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← Revision 189 as of 2017-03-16 14:11:24 → ⇥
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Comment: multimodal diffusion integration and diffusion processing tutorials were merged into one. deleting original diff page that didn't include mulitmodal
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=== Diffusion Use Case: ===
10 MIND subjects (can't use schizophrenia data)

1. Creation of DTI maps with dt_recon (FA, diffusivity, IVC).
 * We should talk about potentially adding more metrics to this.
 * After #1, you need to make sure to point out where the registration file is that represents the correspondence between str and diff spaces. So when you want to do ROI analysis using wmparc or any other FS recon files, people will know how to transform them to the right space.
 *run dtk on data to look at tracts?
----
Example:

setenv SUBJECTS_DIR /your/subjects/directory

pushd /your/diffusion/acquisition/directory

set dicomfile = # a .dcm file

set subj =

set outputdir =

set cmd = (dt_recon --i $dicomfile --s $subj --o $outputdir)

eval $cmd

Stages of dt_recon:

1. Convert dicom to nifti (creates dwi.nii)

2. Eddy current and motion correction using FSLs eddy_correct,
   creates dwi-ec.nii. (Can be turned off with --no-ec)

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)
* dwisynth.nii

4. Registration of lowb to same-subject anatomical using
   bbregister (creates mask.nii and register.dat; can be turned off by
               --no-reg)

5. Map FA and mask to talairach space (creates fa-tal.nii, mask-tal.nii;
               can be turned off by --no-tal)


More:

Resampling structural volumes in diffusion space:

set cmd = (mri_vol2vol --reg $diffdir/register.dat --targ $anatdir/norm.mgz --mov $diffdir/lowb.nii --o $diffdir/anat2diff.nii --inv)

Resampling diffusion volumes in structural space:

set cmd = (mri_vol2vol --reg $diffdir/register.dat --targ $anatdir/norm.mgz --mov $diffdir/lowb.nii --o $anatdir/lowb2anat.nii)
----

2. ROI analysis of #1 with wmparc.mgz
 * need to look a little more closely at what this is doing, and how we might suggest doing this.

3. Comparing FA point by point along the tract (using tracula; need interesting question to test)
 * (I think this technically uses the FSL tools, but I guess various things we do use them.)

4. Recreate importing freesurfer aparc as ROI

5. Ways of registering across subjects - using CVS

6. voxel based statistics with mri_glmfit
 * There might be some things to discuss with regard to procedures- e.g. do we use an FA threshold or something like that, or just compare all voxels, etc.

Study questions:
 *effects of age on FA of a specific tract (These are the ages: 47 57 36 50 46 41 52 63 38 30. Not sure how much age effect we'll be able to see.)
 *gender study



=== Definition of dt_recon output: ===
ADC: apparent diffusion coefficients (ln(S0/S1)/(b1-b0))

RA: relative anisotropy (sqrt(var(lambda))/mean(lambda))

radialdiff: radial diffusivity (lambda2+lambda3)/2

IVC: inter-voxel correlation

where lambda = (lambda1, lambda2, lambda3) the eigenvalues
S0 = signal intensity without the diffusion weighting
S1 = signal with the gradient