#!/bin/sh -xu # print commands with -x and exit if any shell variables are undefined (-u) # All tutorial commands, commented out commands that are listed in the tutorial but are not run for time reasons. date LIBREOFFICE="libreoffice" if [ "$(uname)" = "Darwin" ]; then LIBREOFFICE="/Applications/LibreOffice.app/Contents/MacOS/soffice" fi # FOR DEV BRANCH # -no-auto-load option does not exist in 6.0 # FREEVIEW="freeview -no-auto-load" # 6.0.0 RELEASE: Note that 6.0.0 version of freeview always exits with status 0 when using -quit option FREEVIEW="freeview -quit" # FREEVIEW="strace -e trace=file freeview" # Use AppImage to run latest dev version of freeview - which can exit with non-zero status even with -quit # AppImage file needs -no-auto-load else issues error it cannot find sphere.reg files ? # FREEVIEW="/home/fsuser3/freesurfer/bin/freeview-dev20190624-x86_64.AppImage -no-auto-load" # FREEVIEW="$TUTORIAL_DATA/freeview-dev20190709-x86_64.AppImage -no-auto-load" # FREEVIEW="strace -e trace=file /home/fsuser3/freesurfer/bin/freeview-dev20190624-x86_64.AppImage -no-auto-load" export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs cd $SUBJECTS_DIR set -e # https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/OutputData_freeview echo "Freeview Command 1: load several output volumes" $FREEVIEW -v \ good_output/mri/T1.mgz \ good_output/mri/wm.mgz \ good_output/mri/brainmask.mgz \ good_output/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f good_output/surf/lh.white:edgecolor=blue \ good_output/surf/lh.pial:edgecolor=red \ good_output/surf/rh.white:edgecolor=blue \ good_output/surf/rh.pial:edgecolor=red echo "Freeview Command 2: view surface overlays" $FREEVIEW -f good_output/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ good_output/surf/lh.pial:annot=aparc.a2009s.annot:name=pial_aparc_des:visible=0 \ good_output/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflated_thickness:visible=0 \ good_output/surf/lh.inflated:visible=0 \ good_output/surf/lh.white:visible=0 \ good_output/surf/lh.pial \ --viewport 3d # ADDED 9/2018 from Matt echo "Freeview Command 2.5" $FREEVIEW -v 004/mri/aparc+aseg.mgz:colormap=lut # ADDED 9/2018 from Matt echo "Freeview Command 2.6" $FREEVIEW -f 004/surf/lh.pial:overlay=lh.thickness:overlay_threshold=1,2 --viewport 3d # ADDED 9/2018 from Matt echo "Freeview Command 2.7" $FREEVIEW -v 004/mri/brainmask.mgz 004/mri/wm.mgz:colormap=jet:opacity=.2 -f 004/surf/lh.pial:edgecolor=blue 004/surf/lh.white:edgecolor=red 004/surf/rh.pial:edgecolor # https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice # FINDING THE CORECT INPUT FOR THE FS PIPELINE export SUBJECTS_DIR=$TUTORIAL_DATA/practice_with_data cd $SUBJECTS_DIR # Create scan.log from dicoms cd $TUTORIAL_DATA/practice_with_data/dicoms dcmunpack -src . -scanonly scan.log cat scan.log echo $SUBJECTS_DIR # export SUBJECTS_DIR=$TUTORIAL_DATA/practice_with_data ### takes a long time # recon-all -all -i I50 -s Subj001 # ADDED cd $TUTORIAL_DATA/dicom_challenge/dicoms dcmunpack -src . -scanonly scan.log export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs cd $SUBJECTS_DIR # https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TroubleshootingDataV6.0 echo "Freeview Command 3: open pial_edits_before" $FREEVIEW -v pial_edits_before/mri/T1.mgz \ pial_edits_before/mri/brainmask.mgz \ -f pial_edits_before/surf/lh.white:edgecolor=yellow \ pial_edits_before/surf/lh.pial:edgecolor=red \ pial_edits_before/surf/rh.white:edgecolor=yellow \ pial_edits_before/surf/rh.pial:edgecolor=red echo "Freeview Command 4: open pial_edits_after" $FREEVIEW -v pial_edits_after/mri/T1.mgz \ pial_edits_after/mri/brainmask.mgz \ -f pial_edits_after/surf/lh.white:edgecolor=yellow \ pial_edits_after/surf/lh.pial:edgecolor=red \ pial_edits_after/surf/rh.white:edgecolor=yellow \ pial_edits_after/surf/rh.pial:edgecolor=red echo "Freeview Command 5: look at next subject, wm1_edits_before" $FREEVIEW -v wm1_edits_before/mri/brainmask.mgz \ wm1_edits_before/mri/wm.mgz:colormap=heat:opacity=0.4 \ -f wm1_edits_before/surf/lh.white:edgecolor=yellow \ wm1_edits_before/surf/lh.pial:edgecolor=red \ wm1_edits_before/surf/rh.white:edgecolor=yellow \ wm1_edits_before/surf/rh.pial:edgecolor=red \ wm1_edits_before/surf/rh.inflated:visible=0 \ wm1_edits_before/surf/lh.inflated:visible=0 echo "Freeview Command 6: view problem with white matter segmentation map" $FREEVIEW -v wm1_edits_after/mri/T1.mgz \ wm1_edits_after/mri/brainmask.mgz \ -f wm1_edits_after/surf/lh.white:edgecolor=yellow \ wm1_edits_after/surf/lh.pial:edgecolor=red \ wm1_edits_after/surf/rh.white:edgecolor=yellow \ wm1_edits_after/surf/rh.pial:edgecolor=red : echo "Freeview Command 7: view topo_defect_before" $FREEVIEW -v topo_defect_before/mri/brainmask.mgz \ topo_defect_before/mri/wm.mgz:colormap=heat:opacity=0.4 \ -f topo_defect_before/surf/lh.white:edgecolor=yellow \ topo_defect_before/surf/lh.pial:edgecolor=red \ topo_defect_before/surf/rh.white:edgecolor=yellow \ topo_defect_before/surf/rh.pial:edgecolor=red echo "Freeview Command 8: view topo_defect_after" $FREEVIEW -v topo_defect_after/mri/brainmask.mgz \ topo_defect_after/mri/wm.mgz:colormap=heat:opacity=0.4 \ -f topo_defect_after/surf/lh.white:edgecolor=yellow \ topo_defect_after/surf/lh.pial:edgecolor=red \ topo_defect_after/surf/rh.white:edgecolor=yellow \ topo_defect_after/surf/rh.pial:edgecolor=red echo "Freeview Command 9: view skullstrip_before" $FREEVIEW -v skullstrip_before/mri/T1.mgz \ skullstrip_before/mri/brainmask.mgz:visible=false \ -f skullstrip_before/surf/lh.white:edgecolor=yellow \ skullstrip_before/surf/lh.pial:edgecolor=red \ skullstrip_before/surf/rh.white:edgecolor=yellow \ skullstrip_before/surf/rh.pial:edgecolor=red echo "Freeview Command 10: view skullstrip_after" $FREEVIEW -v skullstrip_after/mri/T1.mgz \ skullstrip_after/mri/brainmask.mgz \ -f skullstrip_after/surf/lh.white:edgecolor=yellow \ skullstrip_after/surf/lh.pial:edgecolor=red \ skullstrip_after/surf/rh.white:edgecolor=yellow \ skullstrip_after/surf/rh.pial:edgecolor=red # Adding control points (intensity normalization) echo "Freeview Command 11: view cp_before" $FREEVIEW -v cp_before/mri/brainmask.mgz \ cp_before/mri/T1.mgz \ -f cp_before/surf/lh.white:edgecolor=blue \ cp_before/surf/lh.pial:edgecolor=red \ cp_before/surf/rh.white:edgecolor=blue \ cp_before/surf/rh.pial:edgecolor=red echo "Freeview Command 12: view cp_after" $FREEVIEW -v cp_after/mri/brainmask.mgz \ cp_after/mri/T1.mgz \ -f cp_after/surf/lh.white:edgecolor=blue \ cp_after/surf/lh.pial:edgecolor=red \ cp_after/surf/rh.white:edgecolor=blue \ cp_after/surf/rh.pial:edgecolor=red echo "Freeview Command 13" #SUB PAGES OF THIS TUTORIAL: $FREEVIEW -v pial_edits_before/mri/T1.mgz \ pial_edits_before/mri/brainmask.mgz \ -f pial_edits_before/surf/lh.white:edgecolor=yellow \ pial_edits_before/surf/lh.pial:edgecolor=red \ pial_edits_before/surf/rh.white:edgecolor=yellow \ pial_edits_before/surf/rh.pial:edgecolor=red #recon-all -autorecon-pial -subjid pial_edits_before #cd /mri #cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz #recon-all -autorecon-pial -subjid pial_edits_before echo "Freeview Command 14" $FREEVIEW -v wm1_edits_before/mri/brainmask.mgz \ wm1_edits_before/mri/wm.mgz:colormap=heat:opacity=0.4 \ -f wm1_edits_before/surf/lh.white:edgecolor=yellow \ wm1_edits_before/surf/lh.pial:edgecolor=red \ wm1_edits_before/surf/rh.white:edgecolor=yellow \ wm1_edits_before/surf/rh.pial:edgecolor=red \ wm1_edits_before/surf/rh.inflated:visible=0 \ wm1_edits_before/surf/lh.inflated:visible=0 echo "Freeview Command 15" $FREEVIEW -v wm1_edits_after/mri/brainmask.mgz \ wm1_edits_after/mri/wm.mgz:colormap=heat:opacity=0.4 \ -f wm1_edits_after/surf/lh.white:edgecolor=yellow \ wm1_edits_after/surf/lh.pial:edgecolor=red \ wm1_edits_after/surf/rh.white:edgecolor=yellow \ wm1_edits_after/surf/rh.pial:edgecolor=red \ wm1_edits_after/surf/rh.inflated:visible=0 \ wm1_edits_after/surf/lh.inflated:visible=0 #recon-all -autorecon2-wm -autorecon3 -subjid wm1_edits_before echo "Freeview Command 16" $FREEVIEW -v topo_defect_before/mri/brainmask.mgz \ topo_defect_before/mri/wm.mgz:colormap=heat:opacity=0.4:visible=0 \ -f topo_defect_before/surf/lh.white:edgecolor=yellow \ topo_defect_before/surf/lh.pial:edgecolor=red \ topo_defect_before/surf/rh.white:edgecolor=yellow \ topo_defect_before/surf/rh.pial:edgecolor=red \ topo_defect_before/surf/lh.smoothwm.nofix:visible=0 echo "Freeview Command 17" $FREEVIEW -v topo_defect_after/mri/brainmask.mgz \ topo_defect_after/mri/wm.mgz:colormap=heat:opacity=0.4:visible=0 \ -f topo_defect_after/surf/lh.white:edgecolor=yellow \ topo_defect_after/surf/lh.pial:edgecolor=red \ topo_defect_after/surf/rh.white:edgecolor=yellow \ topo_defect_after/surf/rh.pial:edgecolor=red \ topo_defect_after/surf/lh.smoothwm.nofix:visible=0 #recon-all -autorecon2-wm -autorecon3 -subjid topo_defect_before echo "Freeview Command 18" $FREEVIEW -v skullstrip_before/mri/T1.mgz \ skullstrip_before/mri/brainmask.mgz:colormap=heat:visible=false \ skullstrip_before/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2 \ -f skullstrip_before/surf/lh.white:edgecolor=yellow \ skullstrip_before/surf/lh.pial:edgecolor=red \ skullstrip_before/surf/rh.white:edgecolor=yellow \ skullstrip_before/surf/rh.pial:edgecolor=red #recon-all -skullstrip -wsthresh -clean-bm -subjid #recon-all -skullstrip -wsthresh -clean-bm -no-wsgcaatlas -subjid skullstrip_before echo "Freeview Command 19" $FREEVIEW -v skullstrip_after/mri/T1.mgz \ skullstrip_after/mri/brainmask.mgz:colormap=heat #recon-all -skullstrip -clean-bm -gcut -subjid #recon-all -autorecon-pial -subjid #recon-all -all -subjid echo "Freeview Command 20" $FREEVIEW -v cp_before/mri/brainmask.mgz \ -f cp_before/surf/lh.white:edgecolor=yellow \ cp_before/surf/lh.pial:edgecolor=red \ cp_before/surf/rh.white:edgecolor=yellow \ cp_before/surf/rh.pial:edgecolor=red #recon-all -autorecon2-cp -autorecon3 -subjid cp_before # Assembling data, mris_preproc export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial cd $SUBJECTS_DIR/glm # takes a while # mris_preproc --fsgd gender_age.fsgd \ # --target fsaverage \ # --hemi lh \ # --meas thickness \ # --out lh.gender_age.thickness.00.mgh # resample the subject left hemisphere data to fsaverage # mri_surf2surf --hemi lh \ # --s fsaverage \ # --sval lh.gender_age.thickness.00.mgh \ # --fwhm 10 \ # --cortex \ # --tval lh.gender_age.thickness.10.mgh # GLM Analysis mri_glmfit \ --y lh.gender_age.thickness.10.mgh \ --fsgd gender_age.fsgd dods \ --C lh-Avg-thickness-age-Cor.mtx \ --surf fsaverage lh \ --cortex \ --glmdir lh.gender_age.glmdir ls lh.gender_age.glmdir ls lh.gender_age.glmdir/lh-Avg-thickness-age-Cor cd $SUBJECTS_DIR/glm echo "Freeview Command 21: view GLM analysis data" $FREEVIEW -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d -layout 1 echo "Freeview Command 22: display F ratio" $FREEVIEW -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/F.mgh:overlay_threshold=20,50 -viewport 3d -layout 1 export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial_perm cd $SUBJECTS_DIR/glm # Same command as before to get initial anaylsis which produces uncorrected results mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods \ --C lh-Avg-thickness-age-Cor.mtx --surf fsaverage lh --cortex --glmdir lh.gender_age.glmdir \ --eres-save # takes a while #mri_glmfit-sim \ # --glmdir lh.gender_age.glmdir \ # --perm 1000 4.0 abs \ # --cwp 0.05\ # --2spaces \ # --bg 1 # ADDED FOR MATT 9/2019 # output file produced that will prevent a 2bd run if it exists # rm -f $TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial_perm/glm/glm_challenge/csd/perm.th40.abs.j001-challenge-Cor.csd