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The purpose of this tutorial is to give you experience with the
integration of Diffusion Tensor Imaging (DTI) with FreeSurfer. The
data were collected at MGH as part of the MIND.

= DTI Basics =

It is assumed that you already have knowledge of DTI and its
analysis. This paragraph is supplied as a summary for completeness.
DTI attempts to measure the diffusion of water in the brain. White
matter tracts tend to be like little straws which contrain the
direction diffusion. The DTI analysis measures the orientation and the
"strength" of the orientation. Eg, CSF will have no strong
orientation. This strength is often measured as the fractional
anisotropy (FA). The diffusivity is ofen measured as the Apparent
Diffusion Coefficient (ADC).

= This Data Set =

This data was acquried at MGH as part of a MIND Consortium study. The
raw data are in dwi.nii.gz. The FreeSurfer anatomical analysis for
this subject is M87102113.v4. Seventy images were acquired (10 low-b
and 60 diffusion weighted). The bvalues and gradient directions are
stored in bvals.dat and bvects.dat, respectively. These data were
analyzed with FreeSurfer's [[dt_recon|dt_recon]] program, which
created the fa.nii, adc.nii, lowb.nii, and register.dat. The data are
located in:
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cd $TUTORIAL/mmtutorial/dti cd $TUTORIAL_DATA/multimodal/dti
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= Check the Registration =

As always, check the registration with the template. In this case, the
template is the low-b image:
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The registration should be accurate. For more information on
registration, see the [[MultiModalRegistration|Registration]]
Tutorial.

= FA Viewing =

View the FA on the subject's anatomical with the white matter
parcellation (wmparc.mgz) as the segmentation:

{{{
tkmedit M87102113.v4 orig.mgz -aux brain.mgz \
  -seg wmparc.mgz \
  -reg register.dat -overlay fa.nii \
  -fthresh 0.1 -fmax 1
}}}

Notes:
  1. The FA is a values between 0 and 1, so the thresholds are set to 0.1 and 1.
  1. When the window first comes up, there will be a lot of activity
  outside the brain. To remove this, set the View->Mask Functional
  Overlay To AuxVolume flag.
  1. In the image below, you can see that white matter tends to have a higher FA.

PIC

= FA ROI Analysis =

As with the [[MultiModalfMRIIndividual| Individual fMRI Analysis]], we
will first resample the FA into the subject's anatomical space:
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Notes:
  1. Nearest neighbor is used to avoid averaging FA across voxels.
  2. The output fa.anat.mgh will be 256^3, 1mm3.

Now run mri_segstats getting a report for each of the following ROIs
(index/name pairs are found in the LUT):
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mri_vol2vol --mov adc.nii \
  --reg register.dat \
  --fstarg --interp nearest \
  --o adc.anat.mgh
251 CC_Posterior (Posterior Corpus Callosum)
3024 wm-lh-precentral
3030 wm-lh-superiortemporal
3021 wm-lh-pericalcarine
4 Left-Lateral-Ventricle
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The wm-lh-precentral, wm-lh-superiortemporal, wm-lh-pericalcarine are
created by the gyral white matter parcellation.
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  --seg $SUBJECTS_DIR/$subject/mri/aseg.mgz \   --seg $SUBJECTS_DIR/M87102113.v4/mri/wmparc.mgz \
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  --nonempty --excludeid 0 \   --id 251 --id 3021 --id 3024 --id 3030 --id 4\
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Click HERE to see the output. The CC has an average FA of about 0.75,
gyral parcellations are about 0.4, and the ventricle is 0.2.

Back to Multimodal Top

The purpose of this tutorial is to give you experience with the integration of Diffusion Tensor Imaging (DTI) with FreeSurfer. The data were collected at MGH as part of the MIND.

DTI Basics

It is assumed that you already have knowledge of DTI and its analysis. This paragraph is supplied as a summary for completeness. DTI attempts to measure the diffusion of water in the brain. White matter tracts tend to be like little straws which contrain the direction diffusion. The DTI analysis measures the orientation and the "strength" of the orientation. Eg, CSF will have no strong orientation. This strength is often measured as the fractional anisotropy (FA). The diffusivity is ofen measured as the Apparent Diffusion Coefficient (ADC).

This Data Set

This data was acquried at MGH as part of a MIND Consortium study. The raw data are in dwi.nii.gz. The FreeSurfer anatomical analysis for this subject is M87102113.v4. Seventy images were acquired (10 low-b and 60 diffusion weighted). The bvalues and gradient directions are stored in bvals.dat and bvects.dat, respectively. These data were analyzed with FreeSurfer's dt_recon program, which created the fa.nii, adc.nii, lowb.nii, and register.dat. The data are located in:

cd $TUTORIAL_DATA/multimodal/dti

Check the Registration

As always, check the registration with the template. In this case, the template is the low-b image:

tkregister2 --mov lowb.nii --reg register.dat --surf

The registration should be accurate. For more information on registration, see the Registration Tutorial.

FA Viewing

View the FA on the subject's anatomical with the white matter parcellation (wmparc.mgz) as the segmentation:

tkmedit M87102113.v4 orig.mgz -aux brain.mgz \
  -seg wmparc.mgz \
  -reg register.dat -overlay fa.nii \
  -fthresh 0.1 -fmax 1 

Notes:

  1. The FA is a values between 0 and 1, so the thresholds are set to 0.1 and 1.
  2. When the window first comes up, there will be a lot of activity

    outside the brain. To remove this, set the View->Mask Functional Overlay To AuxVolume flag.

  3. In the image below, you can see that white matter tends to have a higher FA.

PIC

FA ROI Analysis

As with the Individual fMRI Analysis, we will first resample the FA into the subject's anatomical space:

mri_vol2vol --mov fa.nii \
  --reg register.dat \
  --fstarg --interp nearest \
  --o fa.anat.mgh

Notes:

  1. Nearest neighbor is used to avoid averaging FA across voxels.
  2. The output fa.anat.mgh will be 256^3, 1mm3.

Now run mri_segstats getting a report for each of the following ROIs (index/name pairs are found in the LUT):

251 CC_Posterior (Posterior Corpus Callosum)
3024 wm-lh-precentral 
3030 wm-lh-superiortemporal
3021 wm-lh-pericalcarine 
4   Left-Lateral-Ventricle 

The wm-lh-precentral, wm-lh-superiortemporal, wm-lh-pericalcarine are created by the gyral white matter parcellation.

mri_segstats \
  --seg $SUBJECTS_DIR/M87102113.v4/mri/wmparc.mgz \
  --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \
  --id 251 --id 3021 --id 3024 --id 3030 --id 4\
  --i fa.anat.mgh --sum fa.stats

Click HERE to see the output. The CC has an average FA of about 0.75, gyral parcellations are about 0.4, and the ventricle is 0.2.

FsTutorial/MultiModalDtiIndividual_tktools (last edited 2014-01-28 16:27:11 by LouisVinke)