Dear MRtrix3 users,
I’m working on a fiber bundle, I want to extract the volume of this bundle, and visualize it in 3D volume, Is it possible with MRtrix3?
If so how can I do it?
Your help is highly appreciated,
Best,
Abir.
Hi Abir,
I hope what will be written here do the job for you!!
Here is the same topic that has been answered by @rsmith, https://community.mrtrix.org/t/calculating-the-tract-volume/3936?u=salah.
In terms of the 3D visualization:
You can see the 3D volume of the bundle in mrview > view> Volume render. Then you need to go to Tool > View options > In the section [clip planes], there is + with a little arrow, and when you press it a sublist will appear that has axial, sagittal, and coronal. Choose the plane and you will see the 3D of the bundle.
Dear Salah,
Thank you very much for your response,
So if you understand me, I will measure the volume of the fiber bundle as a quantitative parameter of the tracography, is this possible or not with mrtrix3?
Also for the mrthreshold command, I had difficulty choosing the option to control the thresholding?
Any help or clarification is highly appreciated,
Best,
Abir
1 Like
Hi Abir,
From what has been suggested by @rsmith, yes you can use MRtrix3 to calculate the volume of a specific tract.
For me, I found using fsl to calculate the volume is far easier 
. However, I had a go using mrthreshold, and it shows easy to be used but I found difficulty calculating the volume at the end of the pipeline as it is not straightforward. Here is what I have done:
-
tckmap -image DIR/fa.mif -template DIR.fa.mif DIR/input_tract.tck DIR/out_tract.mif(here I created FA.mif for the interested tract) -
mrthreshold DIR/out_tract.mif Dir/bin_out_tract.mif(here I created a binary image based on the interested tract). -
mrstats Dir/bin_out_tract.mif -output count(here I calculated the number of voxels within the mask.
BUT I was not able to calculate the volume of the tract by multiplying the volume of the voxel that could be found using mrinfo DIR/bin_out_tract.mif. So maybe one of the experts here(@rsmith @jdtournier) or any other expert could correct me and add their input 
.
Regards,
Salah
Dear Salah,
Thank you very much for the information,
I really appreciate it,
Best,
Abir.
One potentially interesting feature of quantifying tract volume is that the measurement can be dependent on the resolution of the voxel grid to which the streamlines are mapped. E.g. Imagine that your template image is a single voxel that encapsulates the entire brain image FoV: you would count at least one streamline within this voxel, and conclude that the volume of the tract is larger than the volume of the brain 
Conversely, if the spatial resolution is too small and/or the number of streamlines is inadequate, then a basic mapping to a voxel grid followed by thresholding may yield a lot of holes within the tract and hence under-estimate volume. Food for thought…
Also for the mrthreshold command, I had difficulty choosing the option to control the thresholding?
By “difficulty”, do you mean that you could not choose which thresholding mechanism was most appropriate for your use case? If so, this is entirely commensurate with the ambiguity of the problem. You would at least not an observation of variations in tract volume across participants to have arisen solely from variations in how such thresholding was computed; so you could probably work backwards from there to think about which approaches are more or less appropriate. I certainly wouldn’t use the -top option, since it’d select the same number of voxels per participant and hence give an identical volume per participant…
BUT I was not able to calculate the volume of the tract by multiplying the volume of the voxel … So maybe one of the experts here … could correct me and add their input
Very well…
echo $(mrstats bin_out_tract.mif -mask bin_out_tract.mif -output count)*$(mrinfo bin_out_tract.mif -spacing | cut -d " " -f 1-3 | tr " " "*") | bc
Rob
1 Like