MRI whole-brain registration to Allen Atlas

This registration method performs the following tasks:

1. Registers in-vivo or ex-vivo MRI data to Allen Reference mouse brain Atlas

2. Warps Allen annotations to the MRI space

GUI

Invoke with $ miraclGUI and select from main menu or run:

$ miracl reg mri_allen_nifty

The following window will open:

Click on Select In-vivo or Ex-vivo MRI and choose the input MRI nii (preferable T2-w) using the dialog window. Then set the registration options:

Parameter	Description	Default
Orient code	Orient nifti from original orientation to ‘standard/Allen’ orientation.	RSP
Labels Hemi	Warp allen labels with hemisphere split (Left different than Right labels) or combined (Left and Right labels are the same/mirrored). Accepted inputs are: split combined	combined
Labels resolution [vox]	Labels voxel size/resolution in um. Accepted inputs are: 10 25 50	10
Olfactory bulb included	Specify whether the olfactory bulb is included in brain. Accepted inputs are: 0 (not included) 1 (included)	0
skull strip	Strip skull. Accepted inputs are: 0 (don’t strip) 1 (strip)	1
No orient	No orientation needed (input image in ‘standard’ orientation). Accepted inputs are: 0 (orient) 1 (don’t orient)	0

Click Enter and Run to start the registration process.

Command-line

Usage:

$ miracl reg mri_allen_nifty -i [ input invivo or exvivo MRI nii ] -o [ orient code ] -m [ hemi mirror ] -v [ labels vox ] -l [ input labels ] -b [ olfactory bulb ] -s [ skull strip ] -n [ no orient needed ]

Example:

$ miracl reg mri_allen_nifty -i inv_mri.nii.gz -o RSP -m combined -v 25

Arguments:

arguments (required):

  i.  input MRI nii
     Preferably T2-weighted

optional arguments:

  o.  orient code (default: RSP)
      to orient nifti from original orientation to "standard/Allen" orientation
  m.  hemisphere mirror (default: combined)
      warp allen labels with hemisphere split (Left different than Right labels) or combined (L & R same labels / Mirrored)
      accepted inputs are: <split> or <combined>
  v.  labels voxel size/Resolution in um (default: 10)
      accepted inputs are: 10, 25 or 50
  l.  input Allen labels to warp (default: annotation_hemi_combined_10um.nii.gz )
      input labels could be at a different depth than default labels
      If l. is specified (m & v cannot be specified)
  b.  olfactory bulb included in brain, binary option (default: 0 -> not included)
  s.  skull strip or not, binary option (default: 1 -> skull-strip)
  f.  FSL skull striping fractional intensity (default: 0.3), smaller values give larger brain outlines
  n.  No orientation needed (input image in "standard" orientation), binary option (default: 0 -> orient)