bet step and dcm2nii

Submitted by Abaexet on Fri, 10/31/2014 - 10:42
Dear all,
 
I'm working with DPARSF in Windows so and I'm asking if it's normal that when I set "bet" step, dcm2nii toolbox starts. Can anybody help me to clarify this step? If it's normal, what I should do then?
 
Thank you in advance!
Anna
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Image icon matlab dcm2nii.png179.98 KB

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YAN Chao-Gan

Mon, 11/03/2014 - 14:48

Hi Anna,

As you are using Windows, then bet is based on Dr. Chris Rorden's work.

See: https://github.com/Chaogan-Yan/DPABI/blob/master/DPARSF_V3.1_141101/Subfunctions/y_Call_bet.m

%Write to target directory
  y_Write(Data,Head,fullfile(OutPath,[OutFile,'BeforeBet.img']));
  %E:\ITraWork\WorkTemp\Bet\mricron>dcm2nii -4 N -g N -m N -n N -r N -s Y -v N -x N -o E:\ITraWork\WorkTemp\Bet\Test E:\ITraWork\WorkTemp\Bet\Test\N.img
   
  %Change to ANALYZE format
  cd([ProgramPath,filesep,'dcm2nii']);
  eval(['!dcm2nii.exe ','-4 N -g N -m N -n N -r N -s Y -v N -x N',' -o ',OutPath,' ',fullfile(OutPath,[OutFile,'BeforeBet.img'])]);
   
  %Bet
  cd([ProgramPath,filesep,'bet']);
  eval(['!bet ',fullfile(OutPath,['f',OutFile,'BeforeBet.img']),' ',fullfile(OutPath,[OutFile,'AfterBet.img']),' ',Option]);
   
  %Write in NIfTI with the reserved header.
  Data = y_Read(fullfile(OutPath,[OutFile,'AfterBet.img']));
  y_Write(Data,Head,OutputFilename);

Best,

Chao-Gan