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.
Open a new ‘MATLAB’ window and type '2' into the command window.
On the network drive, create a folder and name it to describe the type of analysis e.g. ‘Longitudinal_Analysis’.
Within this folder create 2 sub-folders: ‘projects’ and 'stats'.
Within the ‘projects’ folder create a ‘CONTROL’ folder.
Within the ‘CONTROL’ folder create Copy over a folder for your individual subject e.g. ‘LM001_Day2_PostCCI’.
Create a folder named ‘anatomical’ with a sub-folder named ‘coreg (native)’, a folder named ‘T2map' with a subfolder named ‘raw’, a folder named ‘DTI’ with a sub-folder named ‘raw’, a folder named ‘fMRI’ with the subfolders ‘rest01’, ‘stimulus01’ and ‘stimulus02' (etc. depending on how many functional scans were collected), with 'raw’ sub-folders in each of these fMRI subfolders.
To save time, copy and paste the individual subject folder (in this example, the ‘LM001_Day2_PostCCI’ folder) for as many subjects you have i.e. if you have a total of 50 subjects, copy and paste the folder 50 times and then rename each folder with it’s subject’s name. This saves you from having to create all of these subfolders for each subject (would be very time consuming).
Now copy in the necessary files from your ‘Converted data’ folder into each of the folders within the subject folder.sub-folders as outlined in the table below:
Folder | Sub-folders | Files* |
|---|---|---|
'anatomical' | ‘coreg (native)’ |
|
'T2map' | ‘raw’ | Leave empty for now. Refer to STEP X………. |
'DTI' | ‘raw’ |
|
fMRI | ‘rest01'
‘stimulus01'
‘stimulus02’
|
|
*All of these files are 4D nifti images which need to be converted into 3D nifti images. Once you have copied a file into the right folder and renamed it, in the CSPM GUI, click Image → '4D nifti to 3D', paste in the file path and select the 4D nifti file. This will create 13 3D images for the T2map, 82 3D images for the DTI and 136 3D images for the fMRI. Do this 4D to 3D conversion as you go.
Open the first subject’s folder and then click into the ‘anatomical’ folder and the ‘coreg (native)' sub-folder. In the SPM12 GUI, click the ‘Display’ button, paste in this file path and select the first T2map image i.e. the one ending in ‘0000’. It will look something like this:
...
Click the ‘Origin’ button.
You will need to play around with the ‘pitch’, ‘roll', and ‘yaw’ values (trial and error) until the image is realigned and the coronal slice appears in the top left corner, the sagittal on the right and the axial under the coronal, like so:
...
Move the crosshairs to the anterior commissure (just by clicking on the anterior commissure):
...
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)
once you run the ‘Preprocess to Coreg’ step, it will create ‘coreg’ folders in each of these folders