How to judge whether the results of the dwi2fod is right?

1

Hi Community,
I ran the following command:
dwi2fod msmt_csd DWI.mif RF_WM.txt WM_FODs.mif RF_GM.txt GM.mif RF_CSF.txt CSF.mif -mask nodif_brain_mask.nii.gz

I obtained result of FOD as following:

FOD_label.png600×751 231 KB

The red box part as below:

FOD3.png1427×380 188 KB

How to judge whether the results of the dwi2fod is right?

Any suggestions there?
Thanks,
Jian

2

It is pretty hard to tell from these images.

Could you increase the scaling of the fODFs to 2-3 in the ODF display tool and then show full high-resolution orthogonal slices?

Ideally you would show:

axial slice featuring the genu of the corpus callosum
sagittal slice featuring the cingulum
coronal slice featuring the cortico spinal tracts

While you are at it, also increase the detail from 3 to 5 in the ODF display tool.

3

Hi @bjeurissen,
I made the changes, as following:

FOD4.png1181×808 446 KB

axial slice

FOD5.png1181×802 711 KB

sagittal slice

FOD6.png1185×807 485 KB

coronal slice

FOD7.png1187×805 640 KB

Please give me some advice, thank you!
Jian

4

There is definitely something odd-looking about that corpus callosum, particularly in anterior part where it lines the ventricles - the rest of the brain looks good. I doubt it’s anything to do with the CSD itself (I expect you’d find similar issues using a tensor-based analysis - easy enough to verify if you need to).

I recommend you look through your raw data and check whether any of your volumes are corrupted in this region.

Also, maybe you can tell us a bit more about your acquisition parameters (b-value, number of directions, resolution, etc), and what processing you’ve done on these data/

5

How to judge whether the results of the dwi2fod is right?

Please give me some advice, thank you!

More generally, if you’re trying to do a visual assessment of FOD estimation in a healthy brain, what you’re looking for is:
Estimated fibre orientations that are or are not consistent with the spatial continuity of the bundle.

For instance, take a look at this zoomed coronal view of the centrum semiovale where the FODs are clearly “wrong” (looks like pathways with high fibre density just vanish):

Bad_FODs.png710×419 171 KB

If you’re unfamiliar with the anatomy, comparing your images against those presented in relevant journal articles may help.

Cheers
Rob