mne.bem.convert_flash_mris

mne.bem.convert_flash_mris(subject, flash30=True, convert=True, unwarp=False, subjects_dir=None, verbose=None)[source]

Convert DICOM files for use with make_flash_bem.

Parameters
subjectstr

Subject name.

flash30bool

Use 30-degree flip angle data.

convertbool

Assume that the Flash MRI images have already been converted to mgz files.

unwarpbool

Run grad_unwarp with -unwarp option on each of the converted data sets. It requires FreeSurfer’s MATLAB toolbox to be properly installed.

subjects_dirstr | None

The path to the FreeSurfer subjects reconstructions. It corresponds to FreeSurfer environment variable SUBJECTS_DIR.

verbosebool, str, int, or None

If not None, override default verbose level (see mne.verbose() and Logging documentation for more). If used, it should be passed as a keyword-argument only.

Notes

Before running this script do the following: (unless convert=False is specified)

  1. Copy all of your FLASH images in a single directory <source> and

    create a directory <dest> to hold the output of mne_organize_dicom

  2. cd to <dest> and run

    $ mne_organize_dicom <source> to create an appropriate directory structure

  3. Create symbolic links to make flash05 and flash30 point to the

    appropriate series: $ ln -s <FLASH 5 series dir> flash05 $ ln -s <FLASH 30 series dir> flash30 Some partition formats (e.g. FAT32) do not support symbolic links. In this case, copy the file to the appropriate series: $ cp <FLASH 5 series dir> flash05 $ cp <FLASH 30 series dir> flash30

  4. cd to the directory where flash05 and flash30 links are

  5. Set SUBJECTS_DIR and SUBJECT environment variables appropriately

  6. Run this script

This function assumes that the Freesurfer segmentation of the subject has been completed. In particular, the T1.mgz and brain.mgz MRI volumes should be, as usual, in the subject’s mri directory.

Examples using mne.bem.convert_flash_mris