Yes, you can use the siemens STC option (ie, -stc siemens)
On 2/26/2024 9:02 PM, Maria Hakonen wrote:
External Email - Use Caution
Dear all,
Have I understood correctly that the slice delay of each slice is not needed when performing slice time correction with preprocess-sess?
I am processing an open OASIS fMRI dataset. The dataset has fMRI data in nifti format and JSON files that contain information about the data. In the instructions they say: "Slice timing is included in the JSON when available. Some original DICOM files did not have slice timing info. When slice timing information is unavailable use the ratio TR/#slices."
The data is collected with a Siemens scanner. If the slice timing is available it seems to be interleaved:
"SliceTiming": [ 1.1025, 0, 1.165, 0.059999999999999998, 1.2250000000000001, 0.1225, 1.2875000000000001, 0.1825, 1.3474999999999999, 0.245, 1.4099999999999999, 0.30499999999999999, 1.47, 0.36749999999999999, 1.5325, 0.42749999999999999, 1.595, 0.48999999999999999, 1.655, 0.55000000000000004, 1.7175,
Could I just run slice time correction with the siemens option?
Best regards, Maria
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer