Measuring bundle volume

Questions about BrainVisa usage and installation

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houenou
Posts: 62
Joined: Tue May 31, 2005 2:28 pm

Measuring bundle volume

Post by houenou »

Hi,
I can't remember how I can get the "volume" of a bundle created with Brainvisa. By volume, I mean the number of voxels crossed by the bundles.
Is it with comistBundleAnalysis where I can see this -o option:
points_count: the total number of curves points in a bundle
What do you mean by "curves points?"
Thanks
Josselin
denghien
Posts: 209
Joined: Mon Apr 05, 2004 1:35 pm
Location: IFR49 / SHFJ Orsay
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Re: Measuring bundle volume

Post by denghien »

Hi,

Yes you can read the points_count field in the help of comistBundleAnalysis command but in fact the documentation is obsolete.
Additionally, I guess that this value wasn't exactly what you want. The informations were data about the sampling of bundles not for voxels.
So if you want to know the number of voxels corresponding to a bundles, you can use the following steps :
-> convert your .bundles into a binary volume, for example
comistBundles2Ima -i bundles_sujet-2_default_tracking_session.bundles -o mask_bundles -r ../../t2diff_sujet-2.nii -m 1

-> compute "stats" on your binary volume
AimsRoiFeatures -i mask_bundles.nii -o my_result.txt

-> the result wiil something like that :
attributes = {
'format': 'features_1.0',
'content_type': 'roi_features',
'1': {
'point_count': 8487,
'volume': 59674.2,
},
}

Here we have 8487 voxels in the mask of the .bundles.
Be careful of the value of volume because it depends on the voxel size of volume so the volume that you used with the -r option in the comistBundles2Ima command.


I have a question for you too !
Could you give some information about your using of DTI pipeline ? Which model do you use ? Which algo of tracking do you use ....



Isa
houenou
Posts: 62
Joined: Tue May 31, 2005 2:28 pm

Re: Measuring bundle volume

Post by houenou »

Hi,

Thanks for your help. About this 'point_count' statistic: does it count the number of voxels crossed by fibers OR the number of total voxels included in the bundle
i.e. if several fibers cross a single voxel, will this voxel be counted several times ?

About your question about my usage of DTI pipeline, as I am working with Cyril Poupon here in Neurospin, I use mostly his "homemade" (Ptk) routines.
And I am doing mostly deterministic tractography with Q-ball models.

Josselin
denghien
Posts: 209
Joined: Mon Apr 05, 2004 1:35 pm
Location: IFR49 / SHFJ Orsay
Contact:

Re: Measuring bundle volume

Post by denghien »

Hi,

About the 'point_count' field coming from AimsRoiFeatures: in our example, it is the number of voxels in the volume. Your image is a binary mask of your bundles, so it corresponds to number of voxels for all bundles. If many bundles cross the same voxel, you already have one voxel.

Now if you want to have an information about "how many times this voxel is crossed by all bundles ?", you can use comistBundles2Ima with the "m -2" option.
This option can compute a density map : each time a bundle crosses a voxel, so 1 is added to the grey level of this voxel. If you have "3" as value, it means that 3 bundles have crossed this voxel.

Note that the using of AimsRoiFeatures is large enough, you can use other specifc graph/volume to compute other statistics.

I have another question about you using of comistBundleAnalysis. It seems the "points_count" field has been removed perhpas for many years (or months). Did you already used this field ?

Isa
houenou
Posts: 62
Joined: Tue May 31, 2005 2:28 pm

Re: Measuring bundle volume

Post by houenou »

Thanks for your explanations,
Yes I already used this field (or the AImsRoiFeatures I can't remember).
I think this stat is useful to estimate the volume of a bundle. In the literature this kind of metric seems now more used than the the number of reconstructed fibers.

Josselin
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