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Ramesh Babu
2018-01-10
2018-01-20

  • Ramesh Babu

    Ramesh Babu - 2018-01-10

    Dear Experts,

    I am using ANTs for the first time. To learn I used 4 T1 images to crate template. I used .nii files with out skull stripping and "antsMultivariateTemplateConstruction.sh" script to get template. Before proceedig further, I need your suggestions. I have attached 3 template image links; before skull strip and after skull strip (using FSL-Bet) and template_warp.

    Script:
    bash antsMultivariateTemplateConstruction.sh -d 3 -m 30x50x20 -t GR -s CC -c 0 -o -z InitialTemplate.nii.gz *_t1.nii.gz

    https://drive.google.com/open?id=1EzTJmitC2QxUhLV1YahJJw3xiZ9PcgYn
    https://drive.google.com/open?id=1HNdCRU9LtjT_XniCsGlL5vpSUtKpGM_K
    https://drive.google.com/open?id=1QsDdjWt19l2hkhGLw5qAgsVfbZpn12Qs
    Please give your suggestions.

    Thanks
    Ramesh

     

    • Nick Tustison

      Nick Tustison - 2018-01-10

      What's your question?

      Perhaps before you use your own data, you should try to reproduce the examples available here.

       

  • Ramesh Babu

    Ramesh Babu - 2018-01-11

    Dear Nick,

    Thank you for your reply.

    I want to know whether the command which I have used is correct or modification is required?
    Please letme know.

    I have few more questions,I will post it after working on the example data which you mentioned.

    Thanks
    RB

     

  • Ramesh Babu

    Ramesh Babu - 2018-01-13

    Dear Nick,
    I downloaded example data and did analysis using the scritp in the folder. I have comapred with the result provided with the example folder. It is perfectly fine. Could you please help me to create template from my data? I want to select a particular image as initial template and feed into the command line. Please see the image details below and accordingly I want to modify the script/commandline.

    I am using dcm2nii for image conversion and fsl-bet for skull stripping.

    DICOM/IM_0004
    Field Strength: 2
    ProtocolName: T1W3DTFE1X1SENSE (3D image)
    ScanningSequence00180020: GR
    TE: 3.683000088
    TR: 7.494800091
    DimXYZT: 256 256 175 1
    ScanOrder: Interleaved
    VoxelDimensions: 1x1x1

    Thanks
    Ramesh

     

    • Nick Tustison

      Nick Tustison - 2018-01-13

      Did you try adapting the script from the example data to your data? Should be straightforward.

       

  • Ramesh Babu

    Ramesh Babu - 2018-01-15

    Dear Nick,

    I have created a template using the templateCommand.sh script. For a trial I used 3 subjects and created template before and after skull strip. Please see the attached file and give your input.

    https://drive.google.com/open?id=1mtef9p7Gu4jA1Sy4g1OY8ovWoGhsOX07

    https://drive.google.com/open?id=1KPjtkEPBQOyaZghp4Q4SOTrlPd6pm-1y

    Further I want to create tissue probability map for GM, WM and CSF by the samle template. Can I segment the template using fsl-fast segmentation tool?

    And finally I would like to know how to create atlas by using ANTs?

    Waiting for your valuable suggestions.
    Ramesh

     

  • Ramesh Babu

    Ramesh Babu - 2018-01-17

    Dera Nick,
    Happy to see your openion. I have few questions.
    1. For template creation using 40 data which script should I use? is it templateCommand.sh or other scripts?
    2. I want to select one of the data as initial template. How to modify in the script to include initial template?
    3. I have 3 groups including control. Should I select data only from controll group or randomly from all the groups?

    Thanks
    Ramesh

     

    • Nick Tustison

      Nick Tustison - 2018-01-17
      1. For template creation using 40 data which script should I use? is it templateCommand.sh or other scripts?

      Whichever one works best for you.

      1. I want to select one of the data as initial template. How to modify in the script to include initial template?

      Look at the -z option.

      1. I have 3 groups including control. Should I select data only from controll group or randomly from all the groups?

      Depends on your experiment. Standardized templates are typically limited to controls.

       

  • Ramesh Babu

    Ramesh Babu - 2018-01-18

    Dear Nick,

    Thank you for your suggesstions. It is encoursging to me.
    I request you to have a look on the attached log file (which I saved from terminal), in some places I notice "core dumped" (in line 334, 347, ..) and "not found" (in line 2135, 2149....). Is it indicating error? Please clarify.

    And I want to build atlas & label and tissue probability map. Which model/script is best suitable for this?

    Thanks
    Ramesh

     
    MultivariateBsplineSyN-log

  • Ramesh Babu

    Ramesh Babu - 2018-01-19

    Dear Nick,

    I have downloaded example data for Atropos and Brain Extraction example. I found template, priori and mask images in the downloaded folder. By using the scripe I got the same result as given the example.

    I have created tempalte using my data by using various template command. I got a good template.

    But how to create mask from the template and priori to preceed further?

    What are the steps should I follow to create atlas with label?

    Thanks
    Ramesh

     

    • Nick Tustison

      Nick Tustison - 2018-01-20

      The steps are described in this paper.

       

  • Ramesh Babu

    Ramesh Babu - 2018-01-20

    Dear Nick,
    Thank you very much. It will be very helpful for me if you send me the full paper.

    Thanks
    Ramesh