1. Name


dt_recon : dt_recon is used in the processing of native diffusion tensor imaging (DTI) data. It takes original dicom images as input, and can automatically detect the bvalue and direction information from certain Siemens sequences. Other users may have to input the bvalue and direction information using bvec and bval text files with the same format as the files used in FSL diffusion processing. The subjectid refers to the subject's cortical reconstruction directory (from Freesurfer/T1 processing). This is used for registration of the diffusion data to the structural images. dt_recon outputs a variety of maps of interest in the study of neural anatomy and integrity as described in more detail below. Output maps can be entered into a variety of region of interest and voxel based analysis procedures (including TBSS from FSL).

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\