#--------------------------------- # New invocation of recon-all Wed Oct 16 15:51:23 UTC 2019 mri_convert /scratch/03763/oesteban/fmriprep-work/sub-06/fmriprep_wf/single_subject_06_wf/anat_preproc_wf/anat_validate/sub-06_ses-retest_T1w_template_valid.nii.gz /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/mri/orig/001.mgz #-------------------------------------------- #@# MotionCor Wed Oct 16 15:51:35 UTC 2019 cp /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/mri/orig/001.mgz /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/mri/rawavg.mgz mri_convert /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/mri/rawavg.mgz /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/mri/orig.mgz --conform mri_add_xform_to_header -c /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/mri/transforms/talairach.xfm /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/mri/orig.mgz /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/mri/orig.mgz #-------------------------------------------- #@# Talairach Wed Oct 16 15:51:45 UTC 2019 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 Wed Oct 16 15:53:08 UTC 2019 talairach_afd -T 0.005 -xfm transforms/talairach.xfm awk -f /opt/freesurfer/bin/extract_talairach_avi_QA.awk /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/mri/transforms/talairach_avi.log tal_QC_AZS /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/mri/transforms/talairach_avi.log #-------------------------------------------- #@# Nu Intensity Correction Wed Oct 16 15:53:09 UTC 2019 mri_nu_correct.mni --i orig.mgz --o nu.mgz --uchar transforms/talairach.xfm --n 2 mri_add_xform_to_header -c /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/mri/transforms/talairach.xfm nu.mgz nu.mgz #-------------------------------------------- #@# Intensity Normalization Wed Oct 16 15:54:45 UTC 2019 mri_normalize -g 1 -mprage nu.mgz T1.mgz #--------------------------------- # New invocation of recon-all Wed Oct 16 17:21:39 UTC 2019 #------------------------------------- #@# EM Registration Wed Oct 16 17:21:43 UTC 2019 mri_em_register -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/touch/rusage.mri_em_register.dat -uns 3 -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta #-------------------------------------- #@# CA Normalize Wed Oct 16 17:25:01 UTC 2019 mri_ca_normalize -c ctrl_pts.mgz -mask brainmask.mgz nu.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta norm.mgz #-------------------------------------- #@# CA Reg Wed Oct 16 17:26:15 UTC 2019 mri_ca_register -rusage /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/touch/rusage.mri_ca_register.dat -nobigventricles -T transforms/talairach.lta -align-after -mask brainmask.mgz norm.mgz /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca transforms/talairach.m3z #-------------------------------------- #@# SubCort Seg Wed Oct 16 18:45:54 UTC 2019 mri_ca_label -relabel_unlikely 9 .3 -prior 0.5 -align norm.mgz transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca aseg.auto_noCCseg.mgz mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/sub-06/mri/transforms/cc_up.lta sub-06 #-------------------------------------- #@# Merge ASeg Wed Oct 16 19:21:42 UTC 2019 cp aseg.auto.mgz aseg.presurf.mgz #-------------------------------------------- #@# Intensity Normalization2 Wed Oct 16 19:21:42 UTC 2019 mri_normalize -mprage -aseg aseg.presurf.mgz -mask brainmask.mgz norm.mgz brain.mgz #-------------------------------------------- #@# Mask BFS Wed Oct 16 19:23:43 UTC 2019 mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz #-------------------------------------------- #@# WM Segmentation Wed Oct 16 19:23:45 UTC 2019 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 Wed Oct 16 19:24:56 UTC 2019 mri_fill -a ../scripts/ponscc.cut.log -xform transforms/talairach.lta -segmentation aseg.auto_noCCseg.mgz wm.mgz filled.mgz #--------------------------------- # New invocation of recon-all Wed Oct 16 21:20:23 UTC 2019 #-------------------------------------------- #@# Cortical ribbon mask Wed Oct 16 21:20:24 UTC 2019 mris_volmask --aseg_name aseg.presurf --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon sub-06 #----------------------------------------- #@# Parcellation Stats lh Wed Oct 16 21:26:58 UTC 2019 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-06 lh white mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.pial.stats -b -a ../label/lh.aparc.annot -c ../label/aparc.annot.ctab sub-06 lh pial #----------------------------------------- #@# Cortical Parc 2 lh Wed Oct 16 21:27:43 UTC 2019 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.