recon-all-lh.cmd 4.6 KB

123456789101112131415161718192021222324252627282930313233343536373839404142434445464748495051525354555657585960616263646566676869707172737475767778798081828384858687888990919293949596979899100101102103104105106107108109110111112113114115116117118119120121122123124125126127
  1. #---------------------------------
  2. # New invocation of recon-all Wed Oct 16 19:25:28 UTC 2019
  3. #--------------------------------------------
  4. #@# Tessellate lh Wed Oct 16 19:25:29 UTC 2019
  5. mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz
  6. mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix
  7. rm -f ../mri/filled-pretess255.mgz
  8. mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix
  9. #--------------------------------------------
  10. #@# Smooth1 lh Wed Oct 16 19:25:32 UTC 2019
  11. mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix
  12. #--------------------------------------------
  13. #@# Inflation1 lh Wed Oct 16 19:25:36 UTC 2019
  14. mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
  15. #--------------------------------------------
  16. #@# QSphere lh Wed Oct 16 19:25:50 UTC 2019
  17. mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix
  18. #--------------------------------------------
  19. #@# Fix Topology Copy lh Wed Oct 16 19:27:26 UTC 2019
  20. cp ../surf/lh.orig.nofix ../surf/lh.orig
  21. cp ../surf/lh.inflated.nofix ../surf/lh.inflated
  22. #@# Fix Topology lh Wed Oct 16 19:27:26 UTC 2019
  23. mris_fix_topology -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-06 lh
  24. mris_euler_number ../surf/lh.orig
  25. mris_remove_intersection ../surf/lh.orig ../surf/lh.orig
  26. rm ../surf/lh.inflated
  27. #--------------------------------------------
  28. #@# Make White Surf lh Wed Oct 16 19:38:00 UTC 2019
  29. mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-06 lh
  30. #--------------------------------------------
  31. #@# Smooth2 lh Wed Oct 16 19:41:45 UTC 2019
  32. mris_smooth -n 3 -nw -seed 1234 ../surf/lh.white.preaparc ../surf/lh.smoothwm
  33. #--------------------------------------------
  34. #@# Inflation2 lh Wed Oct 16 19:41:49 UTC 2019
  35. mris_inflate -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/touch/rusage.mris_inflate.lh.dat ../surf/lh.smoothwm ../surf/lh.inflated
  36. #--------------------------------------------
  37. #@# Curv .H and .K lh Wed Oct 16 19:42:02 UTC 2019
  38. mris_curvature -w lh.white.preaparc
  39. mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated
  40. #-----------------------------------------
  41. #@# Curvature Stats lh Wed Oct 16 19:42:53 UTC 2019
  42. mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/lh.curv.stats -F smoothwm sub-06 lh curv sulc
  43. #--------------------------------------------
  44. #@# Sphere lh Wed Oct 16 19:42:56 UTC 2019
  45. mris_sphere -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/touch/rusage.mris_sphere.lh.dat -seed 1234 ../surf/lh.inflated ../surf/lh.sphere
  46. #--------------------------------------------
  47. #@# Surf Reg lh Wed Oct 16 19:53:59 UTC 2019
  48. mris_register -curv -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/touch/rusage.mris_register.lh.dat ../surf/lh.sphere /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/lh.sphere.reg
  49. #--------------------------------------------
  50. #@# Jacobian white lh Wed Oct 16 20:13:56 UTC 2019
  51. mris_jacobian ../surf/lh.white.preaparc ../surf/lh.sphere.reg ../surf/lh.jacobian_white
  52. #--------------------------------------------
  53. #@# AvgCurv lh Wed Oct 16 20:13:57 UTC 2019
  54. mrisp_paint -a 5 /opt/freesurfer/average/lh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/lh.sphere.reg ../surf/lh.avg_curv
  55. #-----------------------------------------
  56. #@# Cortical Parc lh Wed Oct 16 20:13:58 UTC 2019
  57. mris_ca_label -l ../label/lh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-06 lh ../surf/lh.sphere.reg /opt/freesurfer/average/lh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.annot
  58. #--------------------------------------------
  59. #@# Make Pial Surf lh Wed Oct 16 20:14:08 UTC 2019
  60. mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-06 lh
  61. #--------------------------------------------
  62. #@# Surf Volume lh Wed Oct 16 20:24:09 UTC 2019
  63. #---------------------------------
  64. # New invocation of recon-all Sat Jul 25 00:14:37 PDT 2020
  65. #--------------------------------------------
  66. #@# Curv .H and .K lh Sat Jul 25 00:14:42 PDT 2020
  67. mris_curvature -w lh.white.preaparc
  68. mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated