= FS Course Laptop Commands =
List of commands to try on course laptops to verify tutorial commands will work.

<<TableOfContents>>

== CHECK BEFORE RUNNING COMMANDS ==
 * Set FREESURFER_HOME before executing this script
 * Also make sure $FREESURFER_HOME/subjects/buckner_data exists or is symlinked to the buckner data directory.

== Interaction with Individual Subject Data ==
{{{
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR

freeview -v good_output/mri/T1.mgz good_output/mri/wm.mgz:colormap=heat:opacity=0.4 \
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 \

tksurfer good_output lh inflated

freeview 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 \
}}}
== Troubleshooting ==
{{{
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR

 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 \

tksurfer pial_edits_before lh inflated

tksurfer pial_edits_before rh inflated

 freeview -v wm1_edits_before/mri/T1.mgz  \
wm1_edits_before/mri/brainmask.mgz  \
-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 \

tksurfer wm1_edits_before lh inflated

tksurfer wm1_edits_before rh inflated

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 \

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 \

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 \

freeview -v skullstrip1_before/mri/T1.mgz \
skullstrip1_before/mri/brainmask.mgz \
-f skullstrip1_before/surf/lh.white:edgecolor=yellow \
skullstrip1_before/surf/lh.pial:edgecolor=red \
skullstrip1_before/surf/rh.white:edgecolor=yellow \
skullstrip1_before/surf/rh.pial:edgecolor=red \

freeview -v cp_before/mri/brainmask.mgz
-f pial_edits_before/surf/lh.white:edgecolor=blue
pial_edits_before/surf/lh.pial:edgecolor=red
pial_edits_before/surf/rh.white:edgecolor=blue
pial_edits_before/surf/rh.pial:edgecolor=red

tksurfer cp_before lh inflated

tksurfer cp_before rh inflated

freeview -v tal_before/mri/T1.mgz tal_before/mri/brainmask.mgz:reg=transforms/talairach.xfm

tksurfer tal_before lh inflated

tksurfer tal_before rh inflated
}}}
== ROI Analysis ==
{{{
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial
cd $SUBJECTS_DIR

freeview -v 004/mri/orig.mgz 004/mri/aparc+aseg.mgz:colormap=lut:opacity=0.4

tksurfer 004 lh inflated -annot aparc.annot

less $FREESURFER_HOME/FreeSurferColorLUT.txt

mri_label2label \
  --srcsubject fsaverage \
  --srclabel fsaverage/label/lh.BA45.label \
  --trgsubject 004 \
  --trglabel 004/label/lh.BA45.label \
  --hemi lh \
  --regmethod surface

less 004/label/lh.BA45.label

freeview -v 004/mri/orig.mgz

tksurfer 004 lh inflated

cd $SUBJECTS_DIR/004/stats

less aseg.stats

less lh.aparc.stats

setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial
cd $SUBJECTS_DIR

asegstats2table --subjects 004 021 040 067 080 092 \
  --segno 11 17 18 \
  --tablefile aseg.vol.table

less $FREESURFER_HOME/FreeSurferColorLUT.txt

less aseg.vol.table

#oocalc aseg.vol.table

#/Applications/OpenOffice.org.app/Contents/MacOS/scalc 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 Tutorial ==
{{{
setenv SUBJECTS_DIR $TUTORIAL_DATA/long-tutorial
cd $SUBJECTS_DIR

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

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

gedit qdec/long.qdec.table.dat

ooffice -calc qdec/long.qdec.table.dat

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

tksurfer fsaverage lh pial -overlay $SUBJECTS_DIR/OAS2_0001/surf/lh.long.thickness-spc.fwhm15.fsaverage.mgh -aparc

freeview -f 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

qdec --table ./qdec/cross.qdec.table.dat

setenv SUBJECTS_DIR $TUTORIAL_DATA/long-tutorial
cd $SUBJECTS_DIR

freeview -v OAS2_0088/mri/T1.mgz \
            OAS2_0088/mri/brainmask.mgz \
         -f OAS2_0088/surf/lh.pial:edgecolor=red \
            OAS2_0088/surf/rh.pial:edgecolor=red \
            OAS2_0088/surf/lh.white:edgecolor=blue \
            OAS2_0088/surf/rh.white:edgecolor=blue

freeview -v OAS2_0088_MR1/mri/T1.mgz \
            OAS2_0088_MR1/mri/brainmask.mgz \
         -f OAS2_0088_MR1/surf/lh.pial:edgecolor=red \
            OAS2_0088_MR1/surf/rh.pial:edgecolor=red \
            OAS2_0088_MR1/surf/lh.white:edgecolor=blue \
            OAS2_0088_MR1/surf/rh.white:edgecolor=blue

freeview -v OAS2_0088_MR2/mri/T1.mgz \
            OAS2_0088_MR2/mri/brainmask.mgz \
         -f OAS2_0088_MR2/surf/lh.pial:edgecolor=red \
            OAS2_0088_MR2/surf/rh.pial:edgecolor=red \
            OAS2_0088_MR2/surf/lh.white:edgecolor=blue \
            OAS2_0088_MR2/surf/rh.white:edgecolor=blue

freeview -v OAS2_0088_MR1.long.OAS2_0004/mri/T1.mgz \
            OAS2_0088_MR1.long.OAS2_0004/mri/brainmask.mgz \
         -f OAS2_0088_MR1.long.OAS2_0004/surf/lh.pial:edgecolor=red \
            OAS2_0088_MR1.long.OAS2_0004/surf/rh.pial:edgecolor=red \
            OAS2_0088_MR1.long.OAS2_0004/surf/lh.white:edgecolor=blue \
            OAS2_0088_MR1.long.OAS2_0004/surf/rh.white:edgecolor=blue

freeview -v OAS2_0088_MR2.long.OAS2_0004/mri/T1.mgz \
            OAS2_0088_MR2.long.OAS2_0004/mri/brainmask.mgz \
         -f OAS2_0088_MR2.long.OAS2_0004/surf/lh.pial:edgecolor=red \
            OAS2_0088_MR2.long.OAS2_0004/surf/rh.pial:edgecolor=red \
            OAS2_0088_MR2.long.OAS2_0004/surf/lh.white:edgecolor=blue \
            OAS2_0088_MR2.long.OAS2_0004/surf/rh.white:edgecolor=blue

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

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

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

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


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

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

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

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

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

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

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

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

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

freeview -v OAS2_0002_MR2/mri/brain.finalsurfs.mgz \
            OAS2_0002_MR2/mri/brainmask.mgz \
            OAS2_0002_MR2/mri/aseg.mgz:colormap=lut:opacity=0.25 \
         -f OAS2_0002_MR2/surf/lh.pial:edgecolor=red \
            OAS2_0002_MR2/surf/rh.pial:edgecolor=red \
            OAS2_0002_MR2/surf/lh.white:edgecolor=blue \
            OAS2_0002_MR2/surf/rh.white:edgecolor=blue
}}}
== Multi-Modal Registration ==
{{{
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR/multimodal/fmri/fbirn-101

tkregister2 --mov template.nii --s fbirn-anat-101.v4 \
 --regheader --reg myregister.dat --surf

 bbregister --mov template.nii --bold \
    --s fbirn-anat-101.v4 \
    --init-fsl --reg register.dat

cat register.dat

tkregister2 --mov template.nii --reg register.dat --surf
}}}
== Multi-Modal fMRI Individual ==
{{{
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR/multimodal/fmri/fbirn-101

tkregister2 --mov template.nii --reg bb.register.dat --surf

freeview -v $SUBJECTS_DIR/fbirn-anat-101.v4/mri/orig.mgz \
$SUBJECTS_DIR/fbirn-anat-101.v4/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2 \
sig.nii:reg=bb.register.dat:colormap=heat:heatscale=2,2,4 -colorscale \

