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mrAnatExtractBrain.m: corrected bugs in calling FSL bet #216

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mrAnatExtractBrain.m: corrected bugs in calling FSL bet #216

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8 changes: 7 additions & 1 deletion mrAnatomy/Segment/mrAnatExtractBrain.m
100644 → 100755
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Original file line number Diff line number Diff line change
Expand Up @@ -71,6 +71,12 @@
end
end

% JB on 19/08/2016: on some systems, calling a system command outputs some text when running .bashrc or .cshrc
remain=bet; % so we remove any additional starting lines
while ~isempty(remain) %if there are more than 2 lines
[bet,remain]=strtok(remain,sprintf('\n')); % isolate first line
end

bet = strtrim(bet); % The name of the bet funciton on the system

% Set temporary file names for the out file and bet script. These will be
Expand Down Expand Up @@ -100,7 +106,7 @@
betOut = tempname;
betCmd = [bet ' ' out ' ' betOut ' -mnf ' num2str(betLevel(ii))];
fid = fopen(betScript,'wt');
fprintf(fid,'#!/bin/bash\nexport FSLOUTPUTTYPE=NIFTI_GZ\n%s\n',betCmd);
fprintf(fid,'#!/bin/bash\nFSLOUTPUTTYPE=NIFTI_GZ\n%s\n',betCmd); %JB on 19/08/2016: should not export FSLOUTPUTTYPE: it has to equal NIFTI_GZ inside the script
fclose(fid);
unix([bash ' ' betScript]);
betOut = [betOut '_mask.nii.gz'];
Expand Down