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- Sharper resolution of FODs (regularization adjustment) - Fixes to command line tools
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,69 @@ | ||
| function mrtd_coordsys_fix(varargin) | ||
| disp('mrtd_coordsys_fix'); | ||
| coptions = varargin; | ||
| % if(length(varargin{1}) > 1) | ||
| % coptions = varargin{1}; | ||
| % end | ||
| % disp(varargin) | ||
|
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||
| if(isempty(coptions) || isempty(coptions{1}) || strcmpi(coptions{1},'-help')) | ||
| help = 'This tools can be used to check whether spatial dimension flip / permute are needed to properly process the given diffusion MRI data'; | ||
| help = [help newline]; | ||
| help = [help newline 'usage: mrtd_coordsys_fix -nii file.nii -out permuted_file.nii']; | ||
| help = [help newline]; | ||
| help = [help newline '-perm: how to permute the spatial dimensions,e.g. "1 2 3" or "2 1 3" etc.']; | ||
| help = [help newline '-flip: how to flip the spatial dimensions, e.g. "0 0 0" or "0 1 0" etc.']; | ||
| help = [help newline '-auto: attempt auto detection (default 0) - overrides perm and flip']; | ||
| help = [help newline]; | ||
| fprintf(help); | ||
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| return | ||
| end | ||
|
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| file_in = GiveValueForName(coptions,'-nii'); | ||
| if(isempty(file_in)) | ||
| error('Need to specify the target .nii file'); | ||
| end | ||
| auto_fix = GiveValueForName(coptions,'-auto'); | ||
| if(isempty(auto_fix)) | ||
| auto_fix = 0; | ||
| end | ||
| output_file = GiveValueForName(coptions,'-out'); | ||
| if(isempty(output_file)) | ||
| error('Need to specify the output name!'); | ||
| end | ||
| if(auto_fix == 0) | ||
| spat_perm = GiveValueForName(coptions,'-perm'); | ||
| if(isempty(spat_perm)) | ||
| spat_perm = [1 2 3]; | ||
| else | ||
| C = strsplit(spat_perm,' '); | ||
| spat_perm = [str2double(C(1)) str2double(C(2)) str2double(C(3))]; | ||
| end | ||
| spat_flip = GiveValueForName(coptions,'-flip'); | ||
| if(isempty(spat_flip)) | ||
| spat_flip = [0 0 0]; | ||
| else | ||
| C = strsplit(spat_flip,' '); | ||
| spat_flip = [str2double(C(1)) str2double(C(2)) str2double(C(3))]; | ||
| end | ||
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| MRTQuant.FlipPermuteSpatialDimensions('nii_file',file_in,'flip',spat_flip,... | ||
| 'permute',spat_perm,'output',output_file); | ||
| else | ||
| MRTQuant.ConformSpatialDimensions('nii_file',file_in,'output',output_file); | ||
| end | ||
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| end | ||
|
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| % Helper: finds a parameter by name when using varargin | ||
| function value = GiveValueForName(coptions,name) | ||
| value = []; | ||
| for ij=1:2:length(coptions) | ||
| if(strcmpi(coptions{ij},name)) | ||
| value = coptions{ij+1}; | ||
| return | ||
| end | ||
| end | ||
| end |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,167 @@ | ||
| function mrtd_deconv_fod(varargin) | ||
| disp('mrtd_deconv_fod'); | ||
| coptions = varargin; | ||
| % if(length(varargin{1}) > 1) | ||
| % coptions = varargin{1}; | ||
| % end | ||
| % disp(varargin) | ||
|
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||
| if(isempty(coptions) || isempty(coptions{1}) || strcmpi(coptions{1},'-help')) | ||
| help = 'This tool performs spherical deconvolution of (multi-shell) diffusion MRI data'; | ||
| help = [help newline]; | ||
| help = [help newline 'usage: mrtd_deconv_fod -method chosen_method -nii file.nii -bval file.bval -bvec file.bvec -out corrected_file.nii (other_options)']; | ||
