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help > RE: aCompCor in batch processing
Aug 28, 2015 02:08 AM | Alfonso Nieto-Castanon - Boston University
RE: aCompCor in batch processing
Hi Kelli,
As far as I can tell the script looks perfectly fine. Could you please clarify what you mean by "the denoised scans appear to retain WM and CSF noise"? If in doubt, in the CONN gui load your project and go to the Denoising tab. Check there if in the 'confounds' list contains the default parameters (typically White, CSF, realignment, scrubbing, rest). If it does, then the denoised scans will have removed all of those effects from every voxel timeseries.
Best
Alfonso
Originally posted by Kelli Cannon:
As far as I can tell the script looks perfectly fine. Could you please clarify what you mean by "the denoised scans appear to retain WM and CSF noise"? If in doubt, in the CONN gui load your project and go to the Denoising tab. Check there if in the 'confounds' list contains the default parameters (typically White, CSF, realignment, scrubbing, rest). If it does, then the denoised scans will have removed all of those effects from every voxel timeseries.
Best
Alfonso
Originally posted by Kelli Cannon:
Hello,
I have written a script implementing the conn_batch function to process my resting state data. I have left the batch.Preprocessing.confounds fields out of the script in attempt to default to using aCompCor and realignment first-level covariates. However, the denoised scans (niftiDATA_Subject001_Condition000.nii) created appear to retain WM and CSF noise, which I thought aCompCor would have removed. Does leaving the batch.Preprocessing.confounds fields out actually default to using aCompCor? If so, why might my denoised images retain this WM/CSF noise? My script is attached for your review.
Best regards,
Kelli Cannon
I have written a script implementing the conn_batch function to process my resting state data. I have left the batch.Preprocessing.confounds fields out of the script in attempt to default to using aCompCor and realignment first-level covariates. However, the denoised scans (niftiDATA_Subject001_Condition000.nii) created appear to retain WM and CSF noise, which I thought aCompCor would have removed. Does leaving the batch.Preprocessing.confounds fields out actually default to using aCompCor? If so, why might my denoised images retain this WM/CSF noise? My script is attached for your review.
Best regards,
Kelli Cannon
Threaded View
| Title | Author | Date |
|---|---|---|
| Kelli Cannon | Aug 26, 2015 | |
| Alfonso Nieto-Castanon | Aug 28, 2015 | |