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I downloaded the Freesurfer ver 5.3.0 and installed it on Mac OS. I run *"recon-all -s <subject> -local GI" *for my subject.. And I run *Matlab Script* about "*Start up" , "make_outer_surface", "make_roi_paths" , "find correspoding center" *as follows: But it exited with same *errors* as follows: Please Could you tell me the way for correcting that error and to calculate the LGI? *the error message is..* Thank you very much. Best Regards, Subin =====================[Mac OS Error]====================== -------- freesurfer-Darwin-lion-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl Chans-iMac:subjects roh$ recon-all -s test01_t1 -localGI Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/test01_t1 Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 roh staff 468188 May 18 16:01 /Applications/freesurfer/subjects/test01_t1/test01_t1/scripts/recon-all.log Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test01_t1/test01_t1/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri May 18 17:36:00 KST 2018 \n mris_compute_lgi --i lh.pial \n ERROR: Matlab is required to run mris_compute_lgi! Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 recon-all -s test01_t1 exited with ERRORS at Fri May 18 17:36:00 KST 2018 For more details, see the log file /Applications/freesurfer/subjects/test01_t1/test01_t1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting =============================================================== *the Matlab Scripts are..* =================[Matlab Script: StartUp]====================== % freesurfer start fshome = getenv('FREESURFER_HOME'); fsmatlab = sprintf('%s/matlab',fshome); if (exist(fsmatlab) == 7) path(path,fsmatlab); end clear fshome fsmatlab; =================[Matlab Script: make_outer_surface]================ function make_outer_surface (filled_volume, se_diameter, output_surface) % Original Author: Marie Schaer % Date: 2007/11/14 % % This function takes as an input the binary volume resulting of the % filling of the any surface (usually the pial one) using mris_fill, and % will close the sulci using morphological operation, with a sphere as the % structural element. % % Parameters: % se_diameter is the diameter of the sphere (in mm), use 15mm by default % to close the sulci. % % Utilities to write the surface to the freesurfer format are modified from % "freesurfer_write_surf" (from Darren Weber's bioelectromagnetism toolbox), % according to a suggestion by Don Hagler in FreeSurfer's mailing list on % August 3, 2007. % % Example: make_outer_surface('lh.pial.mgz',15,'lh.outer-pial') fprintf('reading filled volume...\n'); vol=MRIread(filled_volume); volume=vol.vol; volume(volume==1)=255; fprintf('closing volume...\n'); % first apply a very soft gaussian filter, with sigma = 1mm, in order to % facilitate the closing Gaussian = fspecial('gaussian',[2 2],1); image_f=zeros(256,256,256); for slice=1:256 temp = double(reshape(volume(:,:,slice),256,256)); image_f(:,:,slice) = conv2(temp,Gaussian,'same'); end image2=zeros(size(image_f)); image2(image_f<=25)=0; image2(image_f>25)=255; se=strel('ball',se_diameter,se_diameter); BW2=imclose(image2,se); thresh = max(BW2(:))/2; i=find(BW2<=thresh); BW2(i)=0; i=find(BW2>thresh); BW2(i)=255; [f,v] = isosurface(BW2,100); v2=[129-v(:,1) v(:,3)-129 129-v(:,2)]; % in order to cope with the different orientation v=v2; fprintf('morphological closing done.\n'); fprintf('writing outer surface...\n'); fname=output_surface; vert = v; face = f - 1; vnum = size(vert,1); fnum = size(face,1); % open it as a big-endian file fid = fopen(fname, 'wb', 'b'); TRIANGLE_FILE_MAGIC_NUMBER = 16777214; fwrite3(fid, TRIANGLE_FILE_MAGIC_NUMBER); % Ouput a couple of text lines with creation date str = sprintf('created from matlab on %s\n',datestr(now)); fwrite(fid, str,'char'); fwrite(fid, vnum,'int32'); fwrite(fid, fnum,'int32'); % reshape vert into column array and write vert = reshape(vert',size(vert,1)*size(vert,2),1); fwrite(fid, vert,'float32'); % reshape face into column array and write face = reshape(face',size(face,1)*size(face,2),1); fwrite(fid, face,'int32'); fclose(fid) ; return end =================[Matlab Script: make_roi_paths]=============== function make_roi_paths(pial, outersmoothed, radius, stepsize, outdir, flagf) % Original Author: Marie Schaer % Date: 2007/11/15 % % This function creates multiple circular regions of interest on the outer % surface, measures their area (saved in matlab format) and save path file % containing a set of % corresponding points on the pial surface. The path files are required as % an input