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Batch Processing and Analysis Protocol

The following protocol is modified from the one provided by Robert P. Mackenzie at Dr. Layla Banihashemi's laboratory.

If you have a working protocol that you would like to share with other users, please send it to me at frank.yeh (at) gmail.com

Diffusion MRI Connectometry analysis:

1. Check for proper files

     a. Create a folder for each subject's data and place all folders under a common root folder.

2. Open DSI Studio

3. Default menu is “Diffusion MRI Tractography”

4. Switch to “Tools: batch processing” menu

5. Select second “Rename DICOM Files: Select a directory containing DICOM files and rename them by their sequence” option (Skip this step if using NIFTI files)

     a. This allows you to select a folder. Choose the folder that contains the DICOM files. (If you reach a point where it says “no items match your search” go back one step and select that folder. The current function cannot see the data in this file, but it should be there.)

     b. Selecting this folder renames the data as a whole.

6. Select “Create SRC files” in the same menu

     a. Move through same folder and subfolders and choose the newly created folder containing the .dcm files. (If you reach a point where it says “no items match your search” go back one folder. Same as before, the data is there but this function cannot see it)

* If unsure, enter initial folder on computer and search through the subfolders to find the folder that has the set of data that has the .dcm extension.

     b. This compiles all the data and generates one representative .src file

c. Collect all .src files into a common folder.

d. Run a quality control on the src file using "SRC files Quality Control" under "Tools: batch processing". The b-table should match each other, and the neighboring DWI correlation should be similar. Lower correlation suggests motion and other SNR issue.

7. Go to “Diffusion MRI Tractography” menu

8. Select “STEP2: Reconstruction”

     a. Move through folders until you reach the .src files that was just created.

b. Select all .src files

9. In reconstruction:

     a. Click on “Step 2: Select reconstruction method” tab at bottom of window

     b. Choose QSDR bubble for reconstruction method

     c. Diffusion sampling length ratio: 1.25

     d. Drop menu to the right should be on “No distance weighting”

     e. Registration method: Select “norm 14-18-14”

     f. Output resolution: 2

     g. Open advanced options

     h. ODF sharpening set to off

i. Output: check only ODFs box (unless you want additional output)

     k. ODF tessellation set to 8-fold

     l. Number of fibers resolved: 5

    m. Multi-thread: 2 (next to “run reconstruction”)

     n. Click run reconstruction

* Wait for “fib file created”

- Click OK

- Close out of reconstruction window

9. Collect all fib files

     a. Create a new folder to place all the created .fib files

     b. Navigate to each individual .fib file and add to new folder

           - This puts them all in one place and makes the next step of selecting each .fib file to average easier

10. Quality check: the file name will report the R square value (e.g. R72.fib.gz means a R value of 0.72). All files should have R values greater than 0.6

11. Open DSI Studio:

     a. Switch to “Diffusion MRI Connectometry” menu

     b. Select “STEP1: Create connectometry database”

     c. Click “+ Add”, go to the new folder containing all the .fib files and select all of them

d. Atlas: HCP842_2mm.fib.gz

e. Index of interest: sdf

     d. After all files have been added, click “create database” in bottom right hand corner of current window. A new db.fib.gz file will be created.

12. Connectometry analysis

13. Local connectome fingerprint

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