To Run -lGI without Recon-all - Freesurfer

22 Jan 2021


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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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