| help = [help newline]; | ||
| help = [help newline '-grad_perm: how to permute the diffusion gradients 1=[x y z] 2=[y x z] 3=[z y x]' .... | ||
| ' 4=[x z y] =[y z x] 6=[z x y]']; | ||
| help = [help newline '-grad_flip: how to flip the sign of the diffusion gradients 1=[x y z] 2=[-x y z] 3=[x -y z] 4=[x y -z]']; | ||
| help = [help newline '-method: one in "csd","mscsd","grl","grl_auto","mfod"']; | ||
| help = [help newline '-t1_seg: T1 segmentation file derived from "fsl_anat" (mscsd only)']; | ||
| help = [help newline '-lmax: spherical harmonics order']; | ||
| help = [help newline '-mat: provide an ExploreDTI-compatible .MAT file. Overrides -nii -bval -bvec']; | ||
| help = [help newline]; | ||
| help = [help newline 'GRL - mFOD specific options']; | ||
| help = [help newline]; | ||
| help = [help newline '-aniso_rf_dti: Add an anisotropic RF using the DTI model. Specify the eigenvalues in ms2/um2 as "1.7 0.2 0.2"']; | ||
| help = [help newline '-aniso_rf_dki: Add an anisotropic RF using the DKI model. Specify the eigenvalues in ms2/um2 and the mean kurtosis as "1.7 0.2 0.2 1" or "auto" to estimate from the data']; | ||
| help = [help newline '-aniso_rf_noddi: Add an anisotropic RF using the NODDI model. Specify 6 parameters "intra-cellular-volume free-diffusivity*10^9 watson-concentration isotropic-fraction isotropic-diffusivity b0-amplitude"']; | ||
| help = [help newline '-iso_rf: Add an isotropic RF using the ADC model. Specify the diffusivity in um2/ms, as 0.7 for GM and 3 for CSF']; | ||
| help = [help newline '-shell_weight: Inner-shell weighting factor (GRL only)']; | ||
| help = [help newline]; | ||
| help = [help newline 'GRL default usage: mrtd_deconv_fod -method grl_auto -nii file.nii -bval file.bval -bvec file.bvec -out GRL_processing']; | ||
| help = [help newline 'mFOD default usage: mrtd_deconv_fod -method mfod -nii file.nii -bval file.bval -bvec file.bvec -out mF -aniso_rf_dki "auto" -aniso_rf_noddi "0.4 1.7 1 0 3 1" -iso_rf 3']; | ||
| help = [help newline]; | ||
| fprintf(help); | ||
|
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| return | ||
| end | ||
|
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||
| nii_file = ''; | ||
| bval_file = ''; | ||
| bvec_file = ''; | ||
| mat_file = ''; | ||
| outfile = ''; | ||
| grad_perm = 1; | ||
| grad_flip = 1; | ||
| deconv_method = 'csd'; | ||
| t1_seg = ''; | ||
| aniso_rf = {}; | ||
| iso_rf = {}; | ||
| lmax = 8; | ||
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| for input_id =1:2:length(coptions) | ||
| value = coptions{input_id}; | ||
| if(strcmp(value,'-nii')) | ||
| nii_file = coptions{input_id+1}; | ||
| elseif(strcmp(value,'-bval')) | ||
| bval_file = coptions{input_id+1}; | ||
| elseif(strcmp(value,'-bvec')) | ||
| bvec_file = coptions{input_id+1}; | ||
| elseif(strcmp(value,'-out')) | ||
| outfile = coptions{input_id+1}; | ||
| elseif(strcmp(value,'-grad_perm')) | ||
| grad_perm = str2double(coptions{input_id+1}); | ||
| elseif(strcmp(value,'-grad_flip')) | ||
| grad_flip = str2double(coptions{input_id+1}); | ||
| elseif(strcmp(value,'-method')) | ||
| deconv_method = coptions{input_id+1}; | ||
| elseif(strcmp(value,'-lmax')) | ||
| lmax = str2double(coptions{input_id+1}); | ||
| elseif(strcmp(value,'-t1_seg')) | ||
| t1_seg = coptions{input_id+1}; | ||
| elseif(strcmp(value,'-aniso_rf_dti')) | ||
| aniso_rf(end+1) = {{'dti',coptions{input_id+1}}}; | ||
| elseif(strcmp(value,'-aniso_rf_dki')) | ||
| aniso_rf(end+1) = {{'dki',coptions{input_id+1}}}; | ||
| elseif(strcmp(value,'-aniso_rf_noddi')) | ||
| aniso_rf(end+1) = {{'aniso_rf_noddi',coptions{input_id+1}}}; | ||
| elseif(strcmp(value,'-iso_rf')) | ||
| iso_rf(end+1) = {coptions{input_id+1}}; | ||
