Hi,
I am using Matlab R2014a, and FS7.1.0
and receiving this error when I try to run -localGI. Is there a package I might be missing? Or am I using an outdated version of Matlab?
================= mris_smooth -nw -n 30 /mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/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: 61554 - 184656 + 123104 = 2 --> 0 holes F =2V-4: 123104 = 123108-4 (0) 2E=3F: 369312 = 369312 (0)
total defect index = 0 ================= mris_convert -n lh.pial-outer-smoothed /mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_30700_.m'); exit =================
< M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc. R2014a (8.3.0.532) 64-bit (glnxa64) February 11, 2014 .
.
.
To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit http://secure-web.cisco.com/19tcoYq0b9VO4ndLxRqJ8z0rI8AoZ3PjjUlX3NMoW1hFDf9t....
Warning: Input argument must be a string.
In ver at 41
In freesurfer_read_surf at 70 In find_corresponding_center_FSformat at 26 Error using fprintf Function is not defined for 'struct' inputs.
Error in freesurfer_read_surf (line 70) fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
ERROR: find_corresponding_center_FSformat did not complete successfully! Command exited with non-zero status 1 @#@FSTIME 2021:05:11:17:18:12 mris_compute_lgi N 2 e 31.58 S 6.20 U 53.23 P 188% M 1319608 F 0 R 1468406 W 0 c 71733 w 7023 I 8832 O 30496 L 17.98 17.99 18.00 @#@FSLOADPOST 2021:05:11:17:18:44 mris_compute_lgi N 2 17.35 17.83 17.95 Linux Gamma 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2+deb8u3 (2016-07-02) x86_64 GNU/Linux
recon-all -s 24015_S5437DFD_ASSET exited with ERRORS at Tue May 11 17:18:44 EDT 2021
For more details, see the log file /mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1tb0Ac8lCR6JdEw2vyP10SJNFvPDfcz-cQZjb7S8SDNovcHC...
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
________________________________
This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.
This was fixed in 7.11. You can use that version or copy the attached file to this location $FREESURFER_HOME/matlab/freesurfer_read_surf.m
On 5/11/2021 2:28 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
Hi,
I am using Matlab R2014a, and FS7.1.0
and receiving this error when I try to run -localGI. Is there a package I might be missing? Or am I using an outdated version of Matlab?
================= mris_smooth -nw -n 30 /mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/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: 61554 - 184656 + 123104 = 2 --> 0 holes F =2V-4: 123104 = 123108-4 (0) 2E=3F: 369312 = 369312 (0)
total defect index = 0
mris_convert -n lh.pial-outer-smoothed /mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/surf/tmp-mris_compute_lgi-lh.pial/lh.pial-outer-smoothed-normals.asc ================= ================= find_corresponding_center_FSformat('lh.pial','lh.pial-outer-smoothed',100,'/mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/surf/tmp-mris_compute_lgi-lh.pial','/tmp/mrc_30700_.m'); exit =================
< M A T L A B (R) > Copyright 1984-2014 The MathWorks, Inc. R2014a (8.3.0.532) 64-bit (glnxa64) February 11, 2014 .
.
.
To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com.
Warning: Input argument must be a string.
In ver at 41
In freesurfer_read_surf at 70 In find_corresponding_center_FSformat at 26 Error using fprintf Function is not defined for 'struct' inputs.
Error in freesurfer_read_surf (line 70) fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));
Error in find_corresponding_center_FSformat (line 26) [mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);
ERROR: find_corresponding_center_FSformat did not complete successfully! Command exited with non-zero status 1 @#@FSTIME 2021:05:11:17:18:12 mris_compute_lgi N 2 e 31.58 S 6.20 U 53.23 P 188% M 1319608 F 0 R 1468406 W 0 c 71733 w 7023 I 8832 O 30496 L 17.98 17.99 18.00 @#@FSLOADPOST 2021:05:11:17:18:44 mris_compute_lgi N 2 17.35 17.83 17.95 Linux Gamma 3.16.0-4-amd64 #1 SMP Debian 3.16.7-ckt25-2+deb8u3 (2016-07-02) x86_64 GNU/Linux
recon-all -s 24015_S5437DFD_ASSET exited with ERRORS at Tue May 11 17:18:44 EDT 2021
For more details, see the log file /mnt/V/Datasets/BSNIP2/Processing/Finished/24015_S5437DFD_ASSET/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
Victor Zeng Beth Israel Deaconess Medical Center Keshavan Lab --
This message is intended for the use of the person(s) to whom it may be addressed. It may contain information that is privileged, confidential, or otherwise protected from disclosure under applicable law. If you are not the intended recipient, any dissemination, distribution, copying, or use of this information is prohibited. If you have received this message in error, please permanently delete it and immediately notify the sender. Thank you.
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Douglas N. Greve -
Zeng, Victor (BIDMC - Keshavan - Psychiatry)