4D timetrends
MRIcroN can display timetrends when you click on a brain location, so it's great for exploring data.
Open and view
- Window => 4D Traces
- Select data in 4D *.nii.gz format (see below)
- Optionally, select an events file (to show lines where challenges start, and to do averaging)
- Optionally, select a VOI file (or multiple files); this will show timetrends from the voi's only
- Enter the TR in the menubar
Now if you double-click on the image (assuming you did not select a VOI), it will show the timetrend at that voxel.
Important!!
The data are shown without reslicing, which nearly always means L/R flipped. Further, you should not have any image yoked, otherwise it gets muddled trying to yoke voxel data to MNI space coordinates.
To turn off yoking: View, Yoke (deselect)
Another option if you really want to yoke is to turn off reslicing ("Help" => "Preferences" => deselect "Reorient", restart MRIcroN) - but remember that the all images need to be in the same space with the same slice orientations/locations etc for yoking to work (you can use the coregister, reslice option to create say a T1 file in the same space as an fMRI file).
Creating files
You make the 4D file using CSPM in two steps: 1) Create 4D file: "Image" => "Convert 3D to 4D" (note that the 3D files will be replaced, so you may want to copy them to a new folder first). 2) Convert the 4D *.nii file to *.nii.gz: "Image" => "Convert nii.gz <=> nii" (change the file type to "nii" so you can see the 4D file you created)
The events files are text files with the time, duration (both in seconds) and event number recorded row-by-row, in time sequence - e.g.: 70 40 1 150 40 1 230 40 1 (save as something like events.txt).