1. fMRI: Biological Basis and Experiment Design Lecture 19: Data formats and data path DICOM DICOM servers Conversion between formats Slice-time correction and trend removal 1 light year = 5,913,000,000,000 miles?

2. DICOM – it's not just a file format

3. Typical directory after a scan

4. Mosaics time MR-ST001-SE005-0007.dcm MR-ST001-SE005-0006.dcm MR-ST001-SE005-0005.dcm MR-ST001-SE005-0004.dcm MR-ST001-SE005-0003.dcm MR-ST001-SE005-0002.dcm MR-ST001-SE005-0001.dcm

5. Getting the data home Plan A: push data to a convenient DICOM server in your department Plan B: push data to Drei (PC in console room); zip scanning session together and ftp it home. Plan C: burn CDs with data (directly from scanner, or from Drei)

6. Useful file formats and analysis packages Analyze (.hdr/.img pair) Nifti (.hdr/.img pair) ???.fmr;.amr;.vmr ??? SPM FSL AFNI BrainVoyager Freesurfer AIR, NIS

7. Converting between formats Some packages will read DICOM and convert to their preferred format Some command line tools exist (e.g. dinifti from NYU) Some tools exist (e.g. MRIcro)

9. Typical pre-processing path Slice-time correction Motion compensation Normalization by mean Trend removal –Linear? –High-pass filter?

10. Slice-time correction TR 1 3 5 2 4Slice order:1 3 5 2 4... Uncorrected data: erroneously assign acquired signal to start of TR Corrected data: interpolate to estimate signal at start of TR True signal Interpolate to estimate signal at start of TR

11. Trend removal - frequency domain Sgl pixel FFT Stimulus response affected because cut-off was too close to stim frequency BeforeAfter