| elseif(strcmp(value,'-mat')) | ||
| mat_file = {coptions{input_id+1}}; | ||
| end | ||
|
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||
| end | ||
|
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| if(isempty(deconv_method)) | ||
| error('Missing mandatory argument -method'); | ||
| end | ||
|
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| if(isempty(mat_file)) | ||
| if(isempty(nii_file)) | ||
| error('Missing mandatory argument -nii'); | ||
| elseif(isempty(bval_file)) | ||
| error('Missing mandatory argument -bval'); | ||
| elseif(isempty(bvec_file)) | ||
| error('Missing mandatory argument -bvec'); | ||
| end | ||
| temp_mat_file = MRTD.QuickNiiBvalBvecToMat('nii_file',nii_file,... | ||
| 'bval_file',bval_file,'bvec_file',bvec_file,'grad_perm',grad_perm,... | ||
| 'grad_flip',grad_flip); | ||
| else | ||
| temp_mat_file = mat_file; | ||
| end | ||
|
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||
| if(strcmp(deconv_method,'csd') || strcmp(deconv_method,'mscsd')) | ||
| if(strcmp(deconv_method,'mscsd')) | ||
| mscsd = 1; | ||
| else | ||
| mscsd = 0; | ||
| end | ||
| EDTI.PerformCSD('mat_file',temp_mat_file,'mscsd',mscsd,... | ||
| 'T1seg',t1_seg,'output',outfile,'lmax',lmax); | ||
|
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| elseif(strcmp(deconv_method,'grl') || strcmp(deconv_method,'mfod')) | ||
| % Converts a .MAT to the MRIToolkit format | ||
| mrt_data = EDTI.EDTI_Data_2_MRIToolkit('mat_file',temp_mat_file); | ||
| other_props = load(temp_mat_file,'FA'); | ||
| % Prepare the spherical deconvolution class on this dataset | ||
| SD = MRTTrack('data',mrt_data); | ||
| % Add an anisotropic response function using the DKI model | ||
| for rf_id=1:length(aniso_rf) | ||
| requested_rf = aniso_rf{rf_id}; | ||
| eigvals = requested_rf{2}; | ||
| if(contains(requested_rf{1},'dki') > 0 && contains(eigvals,'auto')) | ||
| [eigvals,isok] = MRTTrack.Eigenval_IsoK_WM_FromData(mrt_data,other_props.FA,~isnan(other_props.FA)); | ||
| SD.AddAnisotropicRF_DKI(eigvals,isok); % WM | ||
| else | ||
| J = strsplit(eigvals,' '); | ||
| eigvals = []; | ||
| for ikk=1:length(J) | ||
| eigvals = [eigvals str2double(J{ikk})]; | ||
| end | ||
| if(contains(requested_rf{1},'dti')) | ||
| isok = 0; | ||
| eigvals = eigvals(1:3)*1e-3; | ||
| SD.AddAnisotropicRF_DKI(eigvals,isok); % WM | ||
| elseif(contains(requested_rf{1},'dki')) | ||
| isok = eigvals(4); | ||
| eigvals = eigvals(1:3)*1e-3; | ||
| SD.AddAnisotropicRF_DKI(eigvals,isok); % WM | ||
| elseif(contains(requested_rf{1},'noddi')) | ||
| SD.AddAnisotropicRF_NODDI(eigvals); | ||
| end | ||
| end | ||
| end | ||
|
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| for rf_id=1:length(iso_rf) | ||
| SD.AddIsotropicRF(str2double(iso_rf{rf_id})*1e-3); | ||
| end | ||
|
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| if(strcmp(deconv_method,'grl')) | ||
| SD.setInnerShellWeighting(0.2); % Do not loose angular resolution due to the lower shells | ||
| SD.AutomaticDRLDamping(); % see Dell'Acqua 2013 | ||
| SD.setDeconvMethod('dRL'); % damped Richardson Lucy | ||
| elseif(strcmp(deconv_method,'mfod')) | ||
| SD.setInnerShellWeighting(1.0); % in mFOD this parameter has not been investigated | ||
| SD.setDeconvMethod('L2LSQ'); | ||
| end | ||
|
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| GRL_Results = SD.PerformDeconv(); | ||
| MRTTrack.SaveOutputToNii(SD,GRL_Results,outfile); | ||
|
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| else | ||
| error(['Unknown deconvolution method ' method]); | ||
| end | ||
|
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||
| end | ||
|
|
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