[Mristudio-users] Analyze ROIs

[susumu]

Hi Graeme,

I want to follow up Xin's comments. First, please don't be confused by "binary" and "binary map" formats. The "binary" format simply saves the ROI as 0/1 maps (default extension is *.dat). The "binary map" format saves not only the binary ROI files (*.dat files) but also an additional text file, (*.map file)  which you can open and see. To load all files saved as the "binary map" format to DtiStudio, you have to load it as, of course, "binary map" format in DtiStudio. Then DtiStudio looks for the ".map" text file, not the actual 1/0 binary ROI files (*.dat files).

There is one catch, though. When you saved the ROI files by RoiEditor, you can't specify which ROI is for "AND" and which ROI is for "OR". There are "AND", "OR", "NOT", and "CUT" operations you can choose to combine multiple ROIs. Without this information in the *.map text file, DtiStudio doesn't know what to do.

The best way to learn the syntax of the "*.map" file is to create this file using DtiStudio and study the inside. You can do usual fiber tracking by DtiStudio manually. Please make sure that you draw more than 1 ROI and combine them "AND" or "NOT", as you want. Then try "save"->"Binary Map" in the ROI operation section. Once you saved your ROIs using DtiStudio, look for the saved ROI files. You should be able to find a "*.map" file you just saved. Open the "*.map" file by a texteditor. The file contains not only information about your ROI data, but also some explanation about the syntax at the bottom.

Please let me know, if you have any more questions.

Susumu
  ----- Original Message ----- 
  From: Graeme Schwindt 
  To: mristudio-users at mristudio.org 
  Sent: Friday, April 18, 2008 12:28 PM
  Subject: [Mristudio-users] Analyze ROIs


  Hello,

  I am a new DTIStudio user, and am experiencing some confusion regarding ROI data formats. I have two issues:

  1) I would like to import ROIs drawn in MRICro (analyze format) into ROIEditor for statistics calculation,  However, it appears that ROIEditor will not read the analyze files, and gives an roi header file open error. It also refers to a .roihdr file in the error, rather than a .hdr file. Is there anyway to solve this issue?

  2) I would also like to import ROIs into DTIStudio fiber tracking, in order to delinate seed and target ROIs for tracking of fibers. I noticed an earlier mailing list post about using ROIEditor to make these ROIs, and then save them as binary map files for the fiber tracking ROI module in dtistudio. I did this, and the file was saved as a .dat file by ROIEditor. However, then when I went to load the roi in dtistudio's fiber tracking tab in binary map format, it was asking for a .map file. I  forced it to open the binary map file I had saved in ROIEditor (ending in _map.dat), and while it appeared to load, it did not appear on the image, nor did any fibers appear when the 'selected' radio button was highlighted. I feel I must be making some simple mistake here.

  Thanks for any help or advice and for supporting this mailing list!

  Graeme

  -- 
  Graeme C. Schwindt, HBSc
  MD/PhD Student
  University of Toronto
  graeme.schwindt at gmail.com
  416.546.5453 


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