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?

DICOM – it's not just a file format

Typical directory after a scan

Mosaicstime

MR-ST001-SE005-0007.dcmMR-ST001-SE005-0006.dcm

MR-ST001-SE005-0005.dcmMR-ST001-SE005-0004.dcm

MR-ST001-SE005-0003.dcmMR-ST001-SE005-0002.dcm

MR-ST001-SE005-0001.dcm

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)

Useful file formats and analysis packages

• Analyze (.hdr/.img pair)

• Nifti (.hdr/.img pair)

• ???

• .fmr; .amr; .vmr

• ???

• ???

• SPM

• FSL

• AFNI

• BrainVoyager

• Freesurfer

• AIR, NIS

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)

Typical pre-processing path

• Slice-time correction• Motion compensation• Normalization by mean• Trend removal

– Linear?– High-pass filter?

Slice-time correctionTR

1 3 5 2 4Slice order: 1 3 5 2 4 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

Trend removal - frequency domain

Sglpixel

FFTStimulus response affected because cut-off was too close to stim frequency

Before After