| -n: | functional MR nifti file (path). | |
| -s: | percentage of voxels with the lowest mean time course values (outside the mask) that are used for the SNR calculation (scalar value). | |
| either | ||
| -t: | threshold of minimum mean voxel intensity that should be included in the quality assurance (scalar value). | |
| or | ||
| -k: | binary nifti mask file of voxels that should be included in the quality assurance (path). | |
| optional | ||
| -o: | output directory (path). | |
| -m: | motion parameters file following motion correction with FSL (*.par), SPM (rp*.txt) or AFNI (*.1D) (path). | |
| -x: | if -x is set, the 3D and 4D nifti output files are not saved. | |
| -h, | --help: prints the pyfMRIqc input help to the command window. | |
Figure 1
Example of cubic local signal dropout in the variance image. The grey squares show the position of local signal loss in the example file pyfMRIqc_example_local_signal_loss.nii.gz.
Figure 2
Mask image for file pyfMRIqc_example_local_signal_loss.nii.gz. The blue color shows voxels above the given intensity threshold that are included in the quality assurance. Green voxels are the nth percentage of voxels with the lowest mean time course values used for SNR calculation.
Figure 3
Example of the third scaled squared difference plot: A) In the red box the plot shows that the variance of the SSD (blue line) is related to the head motion of the participant (green line). This is plotted from example file pyfMRIqc_example_motion.nii.gz. B) The negative peaks in the mean voxel intensity are related to global signal intensity loss in two volumes in the example file pyfMRIqc_example_volume_intensity_loss.nii.gz.
Figure 4
Examples of the mean voxel time course of bins plot A) Example file pyfMRIqc_example_motion.nii.gz: Two major vertical patterns show the global effects of head motion on different tissue types (bins 32 and higher). The first vertical pattern after volume 65 is related to a strong movement and the second pattern after volume 175 is related to another small movement. The lower numbered bins (top of the plot) represent voxels covering empty space around the head that are not affected by motion. B) Example file pyfMRIqc_example_volume_intensity_loss.nii.gz: Two major vertical patterns between volumes 100 and 122 show global signal intensity loss.