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tortoise_dti [2014/06/27 12:22]
pmolfese
tortoise_dti [2014/06/27 12:23] (current)
pmolfese
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 Now that we have our data preprocessed,​ you will want to launch DIFF_CALC. ​ You can do this by double clicking on the calcvm program.  ​ Now that we have our data preprocessed,​ you will want to launch DIFF_CALC. ​ You can do this by double clicking on the calcvm program.  ​
  
-{{ :​tortoise_diff_calc_1.png?​direct&​300 |}}+{{ :​tortoise_diff_calc_1.png?​direct&​400 |}}
  
 The first thing you will notice about DIFF_CALC is that the user interface is fairly spartan looking. ​ Don’t be fooled, as part of TORTOISE, this application has plenty of power and is full of features. ​ The second thing that you may notice is there is a tiny floating window with one button for “sensitize the buttons”. ​ Whatever you do, don’t close that tiny floating window, it will help you recover later if you accidentally close a window without clicking “Done”. The first thing you will notice about DIFF_CALC is that the user interface is fairly spartan looking. ​ Don’t be fooled, as part of TORTOISE, this application has plenty of power and is full of features. ​ The second thing that you may notice is there is a tiny floating window with one button for “sensitize the buttons”. ​ Whatever you do, don’t close that tiny floating window, it will help you recover later if you accidentally close a window without clicking “Done”.
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 //Note: If you happen to close the window using the close button in the top of the window, you will notice that you’re locked out of the user interface. ​ Here’s where clicking the “sensitize the buttons” button will save you and restore your access to the user interface. // //Note: If you happen to close the window using the close button in the top of the window, you will notice that you’re locked out of the user interface. ​ Here’s where clicking the “sensitize the buttons” button will save you and restore your access to the user interface. //
  
-{{ :​tortoise_gen_mask.png?​direct&​300 |}} +{{ :​tortoise_gen_mask.png?​direct&​400 |}} 
  
 Now that a mask has been created, you can verify the mask using the “display mask” button. ​ This will display the window below where the mask includes regions in blue and excludes regions in red.  If the mask is not where you want it to be, go back to the mask options and try a different threshold. Now that a mask has been created, you can verify the mask using the “display mask” button. ​ This will display the window below where the mask includes regions in blue and excludes regions in red.  If the mask is not where you want it to be, go back to the mask options and try a different threshold.
  
-{{ :​tortoise_show_mask.png?​direct&​300 |}}+{{ :​tortoise_show_mask.png?​direct&​400 |}}
  
 At this point, you can start to actually fit tensors! ​ Click the “opt” button next to “process tensors” and you will see the window below, which allows you the option of doing linear and nonlinear tensor fitting. ​ You can also do fits via [[http://​www.ncbi.nlm.nih.gov/​pubmed/​15844157|RESTORE]] and [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22287298|iRESTORE]]. ​ For the money, the nonlinear estimation is often recommended over the linear and costs you only marginally more time for the estimation. ​ I also find it useful to display the residuals and to sort them!  It’s important that now that you’ve setup the options, you push the “process tensors” button on the main window. At this point, you can start to actually fit tensors! ​ Click the “opt” button next to “process tensors” and you will see the window below, which allows you the option of doing linear and nonlinear tensor fitting. ​ You can also do fits via [[http://​www.ncbi.nlm.nih.gov/​pubmed/​15844157|RESTORE]] and [[http://​www.ncbi.nlm.nih.gov/​pubmed/​22287298|iRESTORE]]. ​ For the money, the nonlinear estimation is often recommended over the linear and costs you only marginally more time for the estimation. ​ I also find it useful to display the residuals and to sort them!  It’s important that now that you’ve setup the options, you push the “process tensors” button on the main window.
  
-{{ :​tortoise_diff_calc_fit_tensors.png?​direct&​300 |}}+{{ :​tortoise_diff_calc_fit_tensors.png?​direct&​500 |}}
  
 You can now view the resulting tensors (and DTI related metrics like FA) using the triplanar viewer shown below. ​ The viewer has an assistive panel allowing you to choose the metric that you view including the Eigen values, structural, and shown below is the DEC map that we have all come to know and love through publications. You can now view the resulting tensors (and DTI related metrics like FA) using the triplanar viewer shown below. ​ The viewer has an assistive panel allowing you to choose the metric that you view including the Eigen values, structural, and shown below is the DEC map that we have all come to know and love through publications.
  
-{{ :​tortoise_tripalne.png?​direct&​400 |}}+{{ :​tortoise_tripalne.png?​direct&​500 |}}
  
 Once I view the data briefly in this viewer, I usually take the estimated tensors and export them for use in AFNI using the dialogue below. ​ But you can also export them for use with TrackVis and other formats. ​ The AFNI export sends out NIFTI files that go into your _proc directory (in my case dwi_proc), and can be found in a sub-folder. ​ The AFNI export is already named correctly for use with the tractography programs (e.g. 3dProbTrackID),​ which will be the topic of an upcoming post. Once I view the data briefly in this viewer, I usually take the estimated tensors and export them for use in AFNI using the dialogue below. ​ But you can also export them for use with TrackVis and other formats. ​ The AFNI export sends out NIFTI files that go into your _proc directory (in my case dwi_proc), and can be found in a sub-folder. ​ The AFNI export is already named correctly for use with the tractography programs (e.g. 3dProbTrackID),​ which will be the topic of an upcoming post.
tortoise_dti.txt · Last modified: 2014/06/27 12:23 by pmolfese