recon-all-rh.cmd 4.6 KB

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  1. #---------------------------------
  2. # New invocation of recon-all Wed Oct 16 19:48:33 UTC 2019
  3. #--------------------------------------------
  4. #@# Tessellate rh Wed Oct 16 19:48:34 UTC 2019
  5. mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz
  6. mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix
  7. rm -f ../mri/filled-pretess127.mgz
  8. mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix
  9. #--------------------------------------------
  10. #@# Smooth1 rh Wed Oct 16 19:48:37 UTC 2019
  11. mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix
  12. #--------------------------------------------
  13. #@# Inflation1 rh Wed Oct 16 19:48:40 UTC 2019
  14. mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
  15. #--------------------------------------------
  16. #@# QSphere rh Wed Oct 16 19:48:51 UTC 2019
  17. mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix
  18. #--------------------------------------------
  19. #@# Fix Topology Copy rh Wed Oct 16 19:50:01 UTC 2019
  20. cp ../surf/rh.orig.nofix ../surf/rh.orig
  21. cp ../surf/rh.inflated.nofix ../surf/rh.inflated
  22. #@# Fix Topology rh Wed Oct 16 19:50:01 UTC 2019
  23. mris_fix_topology -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-10/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 sub-10 rh
  24. mris_euler_number ../surf/rh.orig
  25. mris_remove_intersection ../surf/rh.orig ../surf/rh.orig
  26. rm ../surf/rh.inflated
  27. #--------------------------------------------
  28. #@# Make White Surf rh Wed Oct 16 19:54:12 UTC 2019
  29. mris_make_surfaces -aseg ../mri/aseg.presurf -white white.preaparc -noaparc -whiteonly -mgz -T1 brain.finalsurfs sub-10 rh
  30. #--------------------------------------------
  31. #@# Smooth2 rh Wed Oct 16 19:57:00 UTC 2019
  32. mris_smooth -n 3 -nw -seed 1234 ../surf/rh.white.preaparc ../surf/rh.smoothwm
  33. #--------------------------------------------
  34. #@# Inflation2 rh Wed Oct 16 19:57:03 UTC 2019
  35. mris_inflate -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-10/touch/rusage.mris_inflate.rh.dat ../surf/rh.smoothwm ../surf/rh.inflated
  36. #--------------------------------------------
  37. #@# Curv .H and .K rh Wed Oct 16 19:57:14 UTC 2019
  38. mris_curvature -w rh.white.preaparc
  39. mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated
  40. #-----------------------------------------
  41. #@# Curvature Stats rh Wed Oct 16 19:57:53 UTC 2019
  42. mris_curvature_stats -m --writeCurvatureFiles -G -o ../stats/rh.curv.stats -F smoothwm sub-10 rh curv sulc
  43. #--------------------------------------------
  44. #@# Sphere rh Wed Oct 16 19:57:56 UTC 2019
  45. mris_sphere -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-10/touch/rusage.mris_sphere.rh.dat -seed 1234 ../surf/rh.inflated ../surf/rh.sphere
  46. #--------------------------------------------
  47. #@# Surf Reg rh Wed Oct 16 20:02:18 UTC 2019
  48. mris_register -curv -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-10/touch/rusage.mris_register.rh.dat ../surf/rh.sphere /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif ../surf/rh.sphere.reg
  49. #--------------------------------------------
  50. #@# Jacobian white rh Wed Oct 16 20:17:44 UTC 2019
  51. mris_jacobian ../surf/rh.white.preaparc ../surf/rh.sphere.reg ../surf/rh.jacobian_white
  52. #--------------------------------------------
  53. #@# AvgCurv rh Wed Oct 16 20:17:45 UTC 2019
  54. mrisp_paint -a 5 /opt/freesurfer/average/rh.folding.atlas.acfb40.noaparc.i12.2016-08-02.tif#6 ../surf/rh.sphere.reg ../surf/rh.avg_curv
  55. #-----------------------------------------
  56. #@# Cortical Parc rh Wed Oct 16 20:17:46 UTC 2019
  57. mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-10 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.annot
  58. #--------------------------------------------
  59. #@# Make Pial Surf rh Wed Oct 16 20:17:54 UTC 2019
  60. mris_make_surfaces -orig_white white.preaparc -orig_pial white.preaparc -aseg ../mri/aseg.presurf -mgz -T1 brain.finalsurfs sub-10 rh
  61. #--------------------------------------------
  62. #@# Surf Volume rh Wed Oct 16 20:25:43 UTC 2019
  63. #---------------------------------
  64. # New invocation of recon-all Sat Jul 25 00:15:20 PDT 2020
  65. #--------------------------------------------
  66. #@# Curv .H and .K rh Sat Jul 25 00:15:21 PDT 2020
  67. mris_curvature -w rh.white.preaparc
  68. mris_curvature -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated