What do the statistical outputs from fiber tracking mean

[akiraw...@gmail.com]

Hi Frank, 

I was wondering what the outputs from fiber tracking mean (see following)?

number of tracts 

mean length(mm) 

span(mm) 

curl 

elongation 

diameter(mm) 

volume(mm^3) 

trunk volume(mm^3) 

branch volume(mm^3) 

total surface area(mm^2) 

total radius of end regions(mm) 

total area of end regions(mm^2)

irregularity 

area of end region 1(mm^2) 

radius of end region 1(mm) 

irregularity of end region 1 

area of end region 2(mm^2) 

radius of end region 2(mm) 

irregularity of end region 2 

qa 

nqa 

dti_fa 

md 

ad 

rd

gfa 

iso 

rdi 

nrdi02L 

nrdi04L 

nrdi06L 

I went through the DSI studio website but could not seem to find any detailed explanation. I was wondering if you happen to have some documents that can help me understand what each variable means. Thank you so much for your help!

Sincerely,

Akira

[Frank Yeh]

Hi Akira,

    You may check out https://www.sciencedirect.com/science/article/pii/S1053811920308156 for details:

Best regards,

Frank

--
You received this message because you are subscribed to the Google Groups "DSI Studio" group.
To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/ac1ac97a-3f29-4b51-b799-274cde93d174o%40googlegroups.com.

[yh]

Hi Frank,

   

    I havd read the paper you recommended and want to use shape analysis in my study. But i got some confusion:

    Q1 Do you mean that the shape analys is based on the three precondition(parameter saturation, atlas-based track recognition/filtering, and topology-informed                  pruning)? If without these 3 measuerment in the data processing, the shape related descriptors is not reliable or should not do shape analysis（garbage in,                garbage out）?

  Q2 If i want to conduct shape analysis in my data, could you please provide more information about parameter saturation(what else tools in addition to DSIstudio              can i use? is there any protocal?   According to what I know, the second and third part(atlas-based track recognition/filtering, and topology-informed                            pruning)has already in the Dsistudio software,  so  no specific procedures are needed?

  Q3 I am extremly intrested in the isssue you mentioned in you papaer about the innervation cortical area, do you have any progress in measure this shape                       descriptor?   when i have a discussion with my teacher about your idea about projecting tract termination  to the gyral surfacea, he shows me a paper "Diffusion         Imaging in the Post-HCPEra",DOI: 10.1002/jmri.27247. The figure 2 shows some innervation related detail that should be take into account.

Best regards,

Hu Yin

在 2021年2月18日星期四 UTC+8上午11:21:32，Frank Yeh写道：

To unsubscribe from this group and stop receiving emails from it, send an email to dsi-s...@googlegroups.com.

[Frank Yeh]

>
> Q1 Do you mean that the shape analys is based on the three precondition(parameter saturation, atlas-based track recognition/filtering, and topology-informed pruning)? If without these 3 measuerment in the data processing, the shape related descriptors is not reliable or should not do shape analysis（garbage in, garbage out）?

Possible. Good test-retest reliability is the prerequisite.

>
> Q2 If i want to conduct shape analysis in my data, could you please provide more information about parameter saturation(what else tools in addition to DSIstudio can i use? is there any protocal? According to what I know, the second and third part(atlas-based track recognition/filtering, and topology-informed pruning)has already in the Dsistudio software, so no specific procedures are needed?

This documents mentioned the steps:
http://dsi-studio.labsolver.org/Manual/automatic-fiber-tracking
They will include all these strategies mentioned.

>
> Q3 I am extremly intrested in the isssue you mentioned in you papaer about the innervation cortical area, do you have any progress in measure this shape descriptor? when i have a discussion with my teacher about your idea about projecting tract termination to the gyral surfacea, he shows me a paper "Diffusion Imaging in the Post-HCPEra",DOI: 10.1002/jmri.27247. The figure 2 shows some innervation related detail that should be take into account.
>

You can export the track end-point from DSI Studio, either from GUI or
the command line.
They should be very close to the gyral surface.
Frank

> To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/9cc4354a-26e6-4913-8ed3-e04a4b66be6eo%40googlegroups.com.

[yh]

Hi Frank,

   

   I got only 1 MRI scan (single shell b=1000, n=64,and  b=0, n= 3) in every subject(30con VS 30pat),  No repeat scan（AVM patient will not come back after receiving surgery）.

