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Dear FreeSurfer Experts,
I happened to have a task to run lGI, however this time, I couldn't run from the very beginning to start with recon-all as usual. I have already prepared ?h.pial from outersurf.vtk using mris_convert. Is this correct? May I know how to deal with the problem in red as below and what else to be prepared essentially other than this? I may figure out more if that's simple files to generate. I've gotten ?h.area, ?h.thickness, ?h.volume, segmentation already. Thank you so much!
~/test-G$ recon-all -s subject-1 -localGI Subject Stamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b Current Stamp: freesurfer-linux-centos6_x86_64-7.1.0-20200511-813297b INFO: SUBJECTS_DIR is /home/xiaoxu/test-G Actual FREESURFER_HOME /home/xiaoxu/freesurfer -rw-rw-r-- 1 xiaoxu xiaoxu 31435 Jan 22 14:19 /home/xiaoxu/test-G/subject-1/scripts/recon-all.log Linux xnVMUbuntu18 5.4.0-59-generic #65~18.04.1-Ubuntu SMP Mon Dec 14 15:59:40 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux '/home/xiaoxu/freesurfer/bin/recon-all' -> '/home/xiaoxu/test-G/subject-1/scripts/recon-all.local-copy' ~/test-G/subject-1/mri/transforms ~/test-G/subject-1 ~/test-G/subject-1 #@# pial curv lh Fri Jan 22 15:59:28 CST 2021 cd /home/xiaoxu/test-G/subject-1/mri mris_place_surface --curv-map ../surf/lh.pial 2 10 ../surf/lh.curv.pial Update not needed #@# pial area lh Fri Jan 22 15:59:28 CST 2021 cd /home/xiaoxu/test-G/subject-1/mri mris_place_surface --area-map ../surf/lh.pial ../surf/lh.area.pial Update not needed #@# pial curv rh Fri Jan 22 15:59:28 CST 2021 cd /home/xiaoxu/test-G/subject-1/mri mris_place_surface --curv-map ../surf/rh.pial 2 10 ../surf/rh.curv.pial Update not needed #@# pial area rh Fri Jan 22 15:59:28 CST 2021 cd /home/xiaoxu/test-G/subject-1/mri mris_place_surface --area-map ../surf/rh.pial ../surf/rh.area.pial Update not needed /home/xiaoxu/test-G/subject-1/surf #-------------------------------------------- #@# Local Gyrification Index lh Fri Jan 22 15:59:28 CST 2021
mris_compute_lgi --i lh.pial
================= rm -Rf /home/xiaoxu/test-G/subject-1/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mkdir -p /home/xiaoxu/test-G/subject-1/surf/tmp-mris_compute_lgi-lh.pial ================= ================= mris_fill -c -r 1 lh.pial /home/xiaoxu/test-G/subject-1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz ================= reading surface from lh.pial... conforming output volume setting resolution for intermediate calculations to 1.0000 error: volume size must be greater than 0 in every dimension ERROR: mris_fill -c -r 1 lh.pial /home/xiaoxu/test-G/subject-1/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz failed! Command exited with non-zero status 1 @#@FSTIME 2021:01:22:15:59:28 mris_compute_lgi N 2 e 0.76 S 0.07 U 0.68 P 100% M 151256 F 0 R 43901 W 0 c 9 w 22 I 0 O 0 L 0.12 0.04 0.06 @#@FSLOADPOST 2021:01:22:15:59:29 mris_compute_lgi N 2 0.19 0.06 0.07 Linux xnVMUbuntu18 5.4.0-59-generic #65~18.04.1-Ubuntu SMP Mon Dec 14 15:59:40 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subject-1 exited with ERRORS at Fri Jan 22 15:59:29 CST 2021
For more details, see the log file /home/xiaoxu/test-G/subject-1/scripts/recon-all.log To report a problem, see http://secure-web.cisco.com/1IirEH-QHYbP-VlpZ8Ta_sE9bJzBhRQSQC9X6cw8h90JlDpW...
Regards, Xiaoxu
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