#!/usr/bin/env bash

# parse command line arguments
for i in "$@"; do
case $i in
  --no-gui)
    gui="echo skipping -"
    shift
  ;;
  -h|--help)
    echo $helptext
    exit 0
  ;;
  *)
    echo "error: unknown option '$i'"
    exit 1
  ;;
esac
done

set -ex

# -------- Introduction to Freesurfer Output --------

export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR

${gui} 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
${gui} 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

# -------- Practice Working with Data --------

cd $TUTORIAL_DATA/practice_with_data/dicoms
export SUBJECTS_DIR=$TUTORIAL_DATA/practice_with_data

dcmunpack -src . -scanonly scan.log

# -------- Troubleshooting --------

export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR

${gui} 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
${gui} 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
${gui} 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
${gui} 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
${gui} 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
${gui} 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
${gui} 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
${gui} 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
${gui} 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
${gui} 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
${gui} 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
${gui} 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
${gui} 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

# -------- Surface Based Group Analysis --------

export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial
cd $SUBJECTS_DIR/glm

mri_surf2surf --hemi lh --s fsaverage --sval lh.gender_age.thickness.00.mgh --fwhm 10 --cortex --tval lh.gender_age.thickness.10.mgh
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
${gui} 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
${gui} 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

# -------- Clusterwise Correction for Multiple Comparisons (Permutation) --------

export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial_perm
cd $SUBJECTS_DIR/glm

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
ls lh.gender_age.glmdir/lh-Avg-thickness-age-Cor
cat lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/perm.th40.abs.sig.cluster.summary
${gui} 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

# -------- QDEC --------

export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial
cd $SUBJECTS_DIR
mri_label2label --srclabel lh.supramarg --srcsubject fsaverage --trgsubject 004 --trglabel lh.supramarg --regmethod surface --hemi lh
mris_anatomical_stats -l lh.supramarg.label -t lh.thickness -b -f 004/stats/lh.supramarg.stats 004 lh

# -------- Multimodal Integration --------

export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR/multimodal/fmri/fbirn-101

${gui} 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
${gui} 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

# -------- Individual fMRI Integration --------

export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR/multimodal/fmri/fbirn-101

${gui} 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
${gui} 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
${gui} 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

# -------- Surface-Based Group fMRI Analysis --------

export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR/multimodal/fmri

${gui} 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
${gui} 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

# -------- Anatomical ROI analysis --------

export SUBJECTS_DIR=$TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial
cd $SUBJECTS_DIR
${gui} freeview -v 004/mri/orig.mgz 004/mri/aparc+aseg.mgz:colormap=lut:opacity=0.4 -f 004/surf/lh.white:annot=aparc.annot
cat $FREESURFER_HOME/FreeSurferColorLUT.txt
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
${gui} freeview -v 004/mri/orig.mgz
${gui} freeview -f 004/surf/lh.inflated
cd $SUBJECTS_DIR/004/stats
cat aseg.stats
cat lh.aparc.stats
cd $SUBJECTS_DIR/004
mris_anatomical_stats -l label/lh.BA45_exvivo.label -f stats/lh.BA45_exvivo.stats 004 lh
ls -l $SUBJECTS_DIR/004/stats/lh.BA45_exvivo.stats
cd $SUBJECTS_DIR
asegstats2table --subjects 004 021 040 067 080 092 --segno 11 17 18 --tablefile aseg.vol.table
cat aseg.vol.table
asegstats2table --subjects 004 021 040 067 080 092 --segno 11 17 18 --meas mean --tablefile aseg.mean-intensity.table
asegstats2table --subjects 004 021 040 067 080 092 --segno 3007 3021 3022 4022 --stats wmparc.stats --tablefile wmparc.vol.table
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

# -------- Longitudinal --------

export SUBJECTS_DIR=$TUTORIAL_DATA/long-tutorial
cd $SUBJECTS_DIR

${gui} 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
${gui} 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
cat qdec/long.qdec.table.dat
${gui} 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
${gui} 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

# -------- Diffusion Imaging Basics --------

export SUBJECTS_DIR=$TUTORIAL_DATA/diffusion_recons
export TUTORIAL_DIR=$TUTORIAL_DATA/diffusion_tutorial
subj=Diff001
cd $TUTORIAL_DIR/$subj/dtrecon

${gui} freeview dwi.nii.gz
${gui} 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
${gui} freeview -v fa.nii adc.nii
${gui} 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
${gui} 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
${gui} 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
${gui} 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
${gui} freeview -v $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz fa-masked.ANAT+CVS-to-avg35.mgz

# -------- TRACULA --------

export SUBJECTS_DIR=$TUTORIAL_DATA/diffusion_recons
cd $TUTORIAL_DATA/diffusion_tutorial

cat $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
${gui} freeview $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/dtifit_FA.nii.gz
cd $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/mni/
${gui} freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz $TUTORIAL_DATA/diffusion_tutorial/elmo.2012/dmri/mni/dtifit_FA.bbr.nii.gz
${gui} 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
${gui} 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
cat $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
cat $TUTORIAL_DATA/diffusion_tutorial/lh.ilf.elmo.2012.All.table
cat $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
cat $TUTORIAL_DATA/diffusion_tutorial/stats/lh.ilf_AS.avg33_mni_bbr.FA_Avg.txt
cat $TUTORIAL_DATA/diffusion_tutorial/stats/lh.ilf_AS.avg33_mni_bbr.log
${gui} freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w $TUTORIAL_DATA/diffusion_tutorial/stats/*.path.mean.txt

