USAGE: dt_recon

$Id: dt_recon,v 1.11 2008/07/29 19:55:17 greve Exp $

Performs DTI reconstruction from the raw DWI in the input file. If bvalues and bvectors are not specified with --b, it is assumed that the input is a Siemens dicom file, and gets gradient directions and bvalues from based on values found in the dicom file. See $FREESURFER_HOME/diffusion/mgh-dti-seqpack/README. If the bvalues and bvectors are specified, then the input volume can be anything.

The bvalues are in a simple text file, one for each direction (including b=0). The bvectors (gradient directions) are also in a simple text file with three components on each row. These also include the b=0 values. There must be as many rows in the bvals/bvecs as there are frames in the input.

Stages: 1. Convert input to nifti (creates dwi.nii) 2. Eddy current and motion correction using FSLs eddy_correct,

3. DTI GLM Fit and tensor construction. Includes creation of:

4. Registration of lowb to same-subject anatomical using

5. Map FA to talairach space (creates fa-tal.nii)

Example usage:

dt_recon --i 6-1025.dcm --s M87102113 --o dti dt_recon --i f.nii --b f.bvals f.bvecs --s M87102113 --o dti

# Check registration tkregister2 --mov dti/lowb.nii --reg dti/register.dat \

# View FA on the subject's anat: tkmedit M87102113 orig.mgz -overlay dti/fa.nii \

# View FA on fsaverage tkmedit fsaverage orig.mgz -overlay dti/fa-tal.nii

# Group/Higher level GLM analysis: # Concatenate fa from individuals into one file # Make sure the order agrees with the fsgd below mri_concat */fa-tal.nii --o group-fa-tal.nii # Create a mask: mri_concat */mask-tal.nii --o group-masksum-tal.nii --mean mri_binarize --i group-masksum-tal.nii --min .999 --o group-mask-tal.nii # GLM Fit mri_glmfit --y group-fa-tal.nii --mask group-mask-tal.nii\