convert_flash_mris(subject, flash30=True, convert=True, unwarp=False, subjects_dir=None, verbose=None)¶
Convert DICOM files for use with make_flash_bem.
Use 30-degree flip angle data.
Assume that the Flash MRI images have already been converted to mgz files.
Run grad_unwarp with -unwarp option on each of the converted data sets. It requires FreeSurfer’s MATLAB toolbox to be properly installed.
The path to the FreeSurfer subjects reconstructions. It corresponds to FreeSurfer environment variable
Before running this script do the following: (unless convert=False is specified)
- Copy all of your FLASH images in a single directory <source> and
create a directory <dest> to hold the output of mne_organize_dicom
- cd to <dest> and run
$ mne_organize_dicom <source> to create an appropriate directory structure
- 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
cd to the directory where flash05 and flash30 links are
Set SUBJECTS_DIR and SUBJECT environment variables appropriately
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.