FA and MD color maps for regions or lesions

[Joshua Adache Ojile]

Hi Dr. Frank,

I am assessing diffusion metrics in specific brain regions and around lesions. I want to generate color maps (for example, using a “jet” colormap) that display only those regions or lesions alone (without the rest of the brain).
Also, instead of just getting summary statistics (mean, min, max) of a parameter (say MD), I want to export the full voxel-wise values (for the region/lesion), and transform those values into z-scores.
Could you provide guidelines or useful resources on how to do these steps in DSI Studio?

Thank you.

Best regards, 

Joshua

[Frank Yeh]

> I am assessing diffusion metrics in specific brain regions and around lesions. I want to generate color maps (for example, using a “jet” colormap) that display only those regions or lesions alone (without the rest of the brain).

Use [Region Misc][Save Region Color] to save color as text file and
the last column is the opacity.
Setting it to zero will make a region entirely transparent and thus not visible.

> Also, instead of just getting summary statistics (mean, min, max) of a parameter (say MD), I want to export the full voxel-wise values (for the region/lesion), and transform those values into z-scores.
> Could you provide guidelines or useful resources on how to do these steps in DSI Studio?

One approach is to read .fz file (sample code at brain.labsolver.org)
directly to get the image volume of each metrics.

Another way is to use [Region Misc][Save Voxel Data as]

Best regards,
Frank

>
> Thank you.
>
> Best regards,
> Joshua
>

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[Frank Yeh]

Currently, DSI Studio renders regions as surfaces, not based on
underlying voxel data. This design means we aren't able to present
specific voxel information beneath the surface. For this reason, we
typically assign a single, unifying color to each region.

I am sorry that I don't have a quick solution to this feature.
Best regards,
Frank

On Wed, Oct 15, 2025 at 10:05 AM Joshua Adache Ojile
<ojile.jos...@gmail.com> wrote:
>
> Hi Dr. Frank Yeh,
>
> Thank you for the quick response.
>
> For the first part of my question, I tried to use [Region Misc][Save Region Color] as mentioned, but it saves the regions as a single static color. I want to apply a transient color map, like 'jet', to the segmented region. For instance, in the image attached, instead of having a single color, I have a jet color to match the color bar.
>
> I tried using [Slices][Load color map], but it applies the map to the entire brain, and not the legion area alone.
> Is there another approach to achieve this using DSI Studio?
>
> Thank again.
>
> Best,
> Joshua