Cheers.

Cheers.

Also included in this release is a command-line tool called “track_vis”. To say it is the command-line version of TrackVis is a little bit exaggerating. It was really just a prototype before TrackVis was built. It has not been updated for a long time and is only maintained for runnability. But there is some value of it in that it can be put in a script for batch data processing and screen captures. It can actually be very helpful in some case. So we decided to put it out there. The only documentation for it is its massive in-program help text. Just run “track_vis” without any flags, you will see it.

Cheers.

• The old way. No b0 (0, 0, 0) vector included in the table. Program will assume all the b0’s are on top of the image list. You need to enter the number of b0’s correctly.
• Put b0 (0, 0, 0) vectors in the table, anywhere. Note once program detects there is b0 vector in the table, it will automatically count its number. You need to make sure the number and the position of each match the input data. For example, if your data has 2 b0’s at the top of the image list, you can not just put one b0 (0, 0, 0) vector at the top of the table, you need to put two in there.
• Put b values in the table. You can now put b values of each gradient vector in the table as the 4th component. A typical table will look like this:

  0, 0, 0, 0
  x1, y1, z1, 700
  x2, y2, z2, 700
  ...
  x10, y10, z10, 1500
  x11, y11, z11, 1500
  ...
  

  You probably have noticed that b values can be different in the table. Thus, data set with b stepping can be reconstructed – something Diffusion Toolkit was not able to do before!

  Please note that once you put b values in the gradient table, the b value you specified in the GUI will be ignored. Also, once you put one b value in, you must put every one in. Do not mix up 3 component vectors and 4 component vectors in the same table.

• The b-values-in-table feature will now allow reconstructing DSI data as DTI. But it would be painful to enter b value for every vector (515 of them!) in the table. That’s why a check box called “Multiple high b value” is created in the GUI. Once it is checked, even if there is no b value given in the table, program will assume the gradient vectors in this table are scaled (so it will not automatically normalize them). Given the maximum b value, it will automatically calculate the b value for each vector by its length (magnitude). For example, a DSI gradient table may look like the following:

  0.2,   0.0,   0.0
  ...
  0.4,   0.0,   0.0
  ...
  0.6,   0.0,   0.0
  ...
  0.8,   0.0,   0.0
  ...
  1.0,   0.0,   0.0
  

  If maximum b value is set as 10,000, the program will automatically compute the b values by the magnitude of each vector. So the b value for each vectors above will be 2,000, 4,000, 6,000, 8,000 and 10,000 respectively.

Remember Diffusion Toolkit’s main GUI is just a front end to wrap up the underneath command-line tools. The real handler of gradient tables is dti_recon command-line program. Click “Preview Scripts” button will show you what will be executed by dti_recon.

All the new changes on gradient table apply to DTI processing only.

track_merge file1 file2 ... fileN output_file

Requirement for this to work is obvious: all the input track files must have the same geometry information in the header.

A nice thing track_merge does behind the scene is when it merges multiple track files, it does not simply add them. An id type property tag is added to each track in the newly merged file, with each unique id representing where the track was originally from. When the merged file is loaded in TrackVis, a property filter will show up in Track Property panel. Users can adjust that to distinguish and sub-group tracks by its id (origin).

TrackVis 0.5.1 is mainly a bug fix release containing a few minor improvements. Diffusion Toolkit 0.6 however has a couple of new features that may help you process DTI data more easily. I will discuss the details in separate posts shortly.

Cheers.