USAGE: dt_recon
- Required Aruments:
- --i invol --b bvals bvecs --s subjectid --o outputdir
- --ecref TP : Use TP as 0-based reference time points for EC --no-ec : turn off eddy/motion correction --no-reg : do not register to subject or resample to talairach --no-tal : do not resample FA to talairch space --sd subjectsdir : specify subjects dir (default env SUBJECTS_DIR) --debug : print out lots of info --version : print version of this script and exit --help : voluminous bits of wisdom
$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,
- creates dwi-ec.nii. Can take 1-2 hours.
3. DTI GLM Fit and tensor construction. Includes creation of:
- tensor.nii -- maps of the tensor (9 frames) eigvals.nii -- maps of the eigenvalues eigvec?.nii -- maps of the eigenvectors adc.nii -- apparent diffusion coefficient fa.nii -- fractional anisotropy ra.nii -- relative anisotropy vr.nii -- volume ratio ivc.nii -- intervoxel correlation lowb.nii -- Low B bvals.dat -- bvalues bvecs.dat -- directions Also creates glm-related images:
- beta.nii - regression coefficients eres.nii - residual error (log of dwi intensity) rvar.nii - residual variance (log) rstd.nii - residual stddev (log) dwires.nii - residual error (dwi intensity) dwirvar.nii - residual variance (dwi intensity)
4. Registration of lowb to same-subject anatomical using
- FSLs flirt (creates mask.nii and register.dat)
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 \
- --surf orig --tag
# View FA on the subject's anat: tkmedit M87102113 orig.mgz -overlay dti/fa.nii \
- -overlay-reg dti/register.dat
# 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\
- --fsgd your.fsgd --C contrast --glmdir groupanadir