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fMRI: Biological Basis and Experiment Design Lecture 19: Data formats and data path

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?. DICOM – it's not just a file format. Typical directory after a scan.

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fMRI: Biological Basis and Experiment Design Lecture 19: Data formats and data path

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  1. fMRI: Biological Basis and Experiment DesignLecture 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 MR-ST001-SE005-0007.dcm time 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. Analyze (.hdr/.img pair) Nifti (.hdr/.img pair) ??? .fmr; .amr; .vmr ??? ??? SPM FSL AFNI BrainVoyager Freesurfer AIR, NIS Useful file formats and analysis packages

  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)

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

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

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

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