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tortoise_dti [2014/06/27 12:20]
pmolfese
tortoise_dti [2014/06/27 12:23]
pmolfese
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 ====== Preprocessing Diffusion Data ====== ====== Preprocessing Diffusion Data ======
  
-Start by launching ​DIFF_CALC.  You can simply double-click on the file prepvm.  ​+Start by launching ​DIFF_PREP.  You can simply double-click on the file prepvm.  ​
  
 The first thing to do is get your data into TORTOISE. ​ You can import a variety of data formats (Phillips PAR/REC, DICOM, NIFTI, and Bruker). ​ I highly recommend importing from either DICOM or FSL NIFTI. ​ If you choose DICOM, you will need to supply TORTOISE with your gradient file, as it will not read the directions from your DICOM headers. ​ If you choose FSL NIFTI, TORTOISE will read your bvec and bval files from text, they just need to have the name (bvec or bval) in the filename and be in the same folder as the NIFTI file.  TORTOISE will search sub-folders for these files, so if you have multiple bvec or bval files in your folder or sub-folders,​ it will give you an error that it found multiple bvec/bval files and you’ll have to tidy up your file structure. The first thing to do is get your data into TORTOISE. ​ You can import a variety of data formats (Phillips PAR/REC, DICOM, NIFTI, and Bruker). ​ I highly recommend importing from either DICOM or FSL NIFTI. ​ If you choose DICOM, you will need to supply TORTOISE with your gradient file, as it will not read the directions from your DICOM headers. ​ If you choose FSL NIFTI, TORTOISE will read your bvec and bval files from text, they just need to have the name (bvec or bval) in the filename and be in the same folder as the NIFTI file.  TORTOISE will search sub-folders for these files, so if you have multiple bvec or bval files in your folder or sub-folders,​ it will give you an error that it found multiple bvec/bval files and you’ll have to tidy up your file structure.
  
-{{ :​tortoise.001.jpg?​direct&​400 |}}+{{ :​tortoise.001.jpg?​direct&​500 |}}
  
 In the image above (click to make bigger), you can see the common settings highlighted with yellow arrows. ​ On the import side, you’ll want to specify your format (FSL NIFTI is my recommendation),​ the file path to your NIFTI file (note – uncompressed NIFTI only -.nii not .nii.gz – as of this post), and then click import. ​ Using NIFTI files imported from dcm2nii and DIMON have worked well for me.  The one advantage to dcm2nii is that it will automatically create the bval and bvec files in the correct format for TORTOISE. In the image above (click to make bigger), you can see the common settings highlighted with yellow arrows. ​ On the import side, you’ll want to specify your format (FSL NIFTI is my recommendation),​ the file path to your NIFTI file (note – uncompressed NIFTI only -.nii not .nii.gz – as of this post), and then click import. ​ Using NIFTI files imported from dcm2nii and DIMON have worked well for me.  The one advantage to dcm2nii is that it will automatically create the bval and bvec files in the correct format for TORTOISE.
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 Next you’re going to click the “Registration param” button to setup the more advanced settings. Next you’re going to click the “Registration param” button to setup the more advanced settings.
  
-{{ :​tortoise.002.jpg?​direct&​400 |}}+{{ :​tortoise.002.jpg?​direct&​500 |}}
  
 Inside your Registration Settings, I highly recommend you keep most of the defaults. ​ The things that I’ve found reason to change (in TORTOISE version 2.0.1) are the final DWI voxelsize resolution, it defaults to 1.5mm^3, but it may not make sense to go to such a fine grid if you collect at say 3mm^3. ​ The other thing that I’ve changed is the initial upsampling setting, if you have a particularly thick slice DWI image, you might consider changing it to slice_only. ​ In the registration settings is also where you will turn off the BSpline correction if you aren’t using a T2-weighted image with fat suppression for your structural image. Inside your Registration Settings, I highly recommend you keep most of the defaults. ​ The things that I’ve found reason to change (in TORTOISE version 2.0.1) are the final DWI voxelsize resolution, it defaults to 1.5mm^3, but it may not make sense to go to such a fine grid if you collect at say 3mm^3. ​ The other thing that I’ve changed is the initial upsampling setting, if you have a particularly thick slice DWI image, you might consider changing it to slice_only. ​ In the registration settings is also where you will turn off the BSpline correction if you aren’t using a T2-weighted image with fat suppression for your structural image.
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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