49. Field mapping

unpack dicom

The dicom files from the field mapping protocol should give you two files:

• magnitude images (two images for two echo time). They are images at run 007 in this example.

• phase image (one image). It is the image at run 008 in this example.

extract brain (magnitude image)

% bet gre/007/f.nii gre/007/f_bet.nii

create a field map

% fsl_prepare_fieldmap SIEMENS gre/008/f.nii gre/007/f_bet.nii.gz fmap_rads 2.46

NOTE Two TE's used in this protocol is 2.64 ms and 5.10 ms. The delta TE is 2.46 ms.

The output file fmap_rads.nii.gz is the field map in radian.

show a field map

• In Matlab, load the field map file and display values in Hz.

d=MRIread('fmap_rads.nii.gz');
figure; fmri_mont(d.vol./2./pi);

• To render a field map on a cortical surface, do the following:

1. register between field map images and indivdual's freesurfer recon.

This can be done by, for example, bbregister, where an initial registration is created (bb_register_init.dat) via an interactive script.

Then, run bbregister to fine tune the registration matrix to generate the fine-tuned registration matrix.

bbregister --s s001 --mov ../data/unpack/gre/007/f.nii --init-reg bb_register_init.dat --reg bb_register.dat --bold

2. transform the field map onto individual's freesurfer recon.

Use this script to transform the field map to surface STC files. Note that STC files for both native and standard (MNI, fsaverage subject) space are created.

3. display the result.

Load the field map overlay using etc_render_fsbrain.m.

Field map in the native space (20 Hz to 100 Hz).

Field map in MNI space (20 Hz to 100 Hz).