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help > RE: Band-pass filter before denoising (to use rshrf toolbox)
Dec 4, 2018 04:12 PM | Alfonso Nieto-Castanon - Boston University
RE: Band-pass filter before denoising (to use rshrf toolbox)
Dear Stephen,
That is a very good question. My impression is that the best place to apply the hrf-estimation and deconvolution step would be after the standard denoising step (including aCompCor, scrubbing, and band-pass filtering). The rsHRF implementation code seems to similarly apply a number of denoising/regression steps before actually estimating the hrf, which I imagine are aimed at reducing possible biases in the hrf estimation step due to residual motion and physiological artifacts.
In practical terms, I would probably suggest to process your data normally in Setup & Denoising, and have CONN export the denoised nifti files, then use the rsHRF toolbox to estimate and deconvolve the hrf on these nifti files, and then re-import the output files into CONN in Setup (but this time skipping CONN denoising steps entirely). I will see if I can provide some simple functionality to extend CONN's default denoising procedures in the next release to simplify this procedure, but in the meantime I believe this should work just fine. Please let me know your thoughts/comments and/or if you run into any issues
Hope this helps
Alfonso
Originally posted by Stephen L.:
That is a very good question. My impression is that the best place to apply the hrf-estimation and deconvolution step would be after the standard denoising step (including aCompCor, scrubbing, and band-pass filtering). The rsHRF implementation code seems to similarly apply a number of denoising/regression steps before actually estimating the hrf, which I imagine are aimed at reducing possible biases in the hrf estimation step due to residual motion and physiological artifacts.
In practical terms, I would probably suggest to process your data normally in Setup & Denoising, and have CONN export the denoised nifti files, then use the rsHRF toolbox to estimate and deconvolve the hrf on these nifti files, and then re-import the output files into CONN in Setup (but this time skipping CONN denoising steps entirely). I will see if I can provide some simple functionality to extend CONN's default denoising procedures in the next release to simplify this procedure, but in the meantime I believe this should work just fine. Please let me know your thoughts/comments and/or if you run into any issues
Hope this helps
Alfonso
Originally posted by Stephen L.:
Dear Alfonso, dear CONN users,
I would like to use the rshrf toolbox to deconvolve the haemodynamic response function: https://github.com/compneuro-da/rsHRF
Unfortunately, it requires a bandpass filter to work. I have thus two options to apply in an analysis pipeline with CONN:
* Either after preprocessing, thus CONN would receive as input functional files already bandpass filtered images (and hrf deconvolved). Can this impact the CompCor denoising or is this OK?
* Either after CONN denoising, but then I have no idea how I can make CONN use the denoised+deconvolved files instead of just denoised, as CONN provides no way to specify custom additional post-processing steps (feature request? ;-) ). However, even if there was a way to do it after denoising, I think the denoising can remove important information to estimate the hrf, so this is probably not the best avenue (but that's only my thoughts?).
Does someone have any suggestion of what would be the best avenue, or the most correct technically?
Thank you very much in advance!
Best regards,
Stephen
I would like to use the rshrf toolbox to deconvolve the haemodynamic response function: https://github.com/compneuro-da/rsHRF
Unfortunately, it requires a bandpass filter to work. I have thus two options to apply in an analysis pipeline with CONN:
* Either after preprocessing, thus CONN would receive as input functional files already bandpass filtered images (and hrf deconvolved). Can this impact the CompCor denoising or is this OK?
* Either after CONN denoising, but then I have no idea how I can make CONN use the denoised+deconvolved files instead of just denoised, as CONN provides no way to specify custom additional post-processing steps (feature request? ;-) ). However, even if there was a way to do it after denoising, I think the denoising can remove important information to estimate the hrf, so this is probably not the best avenue (but that's only my thoughts?).
Does someone have any suggestion of what would be the best avenue, or the most correct technically?
Thank you very much in advance!
Best regards,
Stephen
Threaded View
| Title | Author | Date |
|---|---|---|
| Stephen L. | Nov 29, 2018 | |
| Alfonso Nieto-Castanon | Dec 4, 2018 | |
| Stephen L. | Dec 4, 2018 | |
| Alfonso Nieto-Castanon | Dec 4, 2018 | |
| Stephen L. | Dec 5, 2018 | |