rm -f challenge-Cor.mtx touch challenge-Cor.mtx # gedit challenge-Cor.mtx echo '1 -1 0 0' >> challenge-Cor.mtx cat challenge-Cor.mtx mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C challenge-Cor.mtx --surf fsaverage lh --cortex --glmdir glm_challenge echo "Freeview Command 21.1" $FREEVIEW -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=glm_challenge/challenge-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d -layout 1 # ADDED FOR MATT 9/2019 mri_glmfit --y lh.gender_age.thickness.10.mgh --fsgd gender_age.fsgd dods --C challenge-Cor.mtx --surf fsaverage lh --cortex --glmdir glm_challenge --eres-save # old laptops may be too slow to run and even 1 job will exit uncelanly # mri_glmfit-sim --glmdir glm_challenge --perm 10 4.0 abs --cwp 0.05 --2spaces --bg 1 echo "Freeview Command 21.2" $FREEVIEW -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=glm_challenge/challenge-Cor/perm.th40.abs.sig.cluster.mgh:overlay_threshold=2,5:annot=glm_challenge/challenge-Cor/perm.th40.abs.sig.ocn.annot -viewport 3d -layout 1 # look at corrected results ls lh.gender_age.glmdir/lh-Avg-thickness-age-Cor # less lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.cluster.summary cat lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.cluster.summary echo "Freeview Command 23: load the cluster annotation" $FREEVIEW -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.cluster.mgh:overlay_threshold=2,5:annot=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.ocn.annot -viewport 3d -layout 1 export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial cd $SUBJECTS_DIR # recon-all -s -qcache # No more links outside of ./tutorial_data # ln -sf $FREESURFER_HOME/subjects/fsaverage export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial cd $SUBJECTS_DIR # qdec & mri_label2label --srclabel lh.supramarg --srcsubject fsaverage --trgsubject 004 --trglabel lh.supramarg --regmethod surface --hemi lh cd $SUBJECTS_DIR mris_anatomical_stats -l lh.supramarg.label \ -t lh.thickness -b -f 004/stats/lh.supramarg.stats 004 lh export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial cd $SUBJECTS_DIR # relationship between segmentation, parcellation and LookUp Table (LUT) echo "Freeview Command 24: open orig and aprc+aseg segmentation volumes" $FREEVIEW -v 004/mri/orig.mgz \ 004/mri/aparc+aseg.mgz:colormap=lut:opacity=0.4 \ -f 004/surf/lh.white:annot=aparc.annot # less $FREESURFER_HOME/FreeSurferColorLUT.txt cat $FREESURFER_HOME/FreeSurferColorLUT.txt # map a label to indicidal subjects cd $SUBJECTS_DIR mri_label2label \ --srcsubject fsaverage \ --srclabel $FREESURFER_HOME/subjects/fsaverage/label/lh.BA45_exvivo.label \ --trgsubject 004 \ --trglabel 004/label/lh.BA45_exvivo.label \ --hemi lh \ --regmethod surface echo "Freeview Command 25: view the label for the subject" $FREEVIEW -v 004/mri/orig.mgz echo "Freeview Command 26: load subjects inflated surface" $FREEVIEW -f 004/surf/lh.inflated # look at aseg stats cd $SUBJECTS_DIR/004/stats # less aseg.stats cat aseg.stats # look at aparc stats cd $SUBJECTS_DIR/004/stats # less lh.aparc.stats cat lh.aparc.stats # create a stats file for BA45_exvivo.label cd $SUBJECTS_DIR/004 mris_anatomical_stats \ -l label/lh.BA45_exvivo.label \ -f stats/lh.BA45_exvivo.stats \ 004 \ lh # GROUP STATS FILES export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial cd $SUBJECTS_DIR # Table of segmentation volumes # create a segmentation table for 6 subjects asegstats2table --subjects 004 021 040 067 080 092 \ --segno 11 17 18 \ --tablefile aseg.vol.table # less aseg.vol.table cat aseg.vol.table # ADDED for Matt 9/2018 asegstats2table --subjects 004 021 092 --meas mean --tablefile mean.practice.table less mean.practice.table # gedit aseg.vol.table # open -e aseg.vol.table # Table of white matter parcelation volumes # change the segmentation atlas for stats # asegstats2table \ # --subjects 004 021 040 067 080 092 \ # --segno 11 17 18 \ # --meas mean \ # --tablefile aseg.mean-intensity.table # change the segmentation atlas for stats asegstats2table \ --subjects 004 021 040 067 080 092 \ --segno 3007 3021 3022 4022\ --stats wmparc.stats \ --tablefile wmparc.vol.table # create a table of the surface area of each cortical parcellation in the Desikan/Killiany atlas aparcstats2table --hemi lh \ --subjects 004 021 040 067 080 092 \ --tablefile lh.aparc.area.table aparcstats2table --hemi lh \ --subjects 004 021 040 067 080 092 \ --meas thickness \ --parc aparc.a2009s \ --tablefile lh.aparc.a2009.thickness.table #aparcstats2table --help #asegstats2table --help # ADDED aparcstats2table --subjects 004 021 040 --hemi lh --meas thickness --parc aparc.a2009s --tablefile lh.aparc.a2009s.thickness.table less mean.practice.table # soffice --calc lh.aparc.a2009s.thickness.table export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs cd $SUBJECTS_DIR/multimodal/fmri/fbirn-101 echo "Freeview Command 27" $FREEVIEW -v template.nii \ $SUBJECTS_DIR/fbirn-anat-101.v6/mri/orig.mgz:visible=0 -f \ $SUBJECTS_DIR/fbirn-anat-101.v6/surf/lh.white \ $SUBJECTS_DIR/fbirn-anat-101.v6/surf/rh.white \ -viewport cor -transform-volume bbregister --mov template.nii --bold --s fbirn-anat-101.v6 --lta register.lta cat register.lta cat register.dat.mincost echo "Freeview Command 28" $FREEVIEW -v $SUBJECTS_DIR/fbirn-anat-101.v6/mri/orig.mgz:visible=0 \ template.nii:reg=register.lta -f \ $SUBJECTS_DIR/fbirn-anat-101.v6/surf/lh.white \ $SUBJECTS_DIR/fbirn-anat-101.v6/surf/rh.white \ -viewport cor -transform-volume export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs cd $SUBJECTS_DIR/multimodal/fmri/fbirn-101 echo "Freeview Command 29" $FREEVIEW -v $SUBJECTS_DIR/fbirn-anat-101.v6/mri/orig.mgz:visible=0 \ template.nii:reg=register.lta -f \ $SUBJECTS_DIR/fbirn-anat-101.v6/surf/lh.white \ $SUBJECTS_DIR/fbirn-anat-101.v6/surf/rh.white \ -viewport cor -transform-volume echo "Freeview Command 30" $FREEVIEW -v $SUBJECTS_DIR/fbirn-anat-101.v6/mri/orig.mgz \ $SUBJECTS_DIR/fbirn-anat-101.v6/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2 \ sig.nii:reg=register.lta:colormap=heat:heatscale=2,2,4 -colorscale \ -viewport coronal mri_vol2surf --mov sig.nii \ --reg register.lta \ --projfrac 0.5 --interp nearest \ --hemi lh --o lh.sig.mgh mri_info lh.sig.mgh echo "Freeview Command 31" $FREEVIEW -f $SUBJECTS_DIR/fbirn-anat-101.v6/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.sig.mgh:overlay_threshold=2,5 \ -viewport 3d mri_vol2vol --mov ces.nii \ --reg register.lta \ --fstarg --interp nearest \ --o ces.anat.bb.mgh mri_info ces.anat.bb.mgh mri_segstats \ --seg $SUBJECTS_DIR/fbirn-anat-101.v6/mri/aparc+aseg.