# -------- FSFAST --------

export FSF_OUTPUT_FORMAT=nii.gz
cd $TUTORIAL_DATA/fsfast-functional/sess01.noproc
export SUBJECTS_DIR=$TUTORIAL_DATA/fsfast-tutorial.subjects

cat subjectname
cd bold/001
mri_info --dim f.nii.gz
mri_info --res f.nii.gz
${gui} freeview -v f.nii.gz -timecourse
cat workmem.par
cd $TUTORIAL_DATA/fsfast-functional
cat sessidlist
export SUBJECTS_DIR=$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
${gui} tkregister-sess -s sess02 -fsd bold -per-run
cd $TUTORIAL_DATA/fsfast-functional/sess01/bold/001
mri_info template.nii.gz
mri_info f.nii.gz
${gui} freeview -v template.nii.gz masks/brain.nii.gz:colormap=heat:opacity=0.75 -viewport coronal
${gui} freeview -v template.nii.gz masks/brain.e3.nii.gz:colormap=heat:opacity=0.75 -viewport coronal
mri_info --dim fmcpr.up.sm5.mni305.2mm.nii.gz
mri_info --res fmcpr.up.sm5.mni305.2mm.nii.gz
mri_info --dim fmcpr.up.sm5.fsaverage.lh.nii.gz
mri_info --res fmcpr.up.sm5.fsaverage.lh.nii.gz
export SUBJECTS_DIR=$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
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
ls $TUTORIAL_DATA/fsfast-functional/sess01/bold
${gui} 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
${gui} 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
${gui} tkmedit-sess -s sess01 -analysis workmem.sm05.mni305 -c encode-v-base -c emot.dist-v-base -c emot.dist-v-neut.dist -c probe.avg-v-base
cd sess01/bold
cd workmem.sm05.lh
cd encode-v-base
export SUBJECTS_DIR=$TUTORIAL_DATA/fsfast-tutorial.subjects
cd $TUTORIAL_DATA/fsfast-functional
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
cd $TUTORIAL_DATA/fsfast-functional/group/workmem.sm05.lh
cd $TUTORIAL_DATA/fsfast-functional/group/workmem.sm05.lh/encode-v-base
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm --surface fsaverage lh --glmdir my-glm.wls --save-eres --nii.gz
${gui} tksurferfv fsaverage lh inflated -aparc -overlay my-glm.wls/osgm/sig.nii.gz -fminmax 2 3
mri_glmfit-sim --glmdir my-glm.wls --cache 3 pos --cwp .05 --3spaces
cat my-glm.wls/osgm/cache.th30.pos.sig.cluster.summary
${gui} tksurferfv fsaverage lh inflated -overlay my-glm.wls/osgm/cache.th30.pos.sig.cluster.nii.gz -annot ./my-glm.wls/osgm/cache.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 --wls cesvar.nii.gz --osgm --surface fsaverage rh --glmdir my-glm.wls --save-eres --nii.gz
mri_glmfit-sim --glmdir my-glm.wls --cache 3 pos --cwp 0.5 --3spaces
cat my-glm.wls/osgm/cache.th30.pos.sig.cluster.summary
cd $TUTORIAL_DATA/fsfast-functional/group/workmem.sm05.mni305/encode-v-base
cd $TUTORIAL_DATA/fsfast-functional/group/workmem.sm05.mni305/encode-v-base
mri_glmfit --y ces.nii.gz --wls cesvar.nii.gz --osgm  --glmdir my-glm.wls --nii.gz --save-eres
${gui} tkmeditfv fsaverage orig.mgz -aparc+aseg -overlay my-glm.wls/osgm/sig.nii.gz -fminmax 2 3
mri_glmfit-sim --glmdir my-glm.wls --grf 3 pos --cwp 0.5 --3spaces
cat my-glm.wls/osgm/grf.th3.pos.sig.cluster.summary
${gui} tkmeditfv fsaverage orig.mgz -ov my-glm.wls/osgm/grf.th3.pos.sig.cluster.nii.gz -seg ./my-glm.wls/osgm/grf.th3.pos.sig.ocn.nii.gz  ./my-glm.wls/osgm/grf.th3.pos.sig.ocn.lut -fminmax 1.3 5
cd $TUTORIAL_DATA/fsfast-functional/group
cat workmem.sm05.lh/encode-v-base/my-glm.wls/osgm/cache.th30.pos.sig.cluster.summary
cat workmem.sm05.rh/encode-v-base/my-glm.wls/osgm/cache.th30.pos.sig.cluster.summary
cat workmem.sm05.mni305/encode-v-base/my-glm.wls/osgm/grf.th3.pos.sig.cluster.summary
vlrmerge --o encode.merged.nii.gz --lh workmem.sm05.lh/encode-v-base/my-glm.wls/osgm/cache.th30.pos.sig.cluster.nii.gz --rh workmem.sm05.rh/encode-v-base/my-glm.wls/osgm/cache.th30.pos.sig.cluster.nii.gz --vol workmem.sm05.mni305/encode-v-base/my-glm.wls/osgm/grf.th3.pos.sig.cluster.nii.gz --scm workmem.sm05.mni305/subcort.mask.nii.gz
${gui} tkmeditfv fsaverage orig.mgz -aparc+aseg -ov encode.merged.nii.gz -fminmax 1.3 5 -surfs

set +x
echo "TUTORIALS FINISHED SUCCESSFULLY"