ABIDE_fs-6.0.0/0050309/scripts/recon-all.cmd

#---------------------------------
# New invocation of recon-all Sun Oct 22 20:25:40 CEST 2017 

 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/_orig/raw_nii/UM_1/0050309/session_1/anat_1/mprage.nii.gz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/orig/001.mgz 

#--------------------------------------------
#@# MotionCor Sun Oct 22 20:25:45 CEST 2017

 cp /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/orig/001.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/rawavg.mgz 


 mri_convert /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/rawavg.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/orig.mgz --conform 


 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/transforms/talairach.xfm /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/orig.mgz /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/orig.mgz 

#--------------------------------------------
#@# Talairach Sun Oct 22 20:25:55 CEST 2017

 mri_nu_correct.mni --no-rescale --i orig.mgz --o orig_nu.mgz --n 1 --proto-iters 1000 --distance 50 


 talairach_avi --i orig_nu.mgz --xfm transforms/talairach.auto.xfm 

talairach_avi log file is transforms/talairach_avi.log...

 cp transforms/talairach.auto.xfm transforms/talairach.xfm 

#--------------------------------------------
#@# Talairach Failure Detection Sun Oct 22 20:27:59 CEST 2017

 talairach_afd -T 0.005 -xfm transforms/talairach.xfm 


 awk -f /pasteur/homes/ntraut/bin/freesurfer-6.0.0/bin/extract_talairach_avi_QA.awk /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/transforms/talairach_avi.log 


 tal_QC_AZS /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/transforms/talairach_avi.log 

#--------------------------------------------
#@# Nu Intensity Correction Sun Oct 22 20:27:59 CEST 2017

 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 


 mri_add_xform_to_header -c /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/transforms/talairach.xfm nu.mgz nu.mgz 

#--------------------------------------------
#@# Intensity Normalization Sun Oct 22 20:30:15 CEST 2017

 mri_normalize -g 1 -mprage nu.mgz T1.mgz 

#--------------------------------------------
#@# Skull Stripping Sun Oct 22 20:32:40 CEST 2017

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/touch/rusage.mri_em_register.skull.dat -skull nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta 


 mri_watershed -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/touch/rusage.mri_watershed.dat -T1 -brain_atlas /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_withskull_2016-05-10.vc700.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz 


 cp brainmask.auto.mgz brainmask.mgz 

#-------------------------------------
#@# EM Registration Sun Oct 22 20:55:56 CEST 2017

 mri_em_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta 

#--------------------------------------
#@# CA Normalize Sun Oct 22 21:14:11 CEST 2017

 mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz 

#--------------------------------------
#@# CA Reg Sun Oct 22 21:16:00 CEST 2017

 mri_ca_register -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z 

#--------------------------------------
#@# SubCort Seg Mon Oct 23 00:50:41 CEST 2017

 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /pasteur/homes/ntraut/bin/freesurfer-6.0.0/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz 


 mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/mri/transforms/cc_up.lta 0050309 

#--------------------------------------
#@# Merge ASeg Mon Oct 23 01:57:23 CEST 2017

 cp aseg.auto.mgz aseg.presurf.mgz 

#--------------------------------------------
#@# Intensity Normalization2 Mon Oct 23 01:57:24 CEST 2017

 mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz 

#--------------------------------------------
#@# Mask BFS Mon Oct 23 02:01:19 CEST 2017

 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz 

#--------------------------------------------
#@# WM Segmentation Mon Oct 23 02:01:21 CEST 2017

 mri_segment -mprage brain.mgz wm.seg.mgz 


 mri_edit_wm_with_aseg -keep-in wm.seg.mgz brain.mgz aseg.presurf.mgz wm.asegedit.mgz 


 mri_pretess wm.asegedit.mgz wm norm.mgz wm.mgz 

#--------------------------------------------
#@# Fill Mon Oct 23 02:05:49 CEST 2017