mri_vol2surf --mov sig.nii \
    --reg bb.register.dat \
    --projfrac 0.5 --interp nearest \
    --hemi lh --o lh.sig.mgh


mri_info lh.sig.mgh

tksurfer fbirn-anat-101.v4 lh inflated -annot aparc \
  -overlay lh.sig.mgh

mri_vol2vol --mov ces.nii \
    --reg bb.register.dat \
    --fstarg --interp nearest \
    --o ces.anat.bb.mgh

mri_info ces.anat.bb.mgh

mri_segstats \
   --seg $SUBJECTS_DIR/fbirn-anat-101.v4/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 bb.register.dat \
    --fstarg --interp nearest \
    --o sig.anat.bb.mgh

mri_segstats \
   --seg $SUBJECTS_DIR/fbirn-anat-101.v4/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_segstats \
   --seg $SUBJECTS_DIR/fbirn-anat-101.v4/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
}}}
== Multi-Modal fMRI Group ==
{{{
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR/multimodal/fmri

tkregister2 --mov fbirn-101/template.nii --reg fbirn-101/bb.register.dat --surf

mris_preproc --target fsaverage --hemi lh \
  --iv  fbirn-101/ces.nii fbirn-101/bb.register.dat \
  --iv  fbirn-103/ces.nii fbirn-103/bb.register.dat \
  --iv  fbirn-104/ces.nii fbirn-104/bb.register.dat \
  --iv  fbirn-105/ces.nii fbirn-105/bb.register.dat \
  --iv  fbirn-106/ces.nii fbirn-106/bb.register.dat \
  --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

tksurfer fsaverage lh inflated -annot aparc -ov lh.ces.sm05.osgm/osgm/sig.mgh

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

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

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
}}}
== Multi-Modal DTI Group ==
{{{
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR/multimodal/dti

tkregister2 --mov lowb.nii --reg register.dat --surf

freeview -v $SUBJECTS_DIR/M87102113.v4/mri/brain.mgz $SUBJECTS_DIR/M87102113.v4/mri/orig.mgz $SUBJECTS_DIR/M87102113.v4/mri/wmparc.mgz:colormap=lut:opacity=0.2 fa.nii:reg=register.dat:colormap=heat:heatscale=.2,.2,1 -colorscale

mri_vol2vol --mov fa.nii \
  --reg register.dat \
  --fstarg --interp nearest \
  --o fa.anat.mgh

mri_segstats \
  --seg $SUBJECTS_DIR/M87102113.v4/mri/wmparc.mgz \
  --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt \
  --id 251 --id 3021 --id 3024 --id 3030 --id 12 --id 4 \
  --i fa.anat.mgh --sum fa.stats
}}}
== Group Analysis ==
{{{
setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs/group_analysis_tutorial
cd $SUBJECTS_DIR/glm

mris_preproc --fsgd gender_age.fsgd \
  --cache-in thickness.fwhm10.fsaverage \
  --target fsaverage --hemi lh \
  --out lh.gender_age.thickness.10.mgh

mri_info lh.gender_age.thickness.10.mgh

mris_preproc --fsgd gender_age.fsgd \
  --target fsaverage --hemi lh \
  --meas thickness \
  --out lh.gender_age.thickness.00.mgh

mri_surf2surf --hemi lh \
  --s fsaverage \
  --sval lh.gender_age.thickness.00.mgh \
  --fwhm 10 \
  --cortex \
  --tval lh.gender_age.thickness.10B.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

tksurfer fsaverage lh inflated \
  -annot aparc.annot -fthresh 2 \
  -overlay lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh

mri_glmfit-sim \
  --glmdir lh.gender_age.glmdir \
  --sim mc-z 5 4 mc-z.negative \
  --sim-sign neg --cwpvalthresh 0.4\
  --overwrite

