Slice Visualization

DSI Studio has a built-in image registration function to present T1w or T2w images along with tractography. To use this function, select [Slices][Insert T1W/T2W Images] and assign DICOM or NIFTI files to provide the source data. Image registration will be conducted in the background. Once you load the structural images, DSI Studio starts a background registration. You may need to wait for a while until it reaches a good registration. 

To save the transformation matrix, select [Slices][Save registration]. The transformation matrix can be exported to a text file. You may also load an external transformation matrix in text format by [Slices][Load mapping]. This will stop the background registration and overwrite it.

To visualize image in a different color maps, clicking [Slices][Load Color Map] and select the PET_RGB.txt file.

MNI space statistical mapping

The statistical mapping from fMRI is often in the MNI space, and thus it cannot be added like the subject's T1W or T2W images. DSI Studio can handle this by loading it using [Slice][Insert MNI images...]. DSI Studio will first calculate the registration map between the subject's data and the MNI space and apply this mapping to warp statistical map to the native space. 

The following steps create an overlay from the added image:

(1) Choose the [Slice] at [Step T3b Draw Region] to view the slices that will serve as an overlay image. You may add any T1W or T2W by [Slice][Insert T1W/T2W images] to include external images as additional slices.

(2) Change the contrast color by clicking the contrast color button and adjust the contrast value (see figure to the left). The color for the maximum value can be changed to red or yellow. The two value input box controls the minimum and maximum contrast values. Any value between the maximum and minimum range will be an overlay on other images. 

Image overlay

DSI Studio supports multiple overlays. If you would like to have two overlays (e.g. red or positive value blue for negative value), you will need to duplicate the slices and assign them as the "overlay", respectively. The one assigned later will be on the top overlay.

To create a duplicated slices, you can insert the external slices twice. For internal slices, you can save the slices as an NIFTI file and insert the file using [Regions][Insert T1W/T2W images]

(3) Check the "overlay" checkbox and switch to other image modality to see the overlay result:

(4) The mosaic overlay can be created by changing the  [region window][slice layout] in the Option Window to the right: