Load mask for REST by Xiao-Wei Song
AX, AY, AZ should be the same size as the Volume, this size should be set automatically, but I use this for compatibility. And I specially give the code for many files' use already. And another reason is the null mask need it
AMaskFilename should be the mask filename
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Copyright(c) 2007~2010
State Key Laboratory of Cognitive Neuroscience and Learning in Beijing Normal University
Written by Xiao-Wei Song
http://resting-fmri.sourceforge.net
dawnsong, 20070509
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Vesa.Kiviniemi@ppshp.fi found Yong He's bug in loading a null-mask
Mail to Authors: <a href="Dawnwei.Song@gmail.com">Xiaowei Song</a>; <a href="ycg.yan@gmail.com">Chaogan Yan</a>
Version=1.2;
Release=20081225;
Revised by YAN Chao-Gan 080610: NIFTI compatible
Revised by Yan Chao-Gan 081225: use the new mask files.
Revised by YAN Chao-Gan, 090420. Revise the input mask to ensure that it only contains 0 and 1.0001 function mask=rest_loadmask(AX, AY, AZ, AMaskFilename) 0002 %Load mask for REST by Xiao-Wei Song 0003 % AX, AY, AZ should be the same size as the Volume, this size should be set automatically, but I use this for compatibility. And I specially give the code for many files' use already. And another reason is the null mask need it 0004 % AMaskFilename should be the mask filename 0005 %------------------------------------------------------------------------------------------------------------------------------ 0006 % Copyright(c) 2007~2010 0007 % State Key Laboratory of Cognitive Neuroscience and Learning in Beijing Normal University 0008 % Written by Xiao-Wei Song 0009 % http://resting-fmri.sourceforge.net 0010 % dawnsong, 20070509 0011 %------------------------------------------------------------------------------------------------------------------------------ 0012 %Vesa.Kiviniemi@ppshp.fi found Yong He's bug in loading a null-mask 0013 % Mail to Authors: <a href="Dawnwei.Song@gmail.com">Xiaowei Song</a>; <a href="ycg.yan@gmail.com">Chaogan Yan</a> 0014 % Version=1.2; 0015 % Release=20081225; 0016 % Revised by YAN Chao-Gan 080610: NIFTI compatible 0017 % Revised by Yan Chao-Gan 081225: use the new mask files. 0018 % Revised by YAN Chao-Gan, 090420. Revise the input mask to ensure that it only contains 0 and 1. 0019 0020 0021 %Load mask, copy from reho.m revised by Dawnwei.Song, 20070504 0022 [pathstr, name, ext, versn] = fileparts(mfilename('fullpath')); 0023 0024 if ( strcmp(AMaskFilename, '')|| (isnumeric(AMaskFilename) && AMaskFilename==0) )% like the old parameter, back-compatible Xiaowei Song, 20070421 0025 mask=ones(AX, AY, AZ); 0026 elseif( strcmpi(AMaskFilename, 'Default')||( isnumeric(AMaskFilename) && AMaskFilename==1) ) % like the old parameter , back-compatible Xiaowei Song, 20070421 0027 switch int2str([AX, AY, AZ]) 0028 case '79 95 69' % 'default''[2 2 2]' 0029 [mask, vsizeTmp, Header]=rest_readfile([pathstr '/mask/BrainMask_05_79x95x69.img']); %YAN Chao-Gan 081225: New masks. 0030 case '53 63 46' % 'default''[3 3 3]' 0031 [mask, vsizeTmp, Header]=rest_readfile([pathstr '/mask/BrainMask_05_53x63x46.img']); %YAN Chao-Gan 081225: New masks. 0032 case '91 109 91' % 'template''[2 2 2]' 0033 [mask, vsizeTmp, Header]=rest_readfile([pathstr '/mask/BrainMask_05_91x109x91.img']); %YAN Chao-Gan 081225: New masks. 0034 case '61 73 61' % 'template' '[3 3 3]' 0035 [mask, vsizeTmp, Header]=rest_readfile([pathstr '/mask/BrainMask_05_61x73x61.img']); %YAN Chao-Gan 081225: New masks. 0036 otherwise 0037 error(sprintf('There are no appropriate default mask file:\n\tVolume size=79*95*69 ,Voxel size=2*2*2;\n\tVolume size=53*63*46, Voxel size=3*3*3;\n\tVolume size=91*109*91, Voxel size=2*2*2;\n\tVolume size=61*73*61, Voxel size=3*3*3;\n Please set bMask = 0.')); 0038 end %end switch 0039 else % new, Xiaowei Song, 20070421 0040 if (ischar(AMaskFilename)) 0041 %if is img file, read and load 0042 if strcmpi(AMaskFilename(end-3:end), '.img') 0043 [mask, vsizeTmp, Header]=rest_readfile(AMaskFilename); 0044 else%if is mat file, direct load 0045 load(AMaskFilename); 0046 end 0047 else 0048 error('There are no appropriate mask file. Please set bMask = 0.'); 0049 end 0050 end %mask select end 0051 0052 mask =logical(mask); %Revised by YAN Chao-Gan, 090420. Revise the mask to ensure that it only contains 0 and 1. 0053 0054 %Check whether mask is 3d 0055 if ndims(mask)~=3 0056 error('mask error, mask is not 3d'); 0057 end 0058 0059 % Brutely check the mask's size to make sure whether the mask's size same to the required size 0060 if ~all(size(mask)==[AX, AY, AZ]), 0061 %warning(sprintf('\n\tMask does not match. Brutely use "No Mask".\n\tMask size is %dx%dx%d, not equal to required size %dx%dx%d',size(mask), [AX, AY, AZ])); 0062 0063 %20070820 Zang's advice 0064 error(sprintf('\n\tMask does not match.\n\tMask size is %dx%dx%d, not same with required size %dx%dx%d',size(mask), [AX, AY, AZ])); 0065 0066 mask = ones(AX, AY, AZ); 0067 end