less lh.gender_age.glmdir/csd/mc-z.neg4.j001-lh-Avg-thickness-age-Cor.csd

less lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.cluster.summary

tksurfer fsaverage lh inflated \
  -annot lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/mc-z.neg4.sig.ocn.annot \
  -fthresh 2 -curv -gray
}}}
== Group Analysis (QDEC) ==
{{{
setenv 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

mris_anatomical_stats -l lh.supramarg.label \
  -t lh.thickness -b -f 004/stats/lh.supramarg.stats 004 lh

freeview -v 004/mri/brainmask.mgz -l 004/label/lh.supramarg.label
}}}
== FS FAST ==
{{{
cd $TUTORIAL_DATA/fsfast-functional
ls

cd $TUTORIAL_DATA/fsfast-functional/sess01.noproc
ls

setenv 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

freeview -v f.nii.gz

cat workmem.par

cd $TUTORIAL_DATA/fsfast-functional
cat sessidlist

setenv SUBJECTS_DIR $TUTORIAL_DATA/fsfast-tutorial.subjects
cd $TUTORIAL_DATA/fsfast-functional
preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run

plot-twf-sess -s sess01 -fsd bold -mc

tkregister-sess -s sess01 -s sess02 -s sess03 -fsd bold -per-run -bbr-sum

tkregister-sess -s sess02 -fsd bold -per-run

cd $TUTORIAL_DATA/fsfast-functional/sess01/bold/001

freeview -v template.nii.gz masks/brain.nii.gz:colormap=heat

freeview -v template.nii.gz masks/brain.e3.nii.gz:colormap=heat

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

setenv 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 -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

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

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

setenv 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 my-group

cd $TUTORIAL_DATA/fsfast-functional/my-group
ls

cd $TUTORIAL_DATA/fsfast-functional/my-group/workmem.sm05.lh
ls

mri_glmfit --y ces.nii.gz \
  --wls cesvar.nii.gz \
  --osgm \
  --surface fsaverage lh \
  --glmdir my-glm.wls \
  --nii.gz

tksurfer 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 --cwpvalthresh .0166

cat my-glm.wls/osgm/cache.th30.pos.sig.cluster.summary

tksurfer 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 --nii.gz
mri_glmfit-sim --glmdir my-glm.wls --cache 3 pos --cwpvalthresh .0166

cat my-glm.wls/osgm/cache.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 --wls cesvar.nii.gz --osgm  \
  --glmdir my-glm.wls --nii.gz

freeview -v $SUBJECTS_DIR/fsaverage/mri/orig.mgz $SUBJECTS_DIR/fsaverage/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2 my-glm.wls/osgm/sig.nii.gz:colormap=heat:heatscale=2,2,3

mri_glmfit-sim --glmdir my-glm.wls --grf 3 pos --cwpvalthresh .0166

cat my-glm.wls/osgm/grf.th3.pos.sig.cluster.summary

freeview $SUBJECTS_DIR/fsaverage/mri/orig.mgz my-glm.wls/osgm/grf.th3.pos.sig.ocn.anat.nii.gz:colormap=lut:lut=./my-glm.wls/osgm/grf.th3.pos.sig.ocn.lut:opacity=0 my-glm.wls/osgm/grf.th3.pos.sig.cluster.nii.gz:colormap=heat:heatscale=1.3,1.3,5

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

freeview -v $SUBJECTS_DIR/fsaverage/mri/orig.mgz \
$SUBJECTS_DIR/fsaverage/mri/aparc+aseg.mgz:colormap=lut:opacity=0.2 \
encode.merged.nii.gz:colormap=heat:heatscale=1.3,1.3,5 \
-f $SUBJECTS_DIR/fsaverage/surf/lh.pial:edgecolor=red \
$SUBJECTS_DIR/fsaverage/surf/rh.pial:edgecolor=red \
$SUBJECTS_DIR/fsaverage/surf/lh.white:edgecolor=yellow \
$SUBJECTS_DIR/fsaverage/surf/rh.white:edgecolor=yellow
}}}
== Diffusion Tutorial ==
{{{
setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_recons
setenv TUTORIAL_DIR $TUTORIAL_DATA/diffusion_tutorial
set subj = Diff001

