Extracting DTI from specific spinal cord regions#

Here, we will use the registered PAM50 template to extract and aggregate values from the white matter region of the fractional anisotropy (FA) diffusion tensor image.

sct_extract_metric -i dti_FA.nii.gz -f label/atlas \
                   -l 51 -method map \
                   -vert 2:5 -vertfile label/template/PAM50_levels.nii.gz -perlevel 1 \
                   -o fa_in_wm.csv
Input arguments:
  • -i : Image to extract intensity values from.

  • -f : File or folder used to pick out specific regions from the input image. In this case, we supply the folder of the white matter atlas that was transformed to the space of the DTI data.

  • -l : The IDs of the label (or group of labels) to compute metrics for. In this case, label 51 is a combined label that represents all of the WM tracts together. You can see the full list of labels to choose from by running sct_extract_metric -list-labels.

  • -method : We specify map to choose the Maximum a Posteriori method, which helps to account for the partial volume effect. This method is most suitable for small regions. This method should only be used with the PAM50 white/gray matter atlas (or with any custom atlas) as long as the sum across all overlapping labels equals 1 in each voxel part of the atlas.

  • -vert: This argument further restricts the metric extraction to specific vertebral levels. In this case, 4 levels in total (C2-C5) will be used.

  • -vertfile: This argument specifies the vertebral label file to use when extracting metrics.

  • -perlevel: Providing this argument will extract the metrics for each vertebral level, rather than averaging across the entire region.

  • -o : The name of the output file.

fa_in_wm.csv: FA values in white matter across vertebral levels#

Slice (I->S)

VertLevel

Label

Size [vox]

MAP()

STD()

1:3

5

white matter

213.116278535089

0.816009066700897

0.120189826223487

4:6

4

white matter

211.802946720226

0.816900166267528

0.138645402811017

7:10

3

white matter

269.344772923089

0.812880776349297

0.144916051577843

11:13

2

white matter

190.065023308727

0.830666411104277

0.167349029313301