Hello,

I am new to AFNI and seem to be getting comfortable with the analysis commands and options.

I want to know if we can use it in our rt-fMRI pipeline. I have gone through the previous messages on this board: [afni.nimh.nih.gov].

- We will be using a Seimens scanner (mosaic epi).
- I will have access through the network to the shared folder in which the dicom images arrive but I cannot install anything there.

- The part of the pipeline that I want to implement:
--- read the dicoms from the shared folder and construct a volume
--- pre-processing (registration to anatomical only for 1st epi, motion correction, smoothing etc),
--- write out: average ROI values in a separate file for each volume, motion parameters in a file, registration parameters in a file, and motion corrected volumes

- I have another program that will read the ROI values from the incoming files for further processing.

I would really appreciate if you can tell me what options are available through AFNI to implement this.

Thanks,
Uday