freeview -v $TUTORIAL_DIR/$subj/dtrecon/fa.nii $TUTORIAL_DIR/$subj/dtrecon/adc.nii

mri_vol2vol --mov $TUTORIAL_DIR/$subj/dtrecon/lowb.nii \
            --targ $SUBJECTS_DIR/$subj/mri/wmparc.mgz \
            --inv --interp nearest --o $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \
            --reg $TUTORIAL_DIR/$subj/dtrecon/register.dat --no-save-reg

freeview -v $TUTORIAL_DIR/$subj/dtrecon/fa.nii \
            $SUBJECTS_DIR/$subj/mri/aparc+aseg2diff.mgz:colormap=lut

mri_mask $TUTORIAL_DIR/$subj/dtrecon/fa.nii \
         $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \
         $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz

freeview -v $TUTORIAL_DIR/$subj/dtrecon/fa.nii \
           $TUTORIAL_DIR/$subj/dtrecon/fa-masked.mgz

freeview -v $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz \
            $TUTORIAL_DIR/$subj/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz
}}}
== TRACULA Tutorial ==
{{{
setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_recons
cd $TUTORIAL_DATA/diffusion_tutorial

gedit $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject

set dtroot = $TUTORIAL_DATA/diffusion_tutorial

set subjlist = (Diff001 Diff002 Diff003)

set runlist = (1)

set dcmroot = $TUTORIAL_DATA/diffusion_tutorial/

set dcmlist = (Diff001/orig/6-1.dcm \
               Diff002/orig/312000-6-1.dcm \
               Diff003/orig/781000-6-1.dcm)

trac-all -prep -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject

trac-all -bedp -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject

trac-all -path -c $TUTORIAL_DATA/diffusion_tutorial/scripts/dmrirc_single_subject

cd $TUTORIAL_DATA/diffusion_tutorial/Diff001/dmri

freeview $TUTORIAL_DATA/diffusion_tutorial/Diff001/dmri/dtifit_FA.nii.gz &

cd $TUTORIAL_DATA/diffusion_tutorial/Diff001/dmri/mni/

freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz \
            $TUTORIAL_DATA/diffusion_tutorial/Diff001/dmri/mni/dtifit_FA.bbr.nii.gz &

freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz \
            $TUTORIAL_DATA/diffusion_tutorial/Diff001/dmri/mni/dtifit_FA.flt.nii.gz &

freeview -v $TUTORIAL_DATA/diffusion_tutorial/Diff001/dmri/dtifit_FA.nii.gz \
            $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.ilf_AS_avg32_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' \
            $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/rh.ilf_AS_avg32_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='Red' &

freeview -tv $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/merged_avg32_mni_flt.mgz \
         -v $TUTORIAL_DATA/diffusion_tutorial/Diff001/dmri/dtifit_FA.nii.gz &

cd $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt

gedit $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt &

gedit $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/pathstats.byvoxel.txt &

tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/lh.cst_AS.All.table

gedit $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/lh.cst_AS.All.table &

tractstats2table --inputs $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/pathstats.overall.txt --overall --only-measures FA_Avg --tablefile $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/lh.cst_AS.FA_Avg.table

gedit $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/lh.cst_AS_avg32_mni_flt/lh.cst_AS.FA_Avg.table &

gedit $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.overall.pathstats.list &

tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.overall.pathstats.list --overall --tablefile $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.All.table

ls $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/*.All.table

tractstats2table --load-pathstats-from-file $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.overall.pathstats.list --overall --only-measures FA_Avg --tablefile $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.FA_Avg.table

oocalc $TUTORIAL_DATA/diffusion_tutorial/TraculaStatFiles/lh.cst_AS.All.table
}}}