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Folder | Sub-folders | Files* |
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'anatomical' | ‘coreg (native)’ |
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'T2map' | ‘raw’ | Leave empty for now. Refer to STEP X………step 15. |
'DTI' | ‘raw’ |
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fMRI | ‘rest01'
‘stimulus01'
‘stimulus02’
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|
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Write down the pitch, roll, yaw and crosshair position values the text document file named ‘movement parameters’ in the ‘coreg (native)' subfolder of the subject’s anatomical folder.
In the Display window, click ‘Set Origin’, then click ‘Reorient’ and select all 13 T2map images to have the same movement parameters applied to these images. Now all 13 3D T2map images are realigned i.e. “coregistered”.
Copy and paste the 13 realigned T2map images from the anatomical folder to that subject’s T2 map folder and then delete all but the first T2map image (i.e. the image ending in ‘0000’) from the ‘native (coreg)’ folder.
Repeat steps 9-15 for each subject.
Once all of the T2maps have been realigned i.e. “coregistered” for each subject, go to the CSPM window → Utilities → T2maps from Bruker.
SCREENSHOT AN EG AND CONTINUE INSTRUCTIONS (ALSO PROBABLY CHANGE PAGE NAME TO REFLECT ALL INSTRUCTIONS)
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Paste in the folder path of your method file in the box next to ‘File or Folder’, then paste in the path of your ‘CONTROL’ folder in the box below and in the ‘Folder with nifti files’ box. Make sure to select the ‘Subfolders’ box so that it can process all subjects' T2maps in one go.
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Click through the buttons of the GUI in the following order: ‘Load T2’, ‘Apply T2 to Nifti’, ‘Apply and Create T2maps’.
Open the T2 relaxation image that was created for each subject. It should look like this:
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Move your cursor around the image and check that the relaxation value (the value highlighted in the screenshot) is below 100 throughout (excluding values near the edges of the brain or near CSF).
Add ‘T2map’ to the end of the name of the newly created relaxation image and move the relaxation image from the ‘T2map' folder to the ‘raw’ sub-folder within the 'T2map’ folder.
Delete all files in the ‘raw’ folder except for the ‘0000’ T2map image and the newly created T2map relaxation image.
Now for the DTI images, in CSPM, click ‘DTI’ → DTI Info (Bruker- alpha). Paste in the folder path of your method file in the box next to ‘File or Folder’, paste in the path of your ‘CONTROL’ folder in the box below and in the ‘Folder with nifti files’ box. Tick the ‘Rodent’ box and again, make sure to select the ‘Subfolders’ box so that it can process all subjects' DTI images in one go.
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Click on the ‘Apply DTI to Nifti’ button and then on the ‘Run DTI Processing’ button. This will create a MATLAB file for each of the 82 3D nifti DTI images, a mean image and a standard deviation image, a few text files. a ‘b0_images’ folder and a ‘tensors’ folder, in the ‘raw' folder.
You are now ready to perform preprocessing using the ‘Preclinical’ GUI as outlined in the next confluence page: ‘Preclinical Preprocessing’.