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Hi, probably you need to add MATLAB path to Freesurfer's $PATH variable. The following link may help:

http://www.manuelschutze.com/?p=297

On 18 May 2018 at 12:02, subin oh subin.b.oh@gmail.com wrote:

    External Email - Use Caution

Hello,

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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