Back to PLS HelpPosted on 09/06/18 21:51:21
Number of posts: 9
Hello,
I'm using fmriprep preprocessed data, and I want to verify that this is correct for PLS. I asked this question on NeuroStars, but I'm not sure how many PLS experts visit it (and so on). We can never be too sure.
fmriprep is great because you can have access to all the details about preprocessing steps: https://fmriprep.readthedocs.io/en/latest/workflows.html#bold-preprocessing
In sum (also from the website): "Functional data was motion corrected using mcflirt (FSL v5.0.9 [9]). "Fieldmap-less" distortion correction was performed by co-registering the functional image to the same-subject T1w image with intensity inverted [13,14] constrained with an average fieldmap template [15], implemented with antsRegistration (ANTs). This was followed by co-registration to the corresponding T1w using boundary-based registration [16] with 9 degrees of freedom, using bbregister (FreeSurfer v6.0.1).Motion correcting transformations, field distortion correcting warp, BOLD-to-T1w transformation and T1w-to-template (MNI) warp were concatenated and applied in a single step using antsApplyTransforms(ANTs v2.1.0) using Lanczos interpolation." https://fmriprep.readthedocs.io/en/latest/citing.html
Some preprocessing can be done after in FSL (or other software), no problem (e.g. my voxel size is 2.5 mm3, so smoothing could be 5mm3, right?).
Could I use my data preprocessed with fmriprep and maybe add some spatial smoothing for PLS analyses? (Also: If anyone has already done this and has tips, please let me know!)
Annick
Replies:
Posted on 09/07/18 06:30:37
Number of posts: 394
Hello,
I'm using fmriprep preprocessed data, and I want to verify that this is correct for PLS. I asked this question on NeuroStars, but I'm not sure how many PLS experts visit it (and so on). We can never be too sure.
fmriprep is great because you can have access to all the details about preprocessing steps: https://fmriprep.readthedocs.io/en/latest/workflows.html#bold-preprocessing
In sum (also from the website): "Functional data was motion corrected using mcflirt (FSL v5.0.9 [9]). "Fieldmap-less" distortion correction was performed by co-registering the functional image to the same-subject T1w image with intensity inverted [13,14] constrained with an average fieldmap template [15], implemented with antsRegistration (ANTs). This was followed by co-registration to the corresponding T1w using boundary-based registration [16] with 9 degrees of freedom, using bbregister (FreeSurfer v6.0.1).Motion correcting transformations, field distortion correcting warp, BOLD-to-T1w transformation and T1w-to-template (MNI) warp were concatenated and applied in a single step using antsApplyTransforms(ANTs v2.1.0) using Lanczos interpolation." https://fmriprep.readthedocs.io/en/latest/citing.html
Some preprocessing can be done after in FSL (or other software), no problem (e.g. my voxel size is 2.5 mm3, so smoothing could be 5mm3, right?).
Could I use my data preprocessed with fmriprep and maybe add some spatial smoothing for PLS analyses? (Also: If anyone has already done this and has tips, please let me know!)
Annick
Hi Annick - in general the same preprocessing that you would do for any analysis would be sppropriate for PLS. The only thing is that you don't need as much spatial smoothing as you might for univariate approaches, so what you propose for as spatial filter - twice the voxel size - should be okay.
cheers
Randy
Posted on 09/22/18 15:59:44
Number of posts: 9
Hi Randy,
Thank you for your reply.
Much appreciated.
Annick
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