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Initial import from BMRL internal wiki with mimimum clean up (1) separate sections (1) minor clean up (1) final editing (1)
xjqian

Overview of Provided Scripts and Workflow

parameter file for necessary variables

CSP_dwi1_qa.params (please see detailed comments in the file)

shell scripts

  1. csp_reg.sh
  2. csp_reg_fix.sh
  3. csp_qa.sh
  4. statgen_csp.sh

R script

csp_res.R (can be done in matlab, and etc. as well)

2D schedule file

xytrans.sch (for registration)

Courtesy of Mark Jenkinson at fMRIB Oxford University

Overview of workflow

  1. set up variable in the parameter file
  2. registration mask creation
  3. run registration script: csp_reg.sh
  4. (optional) fix misregistration between dwi -> b0: csp_reg_fix.sh
  5. cord mask generation
  6. iterative outlier rejection: csp_qa.sh + csp_res.R
  7. final interpolation
  8. WM tracts and GM ROI drawing
  9. ROI value extraction: statgen_csp.sh

Details of workflow

registration mask creation

  1. play movie to get a sense of the motion (watch the lowerest slice (slice 0), which typically has the largest motion)
  2. draw a mask that encompasses the potential positions of the moved cord. This usually results in a mask that encompasses the outer edge of the CSF
  3. save the mask as ID###_dwi1_mask

cord mask

  1. remove non-cord voxels (e.g. nerve roots, fold-over artifacts) It's important to look at the entire field-of-view
  2. remove edge voxels

R script

  1. set up parameters at the top of the R script
  2. run initial setup and
  3. remove frames with unreasonable extreme motion (failed registration
  4. write out binary matrix for the next iteration
  5. run csp_qa.sh
  6. repeat step 3-5
  7. write out averaged motion for each slice (ID###_dwi1_tran.csv)

ROI creation

  1. identify the horizontal line and vertical lines based on the central horn in FA
  2. identify dorsal nerve roots (in case not obvious, divide by 45 degree line) to divide the posterior portion into quadrants
  3. exclude delta regions by connecting the midpoints of the quadrant division lines
    outline the cord
  4. all the above lines are assigned to the first material (i.e., integer value 1)
  5. switch the background image from FA to I0 to avoid bias
  6. place ROI in the corresponding tracts in the following order, add new material (i.e., increment ROI integer value) before each ROI assignment: LCST, LPC, RPC, RCST, LGM, RGM (Note: patient's left is on the right of the screen if the image is in Radiological convention).
  7. repeat the above for each slice by keep adding new material (i.e., incrementing ROI integer value)
    for 6 slices, the last ROI should be material 38 (i.e., integer value 37)
  8. save the tracts ROI as ID###_DWI1_ROI

Noise region ROI

draw noise ROI in structure free regions posterior and anterior to the cord in the largest bval image (this image should be the original dwi image without any interpolation).

Curved cord acquisition

MSMA (multi-slice multi-angle) acquisition: break slices into two or more slice groups if necessary. The goal is to make every slice or slice group perpendicular to the long axis of the cord.

Note for Siemens platform: Because MSMA is not compatible with the Siemens DTI ICE EvaFunctor, you have to disable the mosaic, Tensor, FA, ADC, etc in the diffusion card, leaving only the diffusion weighted image checked. Otherwise reconstruction will fail.

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