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help > RE: Are white matter and CSF confounds saved as files?
Mar 19, 2020 01:03 AM | Alfonso Nieto-Castanon - Boston University
RE: Are white matter and CSF confounds saved as files?
Hi Matt,
yes, the order looks perfectly fine; you seem to have realigned first ('u prefix), then skippped slice-timing correction and proceeded to MNI-normalization directly ('w' prefix), then applied functional smoothing ('s' prefix), and last applied denoising ('dp_*.txt' output files). If you followed that sequence then your aCompCor regions are being defined from the MNI-space segmentation masks, which is perfectly fine since your functional data at that point is also in MNI-space. In general, if you apply denoising (or just create the denoising dp_*.txt files) after any of CONN standard preprocessing pipelines you should be perfectly fine (those pipelines always make sure that the aCompCor regions and the functional data are properly coregistered)
Best
Alfonso
Originally posted by Matthew Heard:
yes, the order looks perfectly fine; you seem to have realigned first ('u prefix), then skippped slice-timing correction and proceeded to MNI-normalization directly ('w' prefix), then applied functional smoothing ('s' prefix), and last applied denoising ('dp_*.txt' output files). If you followed that sequence then your aCompCor regions are being defined from the MNI-space segmentation masks, which is perfectly fine since your functional data at that point is also in MNI-space. In general, if you apply denoising (or just create the denoising dp_*.txt files) after any of CONN standard preprocessing pipelines you should be perfectly fine (those pipelines always make sure that the aCompCor regions and the functional data are properly coregistered)
Best
Alfonso
Originally posted by Matthew Heard:
Thanks for the recommendation, Alfonso. I was
able to run the code. It looks to have created a series of .txt
files for each run per subject with the prefix "dp_" as you
said.
One question about the white matter and CSF regressors, should I construct the regressors from the fully preprocessed files (i.e. after smoothing, normalization, and realignment)? The full name of the output files is "dp_swuepi_run1.nii" so I wanted to make sure that this was the correct order to run the pipeline.
Thanks,
Matt
One question about the white matter and CSF regressors, should I construct the regressors from the fully preprocessed files (i.e. after smoothing, normalization, and realignment)? The full name of the output files is "dp_swuepi_run1.nii" so I wanted to make sure that this was the correct order to run the pipeline.
Thanks,
Matt
Threaded View
| Title | Author | Date |
|---|---|---|
| Matthew Heard | Mar 13, 2020 | |
| Alfonso Nieto-Castanon | Mar 13, 2020 | |
| Matthew Heard | Mar 16, 2020 | |
| Alfonso Nieto-Castanon | Mar 19, 2020 | |
| Matthew Heard | Mar 18, 2020 | |