Time reduction and more

Forums Forums General Questions Time reduction and more

This topic contains 9 replies, has 2 voices, and was last updated by  leonidastra86 3 years, 2 months ago.

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  • #606

    leonidastra86
    Participant

    Is there a way to accelerate the procedure? I need sometimes 12-14 hours for just one patient.
    Do I need more Ram or a better processor?

    Is there a way to calculate also tumor-volumes? Or is it made just for normal brain? The results of the segmentation by patients with tumors, are they accurate?

  • #607

    Anand Joshi
    Moderator

    It should take 2-3 hrs for BrainSuite+SvReg on normal brains if there is sufficient memory and processing power available. Please make sure that there is >=4GB RAM free when you are running the software. For this purpose, closing as many programs as possible is helpful. Also make sure that hibernation or sleep modes are disabled.

  • #610

    leonidastra86
    Participant

    I have already tried it in my Macbook with Sierra and my PC with Windows 10, the first one has 8 GB Ram and the second 16. In both cases I have needed many hours for it. Is there something I should change in the configuration of the program? Does it have to do maybe with the patients, which all had a tumor? Does it work only with high resolution MRIs?
    Thank you for your time and responses!

  • #611

    Anand Joshi
    Moderator

    My guess is that due to tumor the surfaces generated by BrainSuite have too many faces or vertices. This is causing slowing down of the processes. You can try clicking surface registration only checkbox at the beginning of svreg sequence if you need only surface labels.
    What is the voxel resolution of the MRIs? As long as it is around 1mm it should not matter too much.

    • This reply was modified 3 years, 2 months ago by  Anand Joshi. Reason: edits
  • #613

    leonidastra86
    Participant

    1mm, its not so much.

  • #614

    Anand Joshi
    Moderator

    ok. it is probably related to the surface generated by BrainSuite is too complicated due to tumor. It would depend on shape of the tumor. I suggest first trying a normal brain. One example can be found here:
    http://brainsuite.org/tutorials/cseexcercise/
    If this brain also takes a lot of time then there is something wrong with the setup otherwise it is related to the tumor related cortical extraction issues.

  • #615

    leonidastra86
    Participant

    So, brain suite cannot be used for brain tumors. Is that right?
    What is the range of the voxel resolution which works with brain suite?

  • #618

    Anand Joshi
    Moderator

    There is no limitation on voxel size but 1mm is generally optimal for T1 brain scans. In our experience, BrainSuite generally works with tumor brains in the sense that the labeling of regions away from the tumor region is relatively unaffected. The execution time can vary for the tumor cases though it should not be too high. Did you get a chance to try normal brains with BrainSuite to make sure that the long execution time on your computer is not related to tumors?
    If possible, it would also be helpful if you can post a screenshot of your results with the tumor.

  • #619

    leonidastra86
    Participant

    With a normal brain I was going to try it today.
    I have already done it with many brains with tumor and the results are the following
    http://i63.tinypic.com/o8f9m9.jpg
    http://i66.tinypic.com/dxmzcg.jpg
    http://i66.tinypic.com/9uvm6c.jpg
    http://i65.tinypic.com/15ev6gl.jpg
    http://i65.tinypic.com/1z1tsgy.jpg
    As we see, the tumor is missing region. I cannot (directly at least) calculate its size or position.
    Furthermore, the tumor is shown normally in the 3D projection and not on the other side (like in mirror) which is mostly in MRI the case.
    Last but not least, it would be really interesting to have at the and of the analysis, at least the localisation of the tumor (parietal, central region, or much better more accurately specified). Thats shouldn’t be a problem for the software, as it is enough to compare the normal side and its structures with the tumor side.

  • #620

    leonidastra86
    Participant

    With the normal brain it took only 2 1/2 hours as you said.

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