freesurfer

freesurfer tools

MRSvoxelStats

MRS.freesurfer.MRSvoxelStats(segfile, MRSfile=None, center=None, dim=None, subjID=None, gareas=[3, 8, 42, 17, 18, 53, 54, 11, 12, 13, 26, 50, 51, 52, 58, 9, 10, 47, 48, 49, 16, 28, 60], wareas=[2, 7, 41, 46], csfareas=[4, 5, 14, 15, 24, 43, 44, 72])

returns grey/white/CSF content within MRS voxel

Parameters:

segfile: nifti file :

path to segmentation file with grey/white matter labels (freesurfer aseg file converted from mgz).

MRSfile: nifti file :

path to MRSfile of MRS voxel. provide either this or center + dim

center : integer array

[x,y,z] where x, y and z are the coordinates of the point of interest. Provide either MRSfile or center+dim

dim : float array

dimensions of voxel in mm. Provide either MRSfile or center+dim

subjID: string :

optional subject identifier. Defaults to nims scan number

gareas, wareas, csfareas: arrays of integers :

arrays of freesurfer labels for gray, white, and csf areas respectively. Determines which areas are considered grey/white/csf. Some areas like brainstem were lumped with grey matter. Did not include hypointensities.

Returns:

raw number of voxels and proportions of grey, white, csf and :

non-grey-or-white-matter :

Notes

See http://miykael.github.io/nipype-beginner-s-guide/regionOfInterest.html

reconall

MRS.freesurfer.reconall(subjfile, subjID=None, subjdir=None, runreconall=True)

Carries out Freesurfer’s reconall on T1 nifti file

WARNING: Reconall takes very long to run!!

http://nipy.sourceforge.net/nipype/users/examples/smri_freesurfer.html

Parameters:

subjfile: nifti file :

Path to subject’s T1 nifti file

subjID: string :

optional name for subject’s output folder

subjdir: string :

The directory to where segmentation results should be saved. Defaults to same directory as subjfile.

runreconall: boolean :

If set to true, runs reconall, otherwise just converts assorted mgz files to nii