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Hello, FreeSurfer Developers.

I run "recon-all -s test01_t1 -local GI" for my subject after the MATLAB path (%PATH = “/Applications/MATLAB_R2014b.app/bin”:”$PATH”)

The original Setting of the FreeSurfer(Mac OS) is like this :

But it exited with errors as follows:

I guess Outer ROI or matrix...but I couldn't know what the problem exactly is..  

Improper assignment with rectangular empty matrix.
 

Error in dsearchn (line 79)
        [d(i),t(i)] = min(sum((x-yi).^2,2));
Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);

Error in reorganize_verticeslist (line 28)
    [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));
    
Error in make_roi_paths (line 93)
    reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
    verticeslist, step);
 
>> 
ERROR:  make_roi_paths did not complete successfully!
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 Mon May 21 09:50:03 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

I attached two relevant MATLAB files (make_roi_pattern.m, SearchProjectionOnPial_Ver2.m) and all the error message are written below..

Could you tell me some advice?

Best regards, 

Subin Oh

-------- [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$ PATH="/Applications/MATLAB_R2014b.app/bin":"$PATH"
Chans-iMac:subjects roh$ 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  484107 May 18 17:36 /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 Mon May 21 09:47:51 KST 2018
\n mris_compute_lgi --i lh.pial \n
=================
rm -Rf /Applications/freesurfer/subjects/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial
=================
=================
mkdir -p /Applications/freesurfer/subjects/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial
=================
=================
mris_fill -c -r 1 lh.pial /Applications/freesurfer/subjects/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=================
reading surface from lh.pial...
writing filled volume to /Applications/freesurfer/subjects/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz...
conforming output volume
setting resolution for intermediate calculations to 1.0000
=================
make_outer_surface('/Applications/freesurfer/subjects/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz',15,'/Applications/freesurfer/subjects/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer'); exit
=================

                            < M A T L A B (R) >
                  Copyright 1984-2014 The MathWorks, Inc.
                   R2014b (8.4.0.150421) 64-bit (maci64)
                             September 15, 2014

 

For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.

 

>> reading filled volume...
closing volume...
morphological closing done.
writing outer surface...

=================
mris_extract_main_component /Applications/freesurfer/subjects/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer /Applications/freesurfer/subjects/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main
=================

counting number of connected components...
   59754 voxel in cpt #1: X=2 [v=59754,e=179256,f=119504] located at (-26.107368, -18.544823, 16.176725)
For the whole surface: X=2 [v=59754,e=179256,f=119504]
One single component has been found
nothing to do
done

=================
mris_smooth -nw -n 30 /Applications/freesurfer/subjects/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-main ./lh.pial-outer-smoothed
=================
smoothing for 30 iterations
smoothing surface tessellation for 30 iterations...
smoothing complete - recomputing first and second fundamental forms...
=================
mris_euler_number ./lh.pial-outer-smoothed
=================
euler # = v-e+f = 2g-2: 59754 - 179256 + 119504 = 2 --> 0 holes
      F =2V-4:          119504 = 119508-4 (0)
      2E=3F:            358512 = 358512 (0)

total defect index = 0
=================
mris_convert -n lh.pial-outer-smoothed /Applications/freesurfer/subjects/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc
=================
=================
find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/Applications/freesurfer/subjects/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_46281_.m'); exit
=================

                            < M A T L A B (R) >
                  Copyright 1984-2014 The MathWorks, Inc.
                   R2014b (8.4.0.150421) 64-bit (maci64)
                             September 15, 2014

 

For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.

 

>> FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.08 sec)

FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial-outer-smoothed
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.01 sec)


deltaT =

    2.5700


=================
make_roi_paths('lh.pial','lh.pial-outer-smoothed',25,100,'/Applications/freesurfer/subjects/test01_t1/test01_t1/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrp_46281_.m'); exit
=================

                            < M A T L A B (R) >
                  Copyright 1984-2014 The MathWorks, Inc.
                   R2014b (8.4.0.150421) 64-bit (maci64)
                             September 15, 2014

 

For online documentation, see http://www.mathworks.com/support
For product information, visit www.mathworks.com.

 

>> loading datas ...
FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.08 sec)

FREESURFER_READ_SURF [v  1.2 ]
...reading surface file: lh.pial-outer-smoothed
...reading triangle file
...adding 1 to face indices for matlab compatibility.
...done (  0.01 sec)

preparing outer mesh structure ...
face 5000 / 119504
face 10000 / 119504
face 15000 / 119504
face 20000 / 119504
face 25000 / 119504
face 30000 / 119504
face 35000 / 119504
face 40000 / 119504
face 45000 / 119504
face 50000 / 119504
face 55000 / 119504
face 60000 / 119504
face 65000 / 119504
face 70000 / 119504
face 75000 / 119504
face 80000 / 119504
face 85000 / 119504
face 90000 / 119504
face 95000 / 119504
face 100000 / 119504
face 105000 / 119504
face 110000 / 119504
face 115000 / 119504

mesh_outer = 

         vertices: [59754x3 double]
            faces: [119504x3 double]
    facesOfVertex: [59754x1 struct]

preparing pial mesh structure ...
...searching for mesh edges...done (76.35 sec).
... creating path file for vertex 1 / 59754
area file for outer ROIs saved at 1
Improper assignment with rectangular empty matrix.

Error in dsearchn (line 79)
        [d(i),t(i)] = min(sum((x-yi).^2,2));

Error in mesh_vertex_nearest (line 29)
nearestIndex = dsearchn(vertices,points);


Error in reorganize_verticeslist (line 28)
    [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertices(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));

    

Error in make_roi_paths (line 93)
    reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim,
    verticeslist, step);

 

>> 
ERROR:  make_roi_paths did not complete successfully!
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 Mon May 21 09:50:03 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