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --id 1021 --id 1022 --id 1030 --id 17 \ --i ces.anat.bb.mgh --sum ces.bb.stats mri_vol2vol --mov sig.nii \ --reg register.lta \ --fstarg --interp nearest \ --o sig.anat.bb.mgh mri_segstats \ --seg $SUBJECTS_DIR/fbirn-anat-101.v6/mri/aparc+aseg.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --id 1021 --id 1022 --id 1030 --id 17 \ --i ces.anat.bb.mgh --sum ces.abs-masked.bb.stats \ --mask sig.anat.bb.mgh --maskthresh 2 --masksign abs mri_vol2vol --mov sig.nii \ --reg register.lta \ --fstarg --interp nearest \ --o sig.anat.bb.mgh mri_segstats \ --seg $SUBJECTS_DIR/fbirn-anat-101.v6/mri/aparc+aseg.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --id 1021 --id 1022 --id 1030 --id 17 \ --i ces.anat.bb.mgh --sum ces.pos-masked.bb.stats \ --mask sig.anat.bb.mgh --maskthresh 2 --masksign pos export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs cd $SUBJECTS_DIR/multimodal/fmri echo "Freeview Command 32" $FREEVIEW -v $SUBJECTS_DIR/fbirn-anat-101.v6/mri/orig.mgz:visible=0 \ fbirn-101/template.nii:reg=fbirn-101/register.lta -f \ $SUBJECTS_DIR/fbirn-anat-101.v6/surf/lh.white \ $SUBJECTS_DIR/fbirn-anat-101.v6/surf/rh.white \ -viewport cor mris_preproc --target fsaverage --hemi lh \ --iv fbirn-101/ces.nii fbirn-101/register.lta \ --iv fbirn-103/ces.nii fbirn-103/register.lta \ --iv fbirn-104/ces.nii fbirn-104/register.lta \ --iv fbirn-105/ces.nii fbirn-105/register.lta \ --iv fbirn-106/ces.nii fbirn-106/register.lta \ --projfrac 0.5 \ --out lh.ces.mgh mri_info lh.ces.mgh mri_surf2surf --hemi lh --s fsaverage --fwhm 5 --cortex \ --sval lh.ces.mgh --tval lh.ces.sm05.mgh mri_glmfit --y lh.ces.sm05.mgh --surf fsaverage lh \ --osgm --glmdir lh.ces.sm05.osgm --cortex echo "Freeview Command 33" $FREEVIEW -f \ $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.ces.sm05.osgm/osgm/sig.mgh:overlay_threshold=2,5 \ -viewport 3d asegstats2table \ --meas volume \ --tablefile ces.pos-masked.vol.stats \ --i fbirn-101/ces.pos-masked.bb.stats \ fbirn-103/ces.pos-masked.bb.stats \ fbirn-104/ces.pos-masked.bb.stats \ fbirn-105/ces.pos-masked.bb.stats \ fbirn-106/ces.pos-masked.bb.stats cat ces.pos-masked.vol.stats asegstats2table \ --meas mean \ --tablefile ces.abs-masked.mean.stats \ --i fbirn-101/ces.abs-masked.bb.stats \ fbirn-103/ces.abs-masked.bb.stats \ fbirn-104/ces.abs-masked.bb.stats \ fbirn-105/ces.abs-masked.bb.stats \ fbirn-106/ces.abs-masked.bb.stats cat ces.abs-masked.mean.stats asegstats2table \ --meas mean \ --tablefile ces.pos-masked.mean.stats \ --i fbirn-101/ces.pos-masked.bb.stats \ fbirn-103/ces.pos-masked.bb.stats \ fbirn-104/ces.pos-masked.bb.stats \ fbirn-105/ces.pos-masked.bb.stats \ fbirn-106/ces.pos-masked.bb.stats cat ces.pos-masked.mean.stats export SUBJECTS_DIR=$TUTORIAL_DATA/long-tutorial cd $SUBJECTS_DIR # recon-all -subjid OAS2_0001_MR1 -all # recon-all -subjid OAS2_0001_MR2 -all # recon-all -base OAS2_0001 -tp OAS2_0001_MR1 -tp OAS2_0001_MR2 -all # recon-all -long OAS2_0001_MR1 OAS2_0001 -all # recon-all -long OAS2_0001_MR2 OAS2_0001 -all echo "Freeview Command 34" $FREEVIEW -v OAS2_0001/mri/norm.mgz \ -f OAS2_0001/surf/lh.pial:edgecolor=red \ OAS2_0001/surf/rh.pial:edgecolor=red \ OAS2_0001/surf/lh.white:edgecolor=blue \ OAS2_0001/surf/rh.white:edgecolor=blue echo "Freeview Command 35" $FREEVIEW -v OAS2_0001_MR1.long.OAS2_0001/mri/norm.mgz \ OAS2_0001_MR2.long.OAS2_0001/mri/norm.mgz \ -f OAS2_0001_MR1.long.OAS2_0001/surf/lh.pial:edgecolor=red \ OAS2_0001_MR1.long.OAS2_0001/surf/lh.white:edgecolor=blue \ OAS2_0001_MR2.long.OAS2_0001/surf/lh.pial:edgecolor=255,128,128 \ OAS2_0001_MR2.long.OAS2_0001/surf/lh.white:edgecolor=lightblue # libreoffice -calc qdec/long.qdec.table.dat # $LIBREOFFICE -calc qdec/long.qdec.table.dat # coment out unless can automatically close # gedit qdec/long.qdec.table.dat # long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR cd qdec long_qdec_table --qdec ./long.qdec.table.dat --split fsid-base cd .. echo "Freeview Command 36" $FREEVIEW -f OAS2_0001/surf/lh.pial:overlay=OAS2_0001/surf/lh.long.thickness-avg.fwhm15.mgh:overlay_threshold=0,3.5:overlay=OAS2_0001/surf/lh.long.thickness-stack.mgh:annot=OAS2_0001/label/lh.aparc.annot:annot_outline=1 --timecourse --colorscale --viewport 3d # Cannot pass quit option # tksurfer OAS2_0001 lh pial -overlay $SUBJECTS_DIR/OAS2_0001/surf/lh.long.thickness-avg.fwhm15.mgh -timecourse $SUBJECTS_DIR/OAS2_0001/surf/lh.long.thickness-stack.mgh -aparc echo "Freeview Command 37" $FREEVIEW -f $FREESURFER_HOME/subjects/fsaverage/surf/lh.pial:overlay=$SUBJECTS_DIR/OAS2_0001/surf/lh.long.thickness-spc.fwhm15.fsaverage.mgh:overlay_threshold=2,5 long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat # time ? # qdec --table ./qdec/cross.qdec.table.dat export SUBJECTS_DIR=$TUTORIAL_DATA/long-tutorial/skullstrip cd $SUBJECTS_DIR # set +e $FREEVIEW -v OAS2_0004/mri/T1.mgz \ OAS2_0004/mri/brainmask.mgz \ -f OAS2_0004/surf/lh.pial:edgecolor=red \ OAS2_0004/surf/rh.pial:edgecolor=red \ OAS2_0004/surf/lh.white:edgecolor=blue \ OAS2_0004/surf/rh.white:edgecolor=blue $FREEVIEW -v OAS2_0004_MR1/mri/T1.mgz \ OAS2_0004_MR1/mri/brainmask.mgz \ -f OAS2_0004_MR1/surf/lh.pial:edgecolor=red \ OAS2_0004_MR1/surf/rh.pial:edgecolor=red \ OAS2_0004_MR1/surf/lh.white:edgecolor=blue \ OAS2_0004_MR1/surf/rh.white:edgecolor=blue $FREEVIEW -v OAS2_0004_MR2/mri/T1.mgz \ OAS2_0004_MR2/mri/brainmask.mgz \ -f OAS2_0004_MR2/surf/lh.pial:edgecolor=red \ OAS2_0004_MR2/surf/rh.pial:edgecolor=red \ OAS2_0004_MR2/surf/lh.white:edgecolor=blue \ OAS2_0004_MR2/surf/rh.white:edgecolor=blue # set -e # recon-all -subjid OAS2_0004_MR1 -skullstrip -wsthresh 20 -clean-bm -no-wsgcaatlas # recon-all -subjid OAS2_0004_MR2 -skullstrip -wsthresh 55 -clean-bm -no-wsgcaatlas # recon-all -subjid OAS2_0004_MR1 -autorecon2 -autorecon3 # recon-all -subjid OAS2_0004_MR2 -autorecon2 -autorecon3 echo "Freeview Command 41" $FREEVIEW -v OAS2_0004_MR1_fixed/mri/T1.mgz OAS2_0004_MR1_fixed/mri/brainmask.mgz echo "Freeview Command 42" $FREEVIEW -v OAS2_0004_MR2_fixed/mri/T1.mgz OAS2_0004_MR2_fixed/mri/brainmask.mgz # recon-all -skullstrip -subjid OAS2_0004_MR2 # recon-all -autorecon2 -autorecon3 -subjid OAS2_0004_MR2 # recon-all -base OAS2_0004 -tp OAS2_0004_MR1 -tp OAS2_0004_MR2 -all # recon-all -long OAS2_0004_MR1 OAS2_0004 -all # recon-all -long OAS2_0004_MR2 OAS2_0004 -all echo "Freeview Command 43" $FREEVIEW -v OAS2_0004_fixed/mri/T1.mgz \ OAS2_0004_fixed/mri/brainmask.mgz \ -f OAS2_0004_fixed/surf/lh.pial:edgecolor=red \ OAS2_0004_fixed/surf/rh.pial:edgecolor=red \ OAS2_0004_fixed/surf/lh.white:edgecolor=blue \ OAS2_0004_fixed/surf/rh.white:edgecolor=blue echo "Freeview Command 44" $FREEVIEW -v OAS2_0004_MR1.long.OAS2_0004_fixed/mri/T1.mgz \ OAS2_0004_MR1.long.OAS2_0004_fixed/mri/brainmask.mgz \ -f OAS2_0004_MR1.long.OAS2_0004_fixed/surf/lh.pial:edgecolor=red \ OAS2_0004_MR1.long.OAS2_0004_fixed/surf/rh.pial:edgecolor=red \ OAS2_0004_MR1.long.OAS2_0004_fixed/surf/lh.white:edgecolor=blue \ OAS2_0004_MR1.long.OAS2_0004_fixed/surf/rh.white:edgecolor=blue echo "Freeview Command 45" $FREEVIEW -v OAS2_0004_MR2.long.OAS2_0004_fixed/mri/T1.mgz \ OAS2_0004_MR2.long.OAS2_0004_fixed/mri/brainmask.mgz \ -f OAS2_0004_MR2.long.OAS2_0004_fixed/surf/lh.pial:edgecolor=red \ OAS2_0004_MR2.long.OAS2_0004_fixed/surf/rh.pial:edgecolor=red \ OAS2_0004_MR2.long.OAS2_0004_fixed/surf/lh.white:edgecolor=blue \ OAS2_0004_MR2.long.OAS2_0004_fixed/surf/rh.white:edgecolor=blue export SUBJECTS_DIR=$TUTORIAL_DATA/long-tutorial/ cd $SUBJECTS_DIR echo "Freeview Command 46" $FREEVIEW -v OAS2_0057/mri/T1.mgz \ OAS2_0057/mri/brainmask.mgz \ -f OAS2_0057/surf/lh.pial:edgecolor=red \ OAS2_0057/surf/rh.pial:edgecolor=red \ OAS2_0057/surf/lh.white:edgecolor=blue \ OAS2_0057/surf/rh.white:edgecolor=blue echo "Freeview Command 47" $FREEVIEW -v OAS2_0057_MR1/mri/T1.mgz \ OAS2_0057_MR1/mri/brainmask.mgz \ -f OAS2_0057_MR1/surf/lh.pial:edgecolor=red \ OAS2_0057_MR1/surf/rh.pial:edgecolor=red \ OAS2_0057_MR1/surf/lh.white:edgecolor=blue \ OAS2_0057_MR1/surf/rh.white:edgecolor=blue echo "Freeview Command 48" $FREEVIEW -v OAS2_0057_MR2/mri/T1.mgz \ OAS2_0057_MR2/mri/brainmask.mgz \ -f OAS2_0057_MR2/surf/lh.pial:edgecolor=red \ OAS2_0057_MR2/surf/rh.pial:edgecolor=red \ OAS2_0057_MR2/surf/lh.white:edgecolor=blue \ OAS2_0057_MR2/surf/rh.white:edgecolor=blue echo "Freeview Command 49" $FREEVIEW -v OAS2_0057_MR1.long.OAS2_0057/mri/T1.mgz \ OAS2_0057_MR1.long.OAS2_0057/mri/brainmask.mgz \ -f OAS2_0057_MR1.long.OAS2_0057/surf/lh.pial:edgecolor=red \ OAS2_0057_MR1.long.OAS2_0057/surf/rh.pial:edgecolor=red \ OAS2_0057_MR1.long.OAS2_0057/surf/lh.white:edgecolor=blue \ OAS2_0057_MR1.long.OAS2_0057/surf/rh.white:edgecolor=blue echo "Freeview Command 50" $FREEVIEW -v OAS2_0057_MR2.long.OAS2_0057/mri/T1.mgz \ OAS2_0057_MR2.long.OAS2_0057/mri/brainmask.mgz \ -f OAS2_0057_MR2.long.OAS2_0057/surf/lh.pial:edgecolor=red \ OAS2_0057_MR2.long.OAS2_0057/surf/rh.pial:edgecolor=red \ OAS2_0057_MR2.long.OAS2_0057/surf/lh.white:edgecolor=blue \ OAS2_0057_MR2.long.OAS2_0057/surf/rh.white:edgecolor=blue # recon-all -base OAS2_0057 -autorecon-pial # recon-all -long OAS2_0057_MR1 OAS2_0057 -all # recon-all -long OAS2_0057_MR2 OAS2_0057 -all echo "Freeview Command 51" $FREEVIEW -v OAS2_0057_MR1.long.OAS2_0057/mri/T1.mgz \ OAS2_0057_MR1.long.OAS2_0057/mri/brainmask.mgz \ -f OAS2_0057_MR1.long.OAS2_0057/surf/lh.pial:edgecolor=red \ OAS2_0057_MR1.long.OAS2_0057/surf/rh.pial:edgecolor=red \ OAS2_0057_MR1.long.OAS2_0057/surf/lh.white:edgecolor=blue \ OAS2_0057_MR1.long.OAS2_0057/surf/rh.white:edgecolor=blue echo "Freeview Command 52" $FREEVIEW -v OAS2_0057_MR1.long.OAS2_0057_fixed/mri/T1.mgz \ OAS2_0057_MR1.long.OAS2_0057_fixed/mri/brainmask.mgz \ -f OAS2_0057_MR1.long.OAS2_0057_fixed/surf/lh.pial:edgecolor=red \ OAS2_0057_MR1.long.OAS2_0057_fixed/surf/rh.pial:edgecolor=red \ OAS2_0057_MR1.long.OAS2_0057_fixed/surf/lh.white:edgecolor=blue \ OAS2_0057_MR1.long.OAS2_0057_fixed/surf/rh.white:edgecolor=blue echo "Freeview Command 53" $FREEVIEW -v OAS2_0121_MR1/mri/T1.mgz \ OAS2_0121_MR1/mri/brainmask.mgz \ -f OAS2_0121_MR1/surf/lh.pial:edgecolor=red \ OAS2_0121_MR1/surf/rh.pial:edgecolor=red \ OAS2_0121_MR1/surf/lh.white:edgecolor=blue \ OAS2_0121_MR1/surf/rh.white:edgecolor=blue echo "Freeview Command 54" $FREEVIEW -v OAS2_0121_MR2/mri/T1.mgz \ OAS2_0121_MR2/mri/brainmask.mgz \ -f OAS2_0121_MR2/surf/lh.pial:edgecolor=red \ OAS2_0121_MR2/surf/rh.pial:edgecolor=red \ OAS2_0121_MR2/surf/lh.white:edgecolor=blue \ OAS2_0121_MR2/surf/rh.white:edgecolor=blue echo "Freeview Command 55" $FREEVIEW -v OAS2_0121/mri/T1.mgz \ OAS2_0121/mri/brainmask.mgz \ -f OAS2_0121/surf/lh.pial:edgecolor=red \ OAS2_0121/surf/rh.pial:edgecolor=red \ OAS2_0121/surf/lh.white:edgecolor=blue \ OAS2_0121/surf/rh.white:edgecolor=blue