to the mri_path2label function % % Parameters: % radius: radius of the circular region of interest on the outer surface. % Most appropriate values between 20 and 25 mm, further documentation % available in the validation publication: "A surface-based approach to % quantify local cortical gyrification" by Schaer M, Bach Cuadra M, % Tamarit L, Eliez E, Thiran JP, IEEE Transactions on Medical Imaging, 2007 % % Utilities to transfer points on the pial surface calls "mesh_vertex_nearest", % a function written by Darren Weber. Utilities to compute matrix adjacency % for the pial surface calls "mesh_adjacency", a program first written by % Darren Weber, then modified by G. Peyre (source: toolbox_graph on % mathworks) % % Example: make_roi_paths('lh.pial','lh.outer-pial-smoothed',25,100,/tmp) t0 = cputime; disp('loading datas ...') [mesh_total.vertices, mesh_total.faces]=freesurfer_read_surf(pial); [mesh_outer.vertices, mesh_outer.faces]=freesurfer_read_surf(outersmoothed); disp('preparing outer mesh structure ...') mesh_outer = createMeshFacesOfVertex (mesh_outer.vertices, mesh_outer.faces) disp('preparing pial mesh structure ...') A = mesh_adjacency(mesh_total); % Keep track of the area for each individual region of interest on the % outer surface: nbVertices = size(mesh_outer.vertices,1); areasOuterROI = zeros(nbVertices,1); areasOuterROI = sparse (areasOuterROI); clear nbVertices % Circular regions of interest are defined each 100 vertex on the outer % surface. Due to the high resolution of the outer mesh (average face area % of ~0.3mm2), calculations are computed each 1 on 100 vertex, to avoid % high redundancies and optimize calculation time. for iV = 1:stepsize: length(mesh_outer.vertices) disp(['... creating path file for vertex ',num2str(iV),' / ' ,num2str(length(mesh_outer.vertices))]) % ------ Part 1: find the ROI on the enveloppe -------------- [verticesInROI, facesInROI] = getVerticesAndFacesInSphere(mesh_outer, iV, radius); % In rare case, the intersection of the enveloppe with the sphere result % in two regions of interest: the one that we expect, circular and % centered in iV; and an aberrant one at the bottom of the sphere % (e.g. near the superior sagittal vault). The next step is used to % control for that and keep only the radial region centered at iV. facesListOuterGeo = MakeGeodesicOuterROI (mesh_outer, iV, facesInROI); % Find the perimeter of the outer ROI verticesOuterGeo=unique(facesListOuterGeo(:)); perim=setdiff(verticesOuterGeo,verticesInROI); % Measure its area areaOuterROI = getFacesArea(mesh_outer,facesListOuterGeo); areasOuterROI(iV) = areaOuterROI; if (mod(iV,50*stepsize) == 1) fname = [outdir '/' pial '.area_intermed.mat']; save(fname, 'areasOuterROI') ; disp(['area file for outer ROIs saved at ',num2str(iV)]) end clear verticesInROI facesInROI facesListOuterGeo verticesOuterGeo areaOuterROI % ----- Part2: Define the corresponding set of points on the pial surface: % Transfer a few points of the perimeter of the hulls ROI from % the envelope to the pial surface, and save them as path file. step = 7; [verticeslist] = SearchProjectionOnPial(mesh_total, mesh_outer, perim, step); % reorganize the set of points in the right order to input them to % mri_path2label reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step); lindex = reorglist'; lxyz = mesh_total.vertices(lindex,:); lindex= lindex-1; p = sprintf ('%06d', iV); write_path(lxyz, lindex,[outdir '/' pial '.' p '.path']); clear verticeslist lindex lxyz end disp(['saving area file in matlab format... ']) fname = [outdir '/' pial '.outer_ROIs_area.mat']; save(fname, 'areasOuterROI') disp('DONE.') deltaT = cputime - t0 % indicate successful completion by deleting flagfile delete(flagf); =======================[find corresponding_center_FSformat]========================= t0 = cputime; [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial); [mesh_outer.vertices, mesh_outer.faces] = freesurfer_read_surf(outersmoothed); fidv = fopen([outdir '/' pial '.center.vertices'], 'w') ; for iV = 1 :stepsize: length(mesh_outer.vertices) centerSeed=mesh_vertex_nearest(mesh_pial.vertices,mesh_outer.vertices(iV,:)); centerSeed = centerSeed - 1; %FreeSurfer-s vertex are 0-based p = sprintf ('%06d', iV); fid = fopen([outdir '/' pial '.' p '.center'], 'w') ; fprintf(fid,'%d\n',centerSeed); fclose(fid) ; fprintf(fidv,'%s\n',p); end fclose(fidv) ; deltaT = cputime - t0 % indicate successful completion by deleting flagfile delete(flagfile); ===================================================================================
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