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.a2009s.annot #----------------------------------------- #@# Parcellation Stats 2 lh Wed Oct 16 21:27:56 UTC 2019 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.a2009s.stats -b -a ../label/lh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-06 lh white #----------------------------------------- #@# Cortical Parc 3 lh Wed Oct 16 21:28:19 UTC 2019 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.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/lh.aparc.DKTatlas.annot #----------------------------------------- #@# Parcellation Stats 3 lh Wed Oct 16 21:28:30 UTC 2019 mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.DKTatlas.stats -b -a ../label/lh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-06 lh white #----------------------------------------- #@# WM/GM Contrast lh Wed Oct 16 21:28:53 UTC 2019 pctsurfcon --s sub-06 --lh-only #----------------------------------------- #@# Relabel Hypointensities Wed Oct 16 21:28:59 UTC 2019 mri_relabel_hypointensities aseg.presurf.mgz ../surf aseg.presurf.hypos.mgz #----------------------------------------- #@# AParc-to-ASeg aparc Wed Oct 16 21:29:13 UTC 2019 mri_aparc2aseg --s sub-06 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt #----------------------------------------- #@# AParc-to-ASeg a2009s Wed Oct 16 21:33:00 UTC 2019 INFO: skipping a2009s aparc2aseg #----------------------------------------- #@# AParc-to-ASeg DKTatlas Wed Oct 16 21:33:00 UTC 2019 INFO: skipping DKTatlas aparc2aseg #----------------------------------------- #@# APas-to-ASeg Wed Oct 16 21:33:00 UTC 2019 apas2aseg --i aparc+aseg.mgz --o aseg.mgz #-------------------------------------------- #@# ASeg Stats Wed Oct 16 21:33:03 UTC 2019 mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /opt/freesurfer/ASegStatsLUT.txt --subject sub-06 #----------------------------------------- #@# WMParc Wed Oct 16 21:33:29 UTC 2019 mri_aparc2aseg --s sub-06 --labelwm --hypo-as-wm --rip-unknown --volmask --o mri/wmparc.mgz --ctxseg aparc+aseg.mgz mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject sub-06 --surf-wm-vol --ctab /opt/freesurfer/WMParcStatsLUT.txt --etiv #-------------------------------------------- #@# BA_exvivo Labels lh Wed Oct 16 21:37:13 UTC 2019 mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA1_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA2_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA3a_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA3a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA3b_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA3b_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA4a_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA4a_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA4p_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA4p_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA6_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA6_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA44_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA44_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA45_exvivo.label --trgsubject sub-06 --trglabel ./lh.BA45_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.V1_exvivo.label --trgsubject sub-06 --trglabel ./lh.V1_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.V2_exvivo.label --trgsubject sub-06 --trglabel ./lh.V2_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.MT_exvivo.label --trgsubject sub-06 --trglabel ./lh.MT_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.entorhinal_exvivo.label --trgsubject sub-06 --trglabel ./lh.entorhinal_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.perirhinal_exvivo.label --trgsubject sub-06 --trglabel ./lh.perirhinal_exvivo.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA1_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA2_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA3a_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA3a_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA3b_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA3b_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA4a_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA4a_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA4p_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA4p_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA6_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA6_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA44_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA44_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.BA45_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.BA45_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.V1_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.V1_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.V2_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.V2_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.MT_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.MT_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.entorhinal_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.entorhinal_exvivo.thresh.label --hemi lh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/lh.perirhinal_exvivo.thresh.label --trgsubject sub-06 --trglabel ./lh.perirhinal_exvivo.thresh.label --hemi lh --regmethod surface mris_label2annot --s sub-06 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.label --l lh.BA2_exvivo.label --l lh.BA3a_exvivo.label --l lh.BA3b_exvivo.label --l lh.BA4a_exvivo.label --l lh.BA4p_exvivo.label --l lh.BA6_exvivo.label --l lh.BA44_exvivo.label --l lh.BA45_exvivo.label --l lh.V1_exvivo.label --l lh.V2_exvivo.label --l lh.MT_exvivo.label --l lh.entorhinal_exvivo.label --l lh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose mris_label2annot --s sub-06 --hemi lh --ctab /opt/freesurfer/average/colortable_BA.txt --l lh.BA1_exvivo.thresh.label --l lh.BA2_exvivo.thresh.label --l lh.BA3a_exvivo.thresh.label --l lh.BA3b_exvivo.thresh.label --l lh.BA4a_exvivo.thresh.label --l lh.BA4p_exvivo.thresh.label --l lh.BA6_exvivo.thresh.label --l lh.BA44_exvivo.thresh.label --l lh.BA45_exvivo.thresh.label --l lh.V1_exvivo.thresh.label --l lh.V2_exvivo.thresh.label --l lh.MT_exvivo.thresh.label --l lh.entorhinal_exvivo.thresh.label --l lh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.stats -b -a ./lh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-06 lh white mris_anatomical_stats -th3 -mgz -f ../stats/lh.BA_exvivo.thresh.stats -b -a ./lh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-06 lh white #--------------------------------- # New invocation of recon-all Wed Oct 16 21:40:48 UTC 2019 #----------------------------------------- #@# Parcellation Stats rh Wed Oct 16 21:40:49 UTC 2019 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-06 rh white mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.pial.stats -b -a ../label/rh.aparc.annot -c ../label/aparc.annot.ctab sub-06 rh pial #----------------------------------------- #@# Cortical Parc 2 rh Wed Oct 16 21:41:36 UTC 2019 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-06 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.CDaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.a2009s.annot #----------------------------------------- #@# Parcellation Stats 2 rh Wed Oct 16 21:41:48 UTC 2019 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.a2009s.stats -b -a ../label/rh.aparc.a2009s.annot -c ../label/aparc.annot.a2009s.ctab sub-06 rh white #----------------------------------------- #@# Cortical Parc 3 rh Wed Oct 16 21:42:12 UTC 2019 mris_ca_label -l ../label/rh.cortex.label -aseg ../mri/aseg.presurf.mgz -seed 1234 sub-06 rh ../surf/rh.sphere.reg /opt/freesurfer/average/rh.DKTaparc.atlas.acfb40.noaparc.i12.2016-08-02.gcs ../label/rh.aparc.DKTatlas.annot #----------------------------------------- #@# Parcellation Stats 3 rh Wed Oct 16 21:42:23 UTC 2019 mris_anatomical_stats -th3 -mgz -cortex ../label/rh.cortex.label -f ../stats/rh.aparc.DKTatlas.stats -b -a ../label/rh.aparc.DKTatlas.annot -c ../label/aparc.annot.DKTatlas.ctab sub-06 rh white #----------------------------------------- #@# WM/GM Contrast rh Wed Oct 16 21:42:46 UTC 2019 pctsurfcon --s sub-06 --rh-only #----------------------------------------- #@# AParc-to-ASeg aparc Wed Oct 16 21:42:51 UTC 2019 mri_aparc2aseg --s sub-06 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt #----------------------------------------- #@# AParc-to-ASeg a2009s Wed Oct 16 21:46:38 UTC 2019 mri_aparc2aseg --s sub-06 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --a2009s #----------------------------------------- #@# AParc-to-ASeg DKTatlas Wed Oct 16 21:50:25 UTC 2019 mri_aparc2aseg --s sub-06 --volmask --aseg aseg.presurf.hypos --relabel mri/norm.mgz mri/transforms/talairach.m3z /opt/freesurfer/average/RB_all_2016-05-10.vc700.gca mri/aseg.auto_noCCseg.label_intensities.txt --annot aparc.DKTatlas --o mri/aparc.DKTatlas+aseg.mgz #-------------------------------------------- #@# BA_exvivo Labels rh Wed Oct 16 21:54:11 UTC 2019 mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA1_exvivo.label --trgsubject sub-06 --trglabel ./rh.BA1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA2_exvivo.label --trgsubject sub-06 --trglabel ./rh.BA2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA3a_exvivo.label --trgsubject