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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”:”$PATH”)
The original Setting of the FreeSurfer(Mac OS) is like this :
But it exited with errors as follows:
I guess Outer ROI or matrix...but I couldn't know what the problem exactly is..
Improper assignment with rectangular empty matrix.
Error in dsearchn (line 79) [d(i),t(i)] = min(sum((x-yi).^2,2)); Error in mesh_vertex_nearest (line 29) nearestIndex = dsearchn(vertices,points);
Error in reorganize_verticeslist (line 28) [nextindex,nextvalue]=mesh_vertex_nearest(mesh_total.vertice s(remaininglist,:),mesh_total.vertices(verticeslist(start_vertex),:));
Error in make_roi_paths (line 93) reorglist = reorganize_verticeslist (mesh_total, A, mesh_outer, perim, verticeslist, step);
ERROR: make_roi_paths did not complete successfully! Darwin Chans-iMac.local 13.4.0 Darwin Kernel Version 13.4.0: Mon Jan 11 18:17:34 PST 2016; root:xnu-2422.115.15~1/RELEASE_X86_64 x86_64 recon-all -s test01_t1 exited with ERRORS at Mon May 21 09:50:03 KST 2018 For more details, see the log file /Applications/freesurfer/subje cts/test01_t1/test01_t1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/ BugReporting
I attached two relevant MATLAB files (*make_roi_pattern.m, SearchProjectionOnPial_Ver2.m*) and all the error message are written below..
Could you tell me some advice?
Best regards,
Subin Oh
-------- [freesurfer-Darwin-lion-stable-pub-v5.3.0]-------------------
Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni FSL_DIR /usr/local/fsl
----------------------------------------------------------------------------------------------------------------------------------------- Chans-iMac:subjects roh$ 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/subje cts/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/subje cts/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/subje cts/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/subje cts/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/subje cts/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/subje cts/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,'/A pplications/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.vertice s(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/subje cts/test01_t1/test01_t1/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/ BugReporting