Batch processing come to no result

[yh]

Hi frank , I got a new question. I have make some tract template and save them into autotrack list to run batch autotracking. eg. I have merged cortical pontine tracts in hcp1065 1mm template and save them as a niity file and save it into autotrack list,finally run batch autotracking (this merged tract) in my 30 CON group data. But 7case show no result. How can it be no reslt considering this is a rather obvious tract?  May be i need to modify the tract template that i made? or changing the batch autotracking parameters? or something else? please help!

Thank You!

[yh]

Hi , Frank

       Maybe I should post more detail about my question so that I can make it clear. 

       Figure 1 shows how I made the track template[cortical-potine tract was generated by merging 3 different component(parietal, frontal, occiptal) of cortical-potine tract with 0.5m seeds and some other parameters shown in the figure). 

       Figure 2 shows how I use tract templat that made by myself  to run batch processing of fiber tracking(by default setting). This step was according the method you have mention before( tracking the fiber in hcp 1065 1mm template and save all of them into a file. 

       Figure 3 shows in some cases come out with no result. 

       For Dentaorubrothalamic_track in figure 4,  I just apply the same tracking parameter(I try to keep the same tracking parameters in major tract template making) in making my own tract template compared with the original default track parameters(no merge, no cut, no additional  pruning).

      Figure 5 shows which tract I have make my own trat template. As you have suggested that Middle cerebellum peduncle and central tegmental tract was no longer tracked.  They were save as region file and will use fslstats to get mean FA.

      Really hope get some hints from you!  Thanks!

[Frank Yeh]

Sorry for the late reply.

You may increase the "tolerance" to see if it works for you.

Frank

On Sat, Aug 14, 2021 at 4:05 PM yh <beijin...@gmail.com> wrote:

Hi frank , I got a new question. I have make some tract template and save them into autotrack list to run batch autotracking. eg. I have merged cortical pontine tracts in hcp1065 1mm template and save them as a niity file and save it into autotrack list,finally run batch autotracking (this merged tract) in my 30 CON group data. But 7case show no result. How can it be no reslt considering this is a rather obvious tract?  May be i need to modify the tract template that i made? or changing the batch autotracking parameters? or something else? please help!

Thank You!

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[Frank Yeh]

replace 16, 18, 20 with 16, 18, 20, 22, 24

[yh]

Hi Frank

     I am so happy that your suggestion worked.Afer setting tolerance into 16,18,20,22,24, 5 of 7 cases that has no result in batch autotracking has result now!  

    But there are 2 cases remain  no result when i repeat the processing of batch autotraching cortex-potine-fiber. As you have suggested QC for another discussion, i have checked the data of the remain 2 cases and cant find any bug。

    So, may i upload the data of these 2 cases to get your help?

[Frank Yeh]

I did not see uploaded data. Can you resend them (*.src.gz)?

Frank

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[Frank Yeh]

Hi Hu Yin,

    The files you uploaded are

Hu yin - HCP1065.tt.gz
Hu yin - HCP1065.tt.gz.txt
Hu yin - HCP1065_tracking_0.5m.ini

    I won't be able to check data for you unless the SRC files are uploaded.

Best regards,

Frank

[yh]

Hi Frank

     For some reason that the uploading process failed several times but now finished, please check!

     By the way, it seems that there is no "track" file folder in the new version of DSI studio(figure1)  but the tract template that made by myself was usually stored  in that file folder in older version of  DSI studio(figure2) . Where is it now? I browsed all related file folder, find no "track" folder. What should we do in the new version now?

Best wishes

Hu yin

[Frank Yeh]

\atlas\ICBM152\ICBM152.tt.gz

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[yh]

HI Frank

      I have uploded 3 cases data, please check. If you cant see, please let me know!

Best wishes

Hu yin

[Frank Yeh]

The problem is due to a low b-value setting (b=1000) and not enough sampling directions (64).

Another user is also having the same problem: https://groups.google.com/g/dsi-studio/c/wfXcuxk1I3g

It is due to data acquisition issues.

Frank

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