Brain Imaging

Field Map Correction

The fieldmap correction is done with two programs: make_fmap and fieldmap_correction. make_fmap creates a fieldmap from two gradient-echo images acquired with echo times that differ by a few milliseconds (usually 3 ms when imaging at 3T). fieldmap_correction uses this fieldmap to correct the EPIs. make_fmap uses the prelude program from FSL to unwrap the phase images.

• Fieldmap Computation
• Correction of EPIs
• Example results.
• User Comments on the lab wiki.
• Matlab GUI (no longer supported)

Applications

• spm_norm: Script for running SPM's spatial normalization from the command line.
• cine: Fast cine display of EPI images. Facilitates evaluation for motion.
• study_info: Scan a directory tree to create a spreadsheet of salient study informaton.
• dump_header: Display file header contents
• dump_hdrkey: Write a single header value to the output. Useful for scripting.
• convert_file: Convert image formats.
• preprocess: Preprocess fmri data.
• upload_data: Upload data from the scanner.

Miscellaneous

• Using Python in the lab

Downloads

• Image file I/O package

Unix

• Useful commands
• Obscure bash syntax

Lectures and Seminars

• Preprocessing EPIs
• Data Analysis

Scanner

• EPI reconstruction
• Development tools

Methods list

(Access to this list is restricted to the UW community.)

Neuroimaging Methods List