• 7tRegistration

3T-7T Registration

Description

A Freesurfer anatomical analysis is performed on a full-brain MP-RAGE collected at 3T. The registration between the partial field-of-view (FoV) 7T T2* data and the freesurfer anatomical (3T, full-brain) is performed in several stages. First, a full-brain volume collected during the same 7T session as the T2* data is registered to the Freesurfer anatomical using the FSL FLIRT registration tool (www.fmrib.ox.ac.uk/fsl). Next, an initial registration between the partial FoV 7T T2* volume and the same-session full-brain volume is computed from the geometry information found in the DICOM header (this is only accurate if the subject does not move between the two acquisitions). An initial registration between the Freesurfer anatomical and the T2* data is then computed by concatenating these first two registrations. Because this is only accurate if the subject does not move, we need to compute the final registration based on the actual intensity values. This is done using a new (not-yet-published as of May 2008) registration procedure called Boundary-Based Registration (BBR). BBR computes the cost function based upon the intensity gradient across tissue boundaries. This boundary information is available from the Freesurfer anatomical analysis. BBR is very robust in the face of impoverished intensity data from an input volume (eg, a partial FoV acquisition). Each of the T2* partial volumes are registered to the anatomical in this way. The partial volumes are then combined into a single volume in the anatomical space (places where the partial volumes overlapped are averaged together). The T2* intensities for the cortical histograms are created by sampling the T2* 1mm inside the pial surface. -- Doug Greve

Workflow

To overlay pial and white-matter surface outlines (produced in Freesurfer from 3T structurals) on a T2* partial-brain hi-res volume (combined from two 7T scans: upper and lower brain).

Assume the following files exist:

7T sample data found in:

/autofs/space/minerva_002/users/nicks/subjects/nicks_dicoms/2007-10-30

3T structurals for same subject found in:

/autofs/space/minerva_002/users/nicks/subjects/nick9

Step 1

Produce the surfaces ?h.white and ?h.pial from the 3T structural:

recon-all -s <subj> -all

Step 2

Register the 7T whole-brain to the 3T structural:

fslregister --s <subj> --mov t1-7t.nii.gz --reg register-7tw-3t.dat

To check results, run:

tkregister2 --mov t1-7t.nii.gz --reg register-7tw-3t.dat --surf white

Step 3

Produce an initial alignment of the pial surface to each the 7T partial-brain scans (via the intermediate registration file 'register-7tw-3t.dat'):

tkregister2 \
  --mov t2star-7t-flash-upper.nii.gz \
  --int t1-7t.nii.gz register-7tw-3t.dat \
  --reg register-upper.dat \
  --surf pial \
  --s <subj>

tkregister2 \
  --mov t2star-7t-flash-lower.nii.gz \
  --int t1-7t.nii.gz register-7tw-3t.dat \
  --reg register-lower.dat \
  --surf pial \
  --s <subj>

Be sure to click 'Save Reg' to save the register-<upper/lower>.dat file.

Step 4

Use the BB registration utility, mri_segreg, to refine the 3T to 7T-(upper/lower) alignments:

mri_segreg \
  --mov t2star-7t-flash-upper.nii.gz \
  --reg register-upper.dat \
  --out-reg segregister-upper.dat \
  --cost cost.upper

mri_segreg \
  --mov t2star-7t-flash-lower.nii.gz \
  --reg register-lower.dat \
  --out-reg segregister-lower.dat \
  --cost cost.lower

Step 5

Create a hi-res template volume from the 3T structural:

mri_vol2vol \
  --mov $SUBJECTS_DIR/<subj>/mri/brain.mgz \
  --crop 3 \
  --o brain-hires-template.nii.gz

The '3' parameter for crop scales the resolution from the default 1mm to the desired .33m (to match t1star-7t-flash-<upper/lower>.nii.gz).

And a registration to it:

tkregister2 \
  --mov brain-hires-template.nii.gz \
  --s <subj> \
  --regheader \
  --reg register-hires-template.dat

And to each of the 7T partial-brain scans:

mri_matrix_multiply \
  -im segregister-upper.dat \
  -iim register-hires-template.dat \
  -om register-upper-hires.dat

mri_matrix_multiply \
  -im segregister-lower.dat \
  -iim register-hires-template.dat \
  -om register-lower-hires.dat

Step 6

Combine the two 7T partial-brain scans into one volume (7T-combined):

mri_vol2vol \
  --mov t2star-7t-flash-upper.nii.gz \
  --targ brain-hires-template.nii.gz \
  --reg register-upper-hires.dat \
  --o t2upper.nii.gz

mri_vol2vol \
  --mov t2star-7t-flash-lower.nii.gz \
  --targ brain-hires-template.nii.gz \
  --reg register-lower-hires.dat \
  --o t2lower.nii.gz

mri_concat \
  --combine \
  --i t2upper.nii.gz \
  --i t2lower.nii.gz \
  --o t2star-7t-flash-combined.nii.gz

mri_create_t2combined script

A script named 'mri_create_t2combined' is included in the Freesurfer distribution to execute the preceding steps. For help on its usage, type:

mri_create_t2combined