Once you have converted the raw data for all subjects, as outlined in the 'MP3 Conversion of Raw Data’ page, follow these instructions to organise your files and folders. An example of what your folder organisation should look like, that you can refer to throughout the process: Y:\Preclinical_PET_MRI\Melbourne_PET_MRI\MRI\Longitudinal\Analysis_All_Subjects. Please take care not to move or delete any files in these folders.
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Write down the pitch, roll, yaw and crosshair position values (make sure to click enter on the mm crosshair position values so that it sets the vx values, otherwise they will change) in 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 9-16 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.
Paste in the folder path of your method file (Anita: the method file you should use is Y:\Preclinical_PET_MRI\Richelle_TBI\Raw_Data\SS3\20200416_191007_ARAMRA007_SS3_006_M_I_1_1_1\5\method) 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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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 (Anita: the method file you should use is in Y:\Preclinical_PET_MRI\Richelle_TBI\Raw_Data\SS3\20200416_191007_ARAMRA007_SS3_006_M_I_1_1_1\6\method) 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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