We are interested in censoring volumes based on a custom filtering of the y translation motion parameter for A/P phase encoded single band rest-fMRI data built off the recommendations described in (Gratton, C., Dworetsky, A., Coalson, R. S., Adeyemo, B., Laumann, T. O., Wig, G. S., ... & Campbell, M. C. (2020). Removal of high-frequency contamination from motion estimates in single-band fMRI saves data without biasing functional connectivity. NeuroImage, 217, 116866.). Ideally, we would hope to implement this through a call in the xcp_engine design file either at the module that generates censoring or in the output that is made for further use.
We believe this is the module that takes commands to generate the "-nFlags.1D" file based on the description here :
###################################################################
2 CONFOUND2
###################################################################
confound2_rps[2]=0
confound2_rms[2]=0
confound2_wm[2]=1
confound2_csf[2]=1
confound2_gsr[2]=0
confound2_acompcor[2]=0
confound2_tcompcor[2]=0
confound2_aroma[2]=1
confound2_past[2]=0
confound2_dx[2]=0
confound2_sq[2]=1
confound2_censor[2]=****HERE as a 1 or 0 to generate "-nFlags.1D" file
confound2_censor_contig[2]=0
confound2_rerun[2]=0
confound2_cleanup[2]=1
We hope to point to a modified "-nFlags.1D" that is generated from the above step for use in censoring volumes. We understand that all xcp_engine design file steps are functionally modular. As we understand it, this would mean we should be able to independently modify module 2 # COUNFOUND2 output of the "-nFlags.1D" file for implementation in the remaining module 3 regression and so on (other appropriate outputs continue to exist). We are open to the idea that this may mean carefully adjusting for additional parameters such as the correct number of contiguous volumes for flagging that may be required when identifying a censored cutoff calculated in module 2 for use in a modified "-nFlags.1D" file. Any and all help is greatly appreciated.
Hello All
Describe the bug
We are interested in censoring volumes based on a custom filtering of the y translation motion parameter for A/P phase encoded single band rest-fMRI data built off the recommendations described in (Gratton, C., Dworetsky, A., Coalson, R. S., Adeyemo, B., Laumann, T. O., Wig, G. S., ... & Campbell, M. C. (2020). Removal of high-frequency contamination from motion estimates in single-band fMRI saves data without biasing functional connectivity. NeuroImage, 217, 116866.). Ideally, we would hope to implement this through a call in the xcp_engine design file either at the module that generates censoring or in the output that is made for further use. We believe this is the module that takes commands to generate the "-nFlags.1D" file based on the description here : ###################################################################
2 CONFOUND2
################################################################### confound2_rps[2]=0 confound2_rms[2]=0 confound2_wm[2]=1 confound2_csf[2]=1 confound2_gsr[2]=0 confound2_acompcor[2]=0 confound2_tcompcor[2]=0 confound2_aroma[2]=1 confound2_past[2]=0 confound2_dx[2]=0 confound2_sq[2]=1 confound2_censor[2]=****HERE as a 1 or 0 to generate "-nFlags.1D" file confound2_censor_contig[2]=0 confound2_rerun[2]=0 confound2_cleanup[2]=1
###################################################################
We hope to point to a modified "-nFlags.1D" that is generated from the above step for use in censoring volumes. We understand that all xcp_engine design file steps are functionally modular. As we understand it, this would mean we should be able to independently modify module 2 # COUNFOUND2 output of the "-nFlags.1D" file for implementation in the remaining module 3 regression and so on (other appropriate outputs continue to exist). We are open to the idea that this may mean carefully adjusting for additional parameters such as the correct number of contiguous volumes for flagging that may be required when identifying a censored cutoff calculated in module 2 for use in a modified "-nFlags.1D" file. Any and all help is greatly appreciated.