   Can I conduct the shape analysis ? I have see the batching autotracking result,  there are lots of indices and i am wondering whether my data is  qualified for shape analysing?

    

Best regards,

Hu Yin

在 2021年2月22日星期一 UTC+8上午11:49:02，Frank Yeh写道：

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/9cc4354a-26e6-4913-8ed3-e04a4b66be6eo%40googlegroups.com.

[Frank Yeh]

Yes, any tractography can be analyzed by shape analysis, but the low
b-value setting of your data may not be able to map all pathways,
particularly some projection pathways.
Frank

> To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/1d15d28a-a46b-4582-b6f4-905a73943b33o%40googlegroups.com.

[yh]

Hi Frank,

I have explored the DSIstudio to do the first step - “parameter saturation“ but it seems cant do that in DSIstudio GUI. I try to find help in command line instruction but failed, So could you please tell me how can I complete “parameter saturation” (in command line or in GUI? random generator means matlab command line? And them insert the command line into DSIstudio command line ?)

    If possible may I know the example command line about “atlas-based track recognition/filtering, and topology-informed pruning” at the same time?

Best Wishes!

Your sincerely Yin Hu.

 

Department of neurosurgery, Beijing Tiantan  Hospital, Capital Medical University.

No.119 West of south 4^th ring road, Fengtai District, Beijing, China.

Tel: +86 18810252625
在 2021年2月22日星期一 UTC+8下午1:22:17，Frank Yeh写道：

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/1d15d28a-a46b-4582-b6f4-905a73943b33o%40googlegroups.com.

[Frank Yeh]

The default parameters with a large number of seeds or tracts are the
"parameter saturation"
Frank

> To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/6398e10e-cb87-4333-bf98-be623b2e30c5o%40googlegroups.com.

[yh]

Hi Frank,

  I am so glad to know this. Since you don’t mention “atlas-based track recognition/filtering, and topology-informed pruning”, is it appoprate that both of these two steps are also integrated into the batch autotracking function in DSIstudio? 

  If not, please tell me how can I do these steps?

Best Wishes!

Your sincerely Yin Hu. 

Department of neurosurgery, Beijing Tiantan  Hospital, Capital Medical University.

No.119 West of south 4^th ring road, Fengtai District, Beijing, China.

Tel: +86 18810252625

在 2021年3月22日星期一 UTC+8上午11:45:01，Frank Yeh写道：

> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/6398e10e-cb87-4333-bf98-be623b2e30c5o%40googlegroups.com.

[Frank Yeh]

Yes, they are.
Frank

> To unsubscribe from this group and stop receiving emails from it, send an email to dsi-studio+...@googlegroups.com.
> To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/315f4a23-8db4-4ae2-b47a-48c1039d8e10o%40googlegroups.com.

[yh]

Hi Frank,

There are another question about your suggest: "export the track end-point". A .txt file containing a lot of numbers will be produced after this procedure. What dose these numbers mean? Are they coordinates of fibre end? If so, it should contain both end coordinates? How can I distinguish a specific end point belong to end1 or end2? In addition, can I get an volume file (.nii)  of end point for further analysis?

By the way, I don’t know is it appropriate to project these endpoint to surface to get innervation area information (different area with different innervation fibre number (or ratio) ).

Hope to hear your advice.

Best Wishes!

Your sincerely Yin Hu. 

Department of neurosurgery, Beijing Tiantan  Hospital, Capital Medical University.

No.119 West of south 4th ring road, Fengtai District, Beijing, China.

Tel: +86 18810252625

[Frank Yeh]

There are another question about your suggest: "export the track end-point". A .txt file containing a lot of numbers will be produced after this procedure. What dose these numbers mean? Are they coordinates of fibre end?

 

Yes 

 

If so, it should contain both end coordinates?

 

Yes

 

How can I distinguish a specific end point belong to end1 or end2?

 

by checking the coordinate values to see which one close to one end.

 

In addition, can I get an volume file (.nii)  of end point for further analysis?

[Tracts][Endpoints to ROI] 

By the way, I don’t know is it appropriate to project these endpoint to surface to get innervation area information (different area with different innervation fibre number (or ratio) ).

The answer depends on the projects and applications.

Best regards,

Frank

 

To view this discussion on the web visit https://groups.google.com/d/msgid/dsi-studio/b061160f-bc27-4329-b96f-f0a590cba056n%40googlegroups.com.