 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz 

#--------------------------------------------
#@# Tessellate lh Mon Oct 23 02:06:38 CEST 2017

 mri_pretess ../mri/filled.mgz 255 ../mri/norm.mgz ../mri/filled-pretess255.mgz 


 mri_tessellate ../mri/filled-pretess255.mgz 255 ../surf/lh.orig.nofix 


 rm -f ../mri/filled-pretess255.mgz 


 mris_extract_main_component ../surf/lh.orig.nofix ../surf/lh.orig.nofix 

#--------------------------------------------
#@# Tessellate rh Mon Oct 23 02:06:43 CEST 2017

 mri_pretess ../mri/filled.mgz 127 ../mri/norm.mgz ../mri/filled-pretess127.mgz 


 mri_tessellate ../mri/filled-pretess127.mgz 127 ../surf/rh.orig.nofix 


 rm -f ../mri/filled-pretess127.mgz 


 mris_extract_main_component ../surf/rh.orig.nofix ../surf/rh.orig.nofix 

#--------------------------------------------
#@# Smooth1 lh Mon Oct 23 02:06:49 CEST 2017

 mris_smooth -nw -seed 1234 ../surf/lh.orig.nofix ../surf/lh.smoothwm.nofix 

#--------------------------------------------
#@# Smooth1 rh Mon Oct 23 02:06:49 CEST 2017

 mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix ../surf/rh.smoothwm.nofix 

#--------------------------------------------
#@# Inflation1 lh Mon Oct 23 02:07:00 CEST 2017

 mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix 

#--------------------------------------------
#@# Inflation1 rh Mon Oct 23 02:07:00 CEST 2017

 mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix 

#--------------------------------------------
#@# QSphere lh Mon Oct 23 02:08:33 CEST 2017

 mris_sphere -q -seed 1234 ../surf/lh.inflated.nofix ../surf/lh.qsphere.nofix 

#--------------------------------------------
#@# QSphere rh Mon Oct 23 02:08:33 CEST 2017

 mris_sphere -q -seed 1234 ../surf/rh.inflated.nofix ../surf/rh.qsphere.nofix 

#--------------------------------------------
#@# Fix Topology Copy lh Mon Oct 23 02:18:13 CEST 2017

 cp ../surf/lh.orig.nofix ../surf/lh.orig 


 cp ../surf/lh.inflated.nofix ../surf/lh.inflated 

#--------------------------------------------
#@# Fix Topology Copy rh Mon Oct 23 02:18:13 CEST 2017

 cp ../surf/rh.orig.nofix ../surf/rh.orig 


 cp ../surf/rh.inflated.nofix ../surf/rh.inflated 

#@# Fix Topology lh Mon Oct 23 02:18:13 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/touch/rusage.mris_fix_topology.lh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050309 lh 

#@# Fix Topology rh Mon Oct 23 02:18:13 CEST 2017

 mris_fix_topology -rusage /pasteur/projets/policy01/cinq/rto/data/abide/fs-6.0.0/0050309/touch/rusage.mris_fix_topology.rh.dat -mgz -sphere qsphere.nofix -ga -seed 1234 0050309 rh 



#---------------------------------
# New invocation of recon-all Tue May 29 16:19:41 CEST 2018 


#---------------------------------
# New invocation of recon-all Tue May 29 16:25:19 CEST 2018 


#---------------------------------
# New invocation of recon-all Tue May 29 16:56:44 CEST 2018 
#--------------------------------------------
#@# Qdec Cache preproc lh w-g.pct.00.mgh fsaverage Tue May 29 16:56:46 CEST 2018

 mris_preproc --s 0050309 --hemi lh --meas w-g.pct.00.mgh --target fsaverage --out lh.w-g.pct.00.mgh.fsaverage.mgh 



#---------------------------------
# New invocation of recon-all Wed May 30 14:45:30 CEST 2018 
#--------------------------------------------
#@# Qdec Cache preproc lh w-g.pct.mgh fsaverage Wed May 30 14:45:36 CEST 2018

 mris_preproc --s 0050309 --hemi lh --meas w-g.pct.mgh --target fsaverage --out lh.w-g.pct.mgh.fsaverage.mgh 



#---------------------------------
# New invocation of recon-all Thu Jul 12 13:52:33 CEST 2018 
#--------------------------------------------
#@# Qdec Cache preproc lh thickness fsaverage Thu Jul 12 13:52:37 CEST 2018

 mris_preproc --s 0050309 --hemi lh --meas thickness --target fsaverage --out lh.thickness.fsaverage.mgh 



#---------------------------------
# New invocation of recon-all Thu Oct 17 17:47:29 CEST 2019 
#--------------------------------------------
#@# Qdec Cache preproc lh thickness fsaverage4 Thu Oct 17 17:47:41 CEST 2019

 mris_preproc --s 0050309 --hemi lh --meas thickness --target fsaverage4 --out lh.thickness.fsaverage4.mgh