echo "Freeview Command 56" $FREEVIEW -v OAS2_0121_MR1.long.OAS2_0121/mri/T1.mgz \ OAS2_0121_MR1.long.OAS2_0121/mri/brainmask.mgz \ -f OAS2_0121_MR1.long.OAS2_0121/surf/lh.pial:edgecolor=red \ OAS2_0121_MR1.long.OAS2_0121/surf/rh.pial:edgecolor=red \ OAS2_0121_MR1.long.OAS2_0121/surf/lh.white:edgecolor=blue \ OAS2_0121_MR1.long.OAS2_0121/surf/rh.white:edgecolor=blue echo "Freeview Command 57" $FREEVIEW -v OAS2_0121_MR2.long.OAS2_0121/mri/T1.mgz \ OAS2_0121_MR2.long.OAS2_0121/mri/brainmask.mgz \ -f OAS2_0121_MR2.long.OAS2_0121/surf/lh.pial:edgecolor=red \ OAS2_0121_MR2.long.OAS2_0121/surf/rh.pial:edgecolor=red \ OAS2_0121_MR2.long.OAS2_0121/surf/lh.white:edgecolor=blue \ OAS2_0121_MR2.long.OAS2_0121/surf/rh.white:edgecolor=blue # recon-all -subjid OAS2_0121_MR1 -autorecon2 -autorecon3 # recon-all -subjid OAS2_0121_MR2 -autorecon2 -autorecon3 echo "Freeview Command 58" $FREEVIEW -v OAS2_0121_MR1_fixed/mri/T1.mgz \ OAS2_0121_MR1_fixed/mri/brainmask.mgz \ -f OAS2_0121_MR1_fixed/surf/lh.pial:edgecolor=red \ OAS2_0121_MR1_fixed/surf/rh.pial:edgecolor=red \ OAS2_0121_MR1_fixed/surf/lh.white:edgecolor=blue \ OAS2_0121_MR1_fixed/surf/rh.white:edgecolor=blue echo "Freeview Command 59" $FREEVIEW -v OAS2_0121_MR2_fixed/mri/T1.mgz \ OAS2_0121_MR2_fixed/mri/brainmask.mgz \ -f OAS2_0121_MR2_fixed/surf/lh.pial:edgecolor=red \ OAS2_0121_MR2_fixed/surf/rh.pial:edgecolor=red \ OAS2_0121_MR2_fixed/surf/lh.white:edgecolor=blue \ OAS2_0121_MR2_fixed/surf/rh.white:edgecolor=blue # recon-all -base OAS2_0121 -tp OAS2_0121_MR1 -tp OAS2_0121_MR2 -all echo "Freeview Command 60" $FREEVIEW -v OAS2_0121_intermediate/mri/T1.mgz \ OAS2_0121_intermediate/mri/brainmask.mgz \ -f OAS2_0121_intermediate/surf/lh.pial:edgecolor=red \ OAS2_0121_intermediate/surf/rh.pial:edgecolor=red \ OAS2_0121_intermediate/surf/lh.white:edgecolor=blue \ OAS2_0121_intermediate/surf/rh.white:edgecolor=blue # recon-all -base OAS2_0121 -autorecon2 -autorecon3 # recon-all -long OAS2_0121_MR1 OAS2_0121 -all # recon-all -long OAS2_0121_MR2 OAS2_0121 -all echo "Freeview Command 61" $FREEVIEW -v OAS2_0121_MR1.long.OAS2_0121/mri/T1.mgz \ OAS2_0121_MR1.long.OAS2_0121/mri/brainmask.mgz \ -f OAS2_0121_MR1.long.OAS2_0121/surf/lh.pial:edgecolor=red \ OAS2_0121_MR1.long.OAS2_0121/surf/rh.pial:edgecolor=red \ OAS2_0121_MR1.long.OAS2_0121/surf/lh.white:edgecolor=blue \ OAS2_0121_MR1.long.OAS2_0121/surf/rh.white:edgecolor=blue echo "Freeview Command 62" $FREEVIEW -v OAS2_0121_MR1.long.OAS2_0121_fixed/mri/T1.mgz \ OAS2_0121_MR1.long.OAS2_0121_fixed/mri/brainmask.mgz \ -f OAS2_0121_MR1.long.OAS2_0121_fixed/surf/lh.pial:edgecolor=red \ OAS2_0121_MR1.long.OAS2_0121_fixed/surf/rh.pial:edgecolor=red \ OAS2_0121_MR1.long.OAS2_0121_fixed/surf/lh.white:edgecolor=blue \ OAS2_0121_MR1.long.OAS2_0121_fixed/surf/rh.white:edgecolor=blue echo "Freeview Command 63" $FREEVIEW -v OAS2_0185/mri/wm.mgz \ OAS2_0185/mri/brainmask.mgz \ -f OAS2_0185/surf/lh.pial:edgecolor=red \ OAS2_0185/surf/rh.pial:edgecolor=red \ OAS2_0185/surf/lh.white:edgecolor=blue \ OAS2_0185/surf/rh.white:edgecolor=blue echo "Freeview Command 64" $FREEVIEW -v OAS2_0185_MR1/mri/wm.mgz \ OAS2_0185_MR1/mri/brainmask.mgz \ -f OAS2_0185_MR1/surf/lh.pial:edgecolor=red \ OAS2_0185_MR1/surf/rh.pial:edgecolor=red \ OAS2_0185_MR1/surf/lh.white:edgecolor=blue \ OAS2_0185_MR1/surf/rh.white:edgecolor=blue echo "Freeview Command 65" $FREEVIEW -v OAS2_0185_MR2/mri/wm.mgz \ OAS2_0185_MR2/mri/brainmask.mgz \ -f OAS2_0185_MR2/surf/lh.pial:edgecolor=red \ OAS2_0185_MR2/surf/rh.pial:edgecolor=red \ OAS2_0185_MR2/surf/lh.white:edgecolor=blue \ OAS2_0185_MR2/surf/rh.white:edgecolor=blue echo "Freeview Command 66" $FREEVIEW -v OAS2_0185_MR1.long.OAS2_0185/mri/wm.mgz \ OAS2_0185_MR1.long.OAS2_0185/mri/brainmask.mgz \ -f OAS2_0185_MR1.long.OAS2_0185/surf/lh.pial:edgecolor=red \ OAS2_0185_MR1.long.OAS2_0185/surf/rh.pial:edgecolor=red \ OAS2_0185_MR1.long.OAS2_0185/surf/lh.white:edgecolor=blue \ OAS2_0185_MR1.long.OAS2_0185/surf/rh.white:edgecolor=blue echo "Freeview Command 67" $FREEVIEW -v OAS2_0185_MR2.long.OAS2_0185/mri/wm.mgz \ OAS2_0185_MR2.long.OAS2_0185/mri/brainmask.mgz \ -f OAS2_0185_MR2.long.OAS2_0185/surf/lh.pial:edgecolor=red \ OAS2_0185_MR2.long.OAS2_0185/surf/rh.pial:edgecolor=red \ OAS2_0185_MR2.long.OAS2_0185/surf/lh.white:edgecolor=blue \ OAS2_0185_MR2.long.OAS2_0185/surf/rh.white:edgecolor=blue # recon-all -base OAS2_0185 -autorecon2-wm -autorecon3 echo "Freeview Command 68" $FREEVIEW -v OAS2_0185_fixed/mri/wm.mgz \ OAS2_0185_fixed/mri/brainmask.mgz \ -f OAS2_0185_fixed/surf/lh.pial:edgecolor=red \ OAS2_0185_fixed/surf/rh.pial:edgecolor=red \ OAS2_0185_fixed/surf/lh.white:edgecolor=blue \ OAS2_0185_fixed/surf/rh.white:edgecolor=blue # recon-all -long OAS2_0185_MR1 OAS2_0185 -all # recon-all -long OAS2_0185_MR2 OAS2_0185 -all echo "Freeview Command 69" $FREEVIEW -v OAS2_0185_MR1.long.OAS2_0185_fixed/mri/wm.mgz \ OAS2_0185_MR1.long.OAS2_0185_fixed/mri/brainmask.mgz \ -f OAS2_0185_MR1.long.OAS2_0185_fixed/surf/lh.pial:edgecolor=red \ OAS2_0185_MR1.long.OAS2_0185_fixed/surf/rh.pial:edgecolor=red \ OAS2_0185_MR1.long.OAS2_0185_fixed/surf/lh.white:edgecolor=blue \ OAS2_0185_MR1.long.OAS2_0185_fixed/surf/rh.white:edgecolor=blue echo "Freeview Command 70" $FREEVIEW -v OAS2_0185_MR2.long.OAS2_0185_fixed/mri/wm.mgz \ OAS2_0185_MR2.long.OAS2_0185_fixed/mri/brainmask.mgz \ -f OAS2_0185_MR2.long.OAS2_0185_fixed/surf/lh.pial:edgecolor=red \ OAS2_0185_MR2.long.OAS2_0185_fixed/surf/rh.pial:edgecolor=red \ OAS2_0185_MR2.long.OAS2_0185_fixed/surf/lh.white:edgecolor=blue \ OAS2_0185_MR2.long.OAS2_0185_fixed/surf/rh.white:edgecolor=blue export SUBJECTS_DIR=$TUTORIAL_DATA/diffusion_recons export TUTORIAL_DIR=$TUTORIAL_DATA/diffusion_tutorial subj=Diff001 cd $TUTORIAL_DIR/$subj/dtrecon # dt_recon --b bvals.dat bvecs.dat --i $TUTORIAL_DIR/$subj/orig/6-1.dcm --s $subj --o $TUTORIAL_DIR/$subj/dtrecon ls echo "Freeview Command 71" $FREEVIEW dwi.nii.gz echo "Freeview Command 72" $FREEVIEW -v $SUBJECTS_DIR/$subj/mri/orig.mgz \ lowb.nii:reg=register.dat \ -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green \ $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green \ -viewport coronal echo "Freeview Command 73" $FREEVIEW -v fa.nii adc.nii echo "Freeview Command 74" $FREEVIEW -v $SUBJECTS_DIR/$subj/mri/brain.mgz \ $SUBJECTS_DIR/$subj/mri/orig.mgz \ $SUBJECTS_DIR/$subj/mri/wmparc.mgz:colormap=lut:opacity=0.2 \ fa.nii:reg=register.dat:colormap=heat:heatscale=.2,.2,1 -colorscale -viewport coronal mri_vol2vol --mov lowb.nii \ --targ $SUBJECTS_DIR/$subj/mri/wmparc.mgz \ --inv --interp nearest --o $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ --reg register.dat --no-save-reg echo "Freeview Command 75" $FREEVIEW -v lowb.nii \ $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz:colormap=lut \ -f $SUBJECTS_DIR/$subj/surf/lh.white:edgecolor=green \ $SUBJECTS_DIR/$subj/surf/rh.white:edgecolor=green \ -viewport coronal echo "Freeview Command 76" $FREEVIEW -v fa.nii \ $SUBJECTS_DIR/$subj/mri/aparc+aseg2diff.mgz:colormap=lut mri_mask fa.nii \ $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ fa-masked.mgz echo "Freeview Command 77" $FREEVIEW -v fa.nii \ fa-masked.mgz mri_segstats \ --seg $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \ --id 251 --id 3021 --id 3024 --id 3030 --id 12 --id 4 \ --i fa.nii --sum fa.stats # mri_vol2vol --targ $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ # --m3z $SUBJECTS_DIR/$subj/cvs/combined_tocvs_avg35_elreg_afteraseg-norm.m3z \ # --noDefM3zPath \ # --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat \ # --mov fa-masked.mgz \ # --o fa-masked.ANAT+CVS-to-avg35.mgz \ # --interp trilin --no-save-reg echo "Freeview Command 78" $FREEVIEW -v $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \ fa-masked.ANAT+CVS-to-avg35.mgz export SUBJECTS_DIR=$TUTORIAL_DATA/diffusion_recons cd $TUTORIAL_DATA/diffusion_tutorial # gedit $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial & # trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial # trac-all -bedp -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial # trac-all -path -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial # cat $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/dwi_motion.txt cd $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri echo "Freeview Command 79" $FREEVIEW $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/dtifit_FA.nii.gz & cd $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/mni/ echo "Freeview Command 80" $FREEVIEW -v $FSL_DIR/data/standard/MNI152_T1_1mm_brain.nii.gz \ $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/mni/dtifit_FA.bbr.nii.gz & # set +e # echo "Freeview Command 81" # $FREEVIEW -v $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/dtifit_FA.nii.gz \ # $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/rh.ilf_AS_avg33_mni_bbr/path.pd.nii.gz:colormap=heat:isosurface=0,0:color='Red':name=rh.ilf \ # $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/path.pd.nii.gz:colormap=heat:isosurface=0,0:color='Red':name=lh.ilf # Remove :color sub-option (which fails in dev branch freeview) echo "Freeview Command 81" $FREEVIEW -v $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/dtifit_FA.nii.gz \ $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/rh.ilf_AS_avg33_mni_bbr/path.pd.nii.gz:colormap=heat:isosurface=0,0:name=rh.ilf \ $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/path.pd.nii.gz:colormap=heat:isosurface=0,0:name=lh.ilf # set -e echo "Freeview Command 82" $FREEVIEW -tv $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/merged_avg33_mni_bbr.mgz \ -v $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/dtifit_FA.nii.gz & # gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt & tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.overall.txt --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.elmo.2012.All.table # gedit $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.elmo.2012.All.table & # gedit $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.list & # NEED TO FIND lh.ilf.list before run these commands ## tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.list --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.All.table # gedit $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.All.table & ## tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.list --overall --only-measures FA_Avg --tablefile $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.FA_Avg.table # localc $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.All.table # gedit $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dpath/lh.ilf_AS_avg33_mni_bbr/pathstats.byvoxel.txt & trac-all -stat -c $TUTORIAL_DATA/diffusion_tutorial/dmrirc.tutorial # gedit $TUTORIAL_DATA/diffusion_tutorial/stats/lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt & # gedit $TUTORIAL_DATA/diffusion_tutorial/stats/lh.ilf_AS.avg33_mni_bbr.log & echo "Freeview Command 83" $FREEVIEW -v $FSL_DIR/data/standard/MNI152_T1_1mm_brain.nii.gz \ -w $TUTORIAL_DATA/diffusion_tutorial/stats/*.path.mean.txt cd $TUTORIAL_DATA/fsfast-functional ls cd $TUTORIAL_DATA/fsfast-functional/sess01.noproc ls export SUBJECTS_DIR=$TUTORIAL_DATA/fsfast-tutorial.subjects cat subjectname ls $SUBJECTS_DIR ls rest ls bold cd bold/001 ls mri_info --dim f.nii.gz mri_info --res f.nii.gz echo "Freeview Command 84" $FREEVIEW -v f.nii.gz -timecourse cat workmem.par cd $TUTORIAL_DATA/fsfast-functional cat sessidlist # preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run export SUBJECTS_DIR=$TUTORIAL_DATA/fsfast-tutorial.subjects cd $TUTORIAL_DATA/fsfast-functional ls $TUTORIAL_DATA/fsfast-functional/sess01/bold/001 tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum # time ? # tkregister-sess -s sess02 -fsd bold -per-run cd $TUTORIAL_DATA/fsfast-functional/sess01/bold/001 ls ls -ltr mri_info template.nii.gz mri_info f.nii.gz echo "Freeview Command 85" $FREEVIEW -v template.nii.gz masks/brain.nii.gz:colormap=heat:opacity=0.75 -viewport coronal echo "Freeview Command 86" $FREEVIEW -v template.nii.gz masks/brain.e3.nii.gz:colormap=heat:opacity=0.75 -viewport coronal mri_info --dim fmcpr.up.sm5.mni305.2mm.nii.gz mri_info --res fmcpr.up.sm5.mni305.2mm.nii.gz mri_info --dim fmcpr.up.sm5.fsaverage.lh.nii.gz mri_info --res fmcpr.up.sm5.fsaverage.lh.nii.gz export SUBJECTS_DIR=$TUTORIAL_DATA/fsfast-tutorial.subjects cd $TUTORIAL_DATA/fsfast-functional mkanalysis-sess \ -fsd bold -stc up -surface fsaverage lh -fwhm 5 \ -event-related -paradigm workmem.par -nconditions 5 \ -spmhrf 0 -TR 2 -refeventdur 16 -nskip 4 -polyfit 2 \ -analysis my-workmem.sm05.lh -per-run -force ls my-workmem.sm05.lh # more analysis.info cat my-workmem.sm05.lh/analysis.info mkcontrast-sess -analysis my-workmem.sm05.lh -contrast encode-v-base -a 1 ls my-workmem.sm05.lh mkcontrast-sess -analysis my-workmem.sm05.lh -contrast emot.dist-v-neut.dist -a 2 -c 3 mkcontrast-sess -analysis my-workmem.sm05.lh -contrast distractor.avg-v-base -a 2 -a 3 mkcontrast-sess -analysis my-workmem.sm05.lh -contrast emot.dist-v-base -a 2 mkcontrast-sess -analysis my-workmem.sm05.lh -contrast probe.avg-v-base -a 4 -a 5 mkanalysis-sess \ -fsd bold -stc up -surface fsaverage rh -fwhm 5 \ -event-related -paradigm workmem.par -nconditions 5 \ -spmhrf 0 -TR 2 -refeventdur 16 -nskip 4 -polyfit 2 \ -analysis my-workmem.sm05.rh -force -per-run mkanalysis-sess \ -fsd bold -stc up -mni305 2 -fwhm 5 \ -event-related -paradigm workmem.par -nconditions 5 \ -spmhrf 0 -TR 2 -refeventdur 16 -nskip 4 -polyfit 2 \ -analysis my-workmem.sm05.mni305 -force -per-run # selxavg3-sess -s sess01 -analysis workmem.sm05.lh ls $TUTORIAL_DATA/fsfast-functional/sess01/bold # Cannot pass quit option # tksurfer-sess, tkmedit-sess have no -quit option # # tksurfer-sess -s sess01 \ # -analysis workmem.sm05.lh \ # -c encode-v-base \ # -c emot.dist-v-base \ # -c probe.avg-v-base \ # -c emot.dist-v-neut.dist # tksurfer-sess -s sess01 -analysis workmem.sm05.rh \ # -c encode-v-base \ # -c emot.dist-v-base \ # -c emot.dist-v-neut.dist \ # -c probe.avg-v-base # tkmedit-sess -s sess01 -analysis workmem.sm05.mni305 \ # -c encode-v-base \ # -c emot.dist-v-base \ # -c emot.dist-v-neut.dist \ # -c probe.avg-v-base cd sess01/bold ls cd workmem.sm05.lh ls cd encode-v-base ls export SUBJECTS_DIR=$TUTORIAL_DATA/fsfast-tutorial.subjects cd $TUTORIAL_DATA/fsfast-functional # miissing nmask.dat file for the .lh subdir, so do not run this commamnd # isxconcat-sess -sf sessidlist -analysis workmem.sm05.lh -contrast encode-v-base -o group isxconcat-sess -sf sessidlist -analysis workmem.sm05.rh -contrast encode-v-base -o group isxconcat-sess -sf sessidlist -analysis workmem.sm05.mni305 -contrast encode-v-base -o group cd $TUTORIAL_DATA/fsfast-functional/group ls cd $TUTORIAL_DATA/fsfast-functional/group/workmem.sm05.lh ls cd $TUTORIAL_DATA/fsfast-functional/group/workmem.sm05.lh/encode-v-base ls mri_glmfit --y ces.nii.gz \ --osgm \ --surface fsaverage lh \ --glmdir my-glm\ --save-eres \ --nii.gz # Cannot pass quit option # tksurferfv fsaverage lh inflated -aparc -overlay my-glm/osgm/sig.nii.gz -fminmax 2 3 # tksurferfv quit fsaverage lh inflated -aparc -overlay my-glm/osgm/sig.nii.gz -fminmax 2 3 # mri_glmfit-sim --glmdir my-glm --perm 1000 3 pos --cwp .05 --3spaces cat my-glm/osgm/perm.th30.pos.sig.cluster.summary # Cannot pass quit option # tksurferfv fsaverage lh inflated \ # tksurferfv quit fsaverage lh inflated \ # -overlay my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz \ # -annot ./my-glm/osgm/perm.th30.pos.sig.ocn.annot -fminmax 1.3 3 cd $TUTORIAL_DATA/fsfast-functional/group/workmem.sm05.rh/encode-v-base mri_glmfit --y ces.nii.gz --osgm \ --surface fsaverage rh --glmdir my-glm --save-eres --nii.gz # mri_glmfit-sim --glmdir my-glm --perm 1000 3 pos --cwp 0.05 --3spaces cat my-glm/osgm/perm.th30.pos.sig.cluster.summary cd $TUTORIAL_DATA/fsfast-functional/group/workmem.sm05.mni305/encode-v-base ls cd $TUTORIAL_DATA/fsfast-functional/group/workmem.sm05.mni305/encode-v-base mri_glmfit --y ces.nii.gz --osgm \ --glmdir my-glm --nii.gz --save-eres # Cannot pass quit option # tkmeditfv fsaverage orig.mgz -aparc+aseg -overlay my-glm/osgm/sig.nii.gz -fminmax 2 3 # tkmeditfv quit fsaverage orig.mgz -aparc+aseg -overlay my-glm/osgm/sig.nii.gz -fminmax 2 3 # mri_glmfit-sim --glmdir my-glm --perm 1000 3 pos --cwp 0.05 --3spaces cat my-glm/osgm/perm.th30.pos.sig.cluster.summary # Cannot pass quit option # tkmeditfv fsaverage orig.mgz \ # tkmeditfv quit fsaverage orig.mgz \ # -ov my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz \ # -seg ./my-glm/osgm/perm.th30.pos.sig.ocn.nii.gz \ # ./my-glm/osgm/perm.th30.pos.sig.ocn.lut \ # -fminmax 1.3 5 cd $TUTORIAL_DATA/fsfast-functional/group cat workmem.sm05.lh/encode-v-base/my-glm/osgm/perm.th30.pos.sig.cluster.summary cat workmem.sm05.rh/encode-v-base/my-glm/osgm/perm.th30.pos.sig.cluster.summary cat workmem.sm05.mni305/encode-v-base/my-glm/osgm/perm.th30.pos.sig.cluster.summary vlrmerge --o encode.merged.nii.gz \ --lh workmem.sm05.lh/encode-v-base/my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz \ --rh workmem.sm05.rh/encode-v-base/my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz \ --vol workmem.sm05.mni305/encode-v-base/my-glm/osgm/perm.th30.pos.sig.cluster.nii.gz \ --scm workmem.sm05.mni305/subcort.mask.nii.gz # cannot pass quit option # tkmeditfv quit fsaverage orig.mgz -aparc+aseg -ov encode.merged.nii.gz -fminmax 1.3 5 -surfs date