You can also check Sample ini config file for resting-state fMRI or task-state fMRI which are always updated with the most up to date Dev version of pipeline.
Flow chart and file names, which will also be shown in pdf/html report.
Regressors details:
| Filename | description | |||||
| 3dvolreg.maxdisplace.mm.1D | max displacement (mm) | |||||
| 3dvolreg.maxdisplace.mm_delt.1D | derivative of max displacement (mm) | |||||
| 3dvolreg.1D | 6 motion parameters | |||||
| r3dvolreg.1D | 6 motion parameters without comment (was used to fix a motion parameter estimation bug, now the fixation was removed) | |||||
| 3dvolreg.6to24.1D | Friston 24 based on user’s choice | |||||
| fd.txt | FSL estimated | |||||
| thrd_fd.1D | ||||||
| thrdPrePost_fd.1D | ||||||
| dvars.txt | FSL estimated | |||||
| thrd_dvars.1D | ||||||
| thrdPrePost_dvars.1D | ||||||
| afniCensor.txt | AFNI estimated | |||||
| thrd_afniCensor.1D | ||||||
| thrdPrePost_afniCensor.1D | ||||||
| refmse.txt | FSL estimated | |||||
| compound_censor.1D | the union of FD/DVARS/AFNI Euclidean | |||||
| compound.pre.post.1D | the union of FD/DVARS/AFNI Euclidean with pre/post censoring option | |||||
| motion_regressors.1D | all motion combined regressors | |||||
| censoredNo.1D | final scrubbing temporal index | |||||
| csf.1D | PCA of CSF | |||||
| csf.PCmean.1D | Mean of CSF | |||||
| wmPCmean.1D | Mean of WM | |||||
| wm.1D | PCA of WM | |||||
| physioNoise_regressors.1D | the union of the Principla components of CSF/WM | |||||
| regressors.1D | final regressors with headers for user to check | |||||
| norm2-regressors.1D | final regressors to have column norm-2 as 1 | |||||