5ttgen hsvs result modification

[KikukoK]

Hello,

I am attempting to create a 5TT.mif file using 5ttgen hsvs for ACT. The resulting image looks quite good overall (Screenshot1), but the cerebellum area could be improved. I would like to replace only this specific section with the results from SynthSeg (Screenshot2).

I tried creating a SynthSeg2ACT.txt file modeled after FreeSurfer2ACT.txt (Screenshot3. I am actually interested in using only the highlighted sections).

I looked into /usr/local/mrtrix3/lib/mrtrix3/_5ttgen/hsvs.py, but the script was quite complex, and I was unsure which part to modify. Any tips or guidance would be greatly appreciated!

Thank you in advance.

[adsouza]

Hello,
Check out the 5ttedit command. If you are able to extract the white-matter and SGM component of the SynthSeg segmentation, something like this might work:

5ttedit <5ttact.mif> -wm <cerebellum_wm_synthseg.mif> -sgm <cerebellum_sgm_synthseg.mif> <modified5TT.mif>

Hope this helps

[adsouza]

and, to extract the relevant structures from SynthSeg, something like this might be helpful

for region_index in <list_of_index_of_interest>
do
mrcalc <synthseg_segmentation> ${region_index} -eq extracted_region_${region_index}.mif
done

Then add all the relevant extracted regions to create a single cerebellum WM image <cerebellum_wm_synthseg.mif>, and repeat for SGM to create <cerebellum_sgm_synthseg.mif>

[KikukoK]

Hi Arkiev,

Thank you very much! Your advice was really helpful.
I put it into practice and got the image I expected.

I’ll list the commands that I used here in case they might be helpful for others.

for i in 8 47; do mrcalc synthseg.nii.gz $i -eq gm_extracted_${i}.mif; done
for i in 7 46; do mrcalc synthseg.nii.gz $i -eq wm_extracted_${i}.mif; done
mrcalc gm_extracted_8.mif gm_extracted_47.mif -add  cerebellum_gm.mif
mrcalc wm_extracted_7.mif wm_extracted_46.mif -add cerebellum_wm.mif
mrtransform cerebellum_wm.mif -template 5TT.mif cerebellum_wm_transformed.mif
mrtransform cerebellum_gm.mif -template 5TT.mif cerebellum_gm_transformed.mif 
5ttedit 5TT.mif -wm cerebellum_wm_transformed.mif -sgm cerebellum_gm_transformed.mif modified_5TT.mif

Best,
Kikuko