to incorporate that information by using a weighted mask so that voxels where you’re very confident that it’s a WM voxel weight more strongly than a voxel where segmentation is less clear.
Secondly you may wont to erode the mask, in order to remove the influence of voxels at the GM/WM boundary. You can do this with fslmaths in -ero out
> Question: We should use filtered_func_data (but not ICA-AROMA-denoised_func_data) as input, correct?
>
No, you would want to use the AROMA-denoised data and then add further denoising to it, not to the filtered_func_data
> 1-b). We can use similar procedure as above to obtain CSF_in_func_bin_timeseries
>
Yes, but the same comments apply
> 1-c). To regress out these two nuisance regressors:
>
> paste WM_in_func_bin_timeseries CSF_in_func_bin_timeseries > nuisance_timeseries
>
> fsl_glm –i denoised_func_data –d nuisance_timeseries –dat_norm –res_out=residual
>
> Questions: The residual is the file with these nuisance regressed out, correct? We should use –dat_norm, correct? (Or –des_norm? What’s their difference?)
>
You also want to switch on demeaning. The des/dat norm is irrelevant as you’re not using the betas but the residuals for further processing. Depending on what you want to do with the residuals later you also need to re-add the mean so it looks like a firm data set
> (2) Linear detrending
>
> The standard procedure of linear detrending in FSL is done via highpass filtering. How to perform linear detrending as suggested in the ICA-AROMA paper? Many thanks!!
>
use fslmaths with the -bptf option, it will also remove the linear trend
hth
Christian
> (3) highpass filtering
>
> Since my TR = 2.0 s and I want highpass filtering of 100 second, this means 50 TR (volume), and thus highpass sigma is 25.0 TR (volumes).
>
> fslmaths input -bptf 25.0 -1 output
>
> Is that correct?
>
> Best,
> Daniel
>
> From: "[log in to unmask]" <[log in to unmask]> on behalf of Daniel Yang <[log in to unmask]>
> Reply-To: "[log in to unmask]" <[log in to unmask]>
> Date: Wednesday, September 2, 2015 at 1:13 AM
> To: "[log in to unmask]" <[log in to unmask]>
> Subject: [FSL] ICA-AROMA questions: the preprocessing steps after ICA-AROMA
>
> Dear all,
>
> In ICA-AROMA steps, after ICA-AROMA, it is suggested that we do:
>
> Nuisance regression: WM, CSF, & linear trend
> Highpass filtering
>
> Could we please provide details how these two can be properly done (e.g., via bash scripts)?
>
> Many thanks!
> Daniel
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