sub-06 --trglabel ./rh.BA3a_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA3b_exvivo.label --trgsubject sub-06 --trglabel ./rh.BA3b_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA4a_exvivo.label --trgsubject sub-06 --trglabel ./rh.BA4a_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA4p_exvivo.label --trgsubject sub-06 --trglabel ./rh.BA4p_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA6_exvivo.label --trgsubject sub-06 --trglabel ./rh.BA6_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA44_exvivo.label --trgsubject sub-06 --trglabel ./rh.BA44_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA45_exvivo.label --trgsubject sub-06 --trglabel ./rh.BA45_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.V1_exvivo.label --trgsubject sub-06 --trglabel ./rh.V1_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.V2_exvivo.label --trgsubject sub-06 --trglabel ./rh.V2_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.MT_exvivo.label --trgsubject sub-06 --trglabel ./rh.MT_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.entorhinal_exvivo.label --trgsubject sub-06 --trglabel ./rh.entorhinal_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.perirhinal_exvivo.label --trgsubject sub-06 --trglabel ./rh.perirhinal_exvivo.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA1_exvivo.thresh.label --trgsubject sub-06 --trglabel ./rh.BA1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA2_exvivo.thresh.label --trgsubject sub-06 --trglabel ./rh.BA2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA3a_exvivo.thresh.label --trgsubject sub-06 --trglabel ./rh.BA3a_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA3b_exvivo.thresh.label --trgsubject sub-06 --trglabel ./rh.BA3b_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA4a_exvivo.thresh.label --trgsubject sub-06 --trglabel ./rh.BA4a_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA4p_exvivo.thresh.label --trgsubject sub-06 --trglabel ./rh.BA4p_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA6_exvivo.thresh.label --trgsubject sub-06 --trglabel ./rh.BA6_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA44_exvivo.thresh.label --trgsubject sub-06 --trglabel ./rh.BA44_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.BA45_exvivo.thresh.label --trgsubject sub-06 --trglabel ./rh.BA45_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.V1_exvivo.thresh.label --trgsubject sub-06 --trglabel ./rh.V1_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.V2_exvivo.thresh.label --trgsubject sub-06 --trglabel ./rh.V2_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.MT_exvivo.thresh.label --trgsubject sub-06 --trglabel ./rh.MT_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.entorhinal_exvivo.thresh.label --trgsubject sub-06 --trglabel ./rh.entorhinal_exvivo.thresh.label --hemi rh --regmethod surface mri_label2label --srcsubject fsaverage --srclabel /corral-repl/utexas/poldracklab/data/OpenNeuro/ds000114/derivatives/freesurfer-6.0.1/fsaverage/label/rh.perirhinal_exvivo.thresh.label --trgsubject sub-06 --trglabel ./rh.perirhinal_exvivo.thresh.label --hemi rh --regmethod surface mris_label2annot --s sub-06 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.label --l rh.BA2_exvivo.label --l rh.BA3a_exvivo.label --l rh.BA3b_exvivo.label --l rh.BA4a_exvivo.label --l rh.BA4p_exvivo.label --l rh.BA6_exvivo.label --l rh.BA44_exvivo.label --l rh.BA45_exvivo.label --l rh.V1_exvivo.label --l rh.V2_exvivo.label --l rh.MT_exvivo.label --l rh.entorhinal_exvivo.label --l rh.perirhinal_exvivo.label --a BA_exvivo --maxstatwinner --noverbose mris_label2annot --s sub-06 --hemi rh --ctab /opt/freesurfer/average/colortable_BA.txt --l rh.BA1_exvivo.thresh.label --l rh.BA2_exvivo.thresh.label --l rh.BA3a_exvivo.thresh.label --l rh.BA3b_exvivo.thresh.label --l rh.BA4a_exvivo.thresh.label --l rh.BA4p_exvivo.thresh.label --l rh.BA6_exvivo.thresh.label --l rh.BA44_exvivo.thresh.label --l rh.BA45_exvivo.thresh.label --l rh.V1_exvivo.thresh.label --l rh.V2_exvivo.thresh.label --l rh.MT_exvivo.thresh.label --l rh.entorhinal_exvivo.thresh.label --l rh.perirhinal_exvivo.thresh.label --a BA_exvivo.thresh --maxstatwinner --noverbose mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.stats -b -a ./rh.BA_exvivo.annot -c ./BA_exvivo.ctab sub-06 rh white mris_anatomical_stats -th3 -mgz -f ../stats/rh.BA_exvivo.thresh.stats -b -a ./rh.BA_exvivo.thresh.annot -c ./BA_exvivo.thresh.ctab sub-06 rh white #--------------------------------- # New invocation of recon-all Wed Oct 16 21:57:47 UTC 2019 #----------------------------------------- #@# APas-to-ASeg Wed Oct 16 21:57:48 UTC 2019 apas2aseg --i aparc+aseg.mgz --o aseg.mgz