FS Course Laptop Commands

List of commands to try on course laptops to verify tutorial commands will work.

Contents

  1. FS Course Laptop Commands
    1. CHECK BEFORE RUNNING COMMANDS
    2. Interaction with Individual Subject Data
    3. Troubleshooting
    4. ROI Analysis
    5. Longitudinal Tutorial
    6. Multi-Modal Registration
    7. Multi-Modal fMRI Individual
    8. Multi-Modal fMRI Group
    9. Multi-Modal DTI Group
    10. Group Analysis
    11. Group Analysis (QDEC)
    12. FS FAST
    13. Diffusion Tutorial
    14. TRACULA Tutorial

CHECK BEFORE RUNNING COMMANDS

Interaction with Individual Subject Data

setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR

tkmedit good_output brainmask.mgz lh.white -aux T1.mgz -aux-surface rh.white -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

tksurfer good_output lh inflated

Troubleshooting

setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_subjs
cd $SUBJECTS_DIR

tkmedit topo_defect_before brainmask.mgz lh.white -aux wm.mgz -aux-surface rh.white

tksurfer pial_edits_before lh inflated

#EXTRA COMMANDS TO TRY
#tkmedit topo_defect_after brainmask.mgz \
#  lh.white -aux wm.mgz -aux-surface rh.white
#
#
#tkmedit wm1_edits_before brainmask.mgz \
#  lh.white -aux T1.mgz -aux-surface rh.white
#
#
#tksurfer wm1_edits_before lh inflated
#
#tkmedit pial_edits_before brainmask.mgz \
#  lh.white -aux T1.mgz -aux-surface rh.white
#
#
#tkmedit skullstrip1_before brainmask.mgz \
#  lh.white -aux T1.mgz -aux-surface rh.white
#
#
#tkmedit cp_before brainmask.mgz \
#  lh.white -aux T1.mgz -aux-surface rh.white
#
#
#tksurfer cp_before lh inflated &
#tksurfer cp_before rh inflated &
#
#tkmedit tal_before brainmask.mgz \
#  lh.white -aux T1.mgz -aux-surface rh.white
#
#
#tksurfer tal_before lh inflated

ROI Analysis

setenv SUBJECTS_DIR $TUTORIAL_DATA/group_analysis_tutorial
cd $SUBJECTS_DIR

tkmedit 004 orig.mgz -aux aparc+aseg.mgz -seg aparc+aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

tksurfer 004 lh inflated -annot aparc.annot

cat $FREESURFER_HOME/FreeSurferColorLUT.txt

cat 004/label/lh.BA45.label

#tkmedit 004 orig.mgz

#tksurfer 004 lh inflated

cd $SUBJECTS_DIR/004/stats
cat aseg.stats

cd $SUBJECTS_DIR/004/stats
cat lh.aparc.stats

setenv SUBJECTS_DIR $TUTORIAL_DATA/group_analysis_tutorial
cd $SUBJECTS_DIR

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

cat $FREESURFER_HOME/FreeSurferColorLUT.txt

cat 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

cat $FREESURFER_HOME/FreeSurferColorLUT.txt

asegstats2table \
  --subjects 004 021 040 067 080 092 \
  --segno 3007 3021 3022 4022 \
  --stats wmparc.stats \
  --tablefile wmparc.vol.table

cat $FREESURFER_HOME/FreeSurferColorLUT.txt

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

long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat

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

gedit qdec/.Qdecrc

tkmedit OAS2_0088 brainmask.mgz  -aux T1.mgz -surfs

#tkmedit OAS2_0088_MR1 brainmask.mgz  -aux T1.mgz -surfs
#tkmedit OAS2_0088_MR2 brainmask.mgz  -aux T1.mgz -surfs

#tkmedit OAS2_0088_MR1.long.OAS2_0004 brainmask.mgz  -aux T1.mgz -surfs
#tkmedit OAS2_0088_MR2.long.OAS2_0004 brainmask.mgz  -aux T1.mgz -surfs

tkmedit OAS2_0002_MR2 brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

tkmedit OAS2_0002 brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

tkmedit OAS2_0002_MR2.long.OAS2_0002 brainmask.mgz -aux brain.finalsurfs.mgz -surfs -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

Multi-Modal Registration

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

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

tkmedit fbirn-anat-101.v4 orig.mgz -aux brain.mgz -seg aparc+aseg.mgz -overlay sig.nii -reg bb.register.dat -fthresh 2 -fmax 4

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
cd $TUTORIAL_DATA/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
cd $TUTORIAL_DATA/multimodal/dti

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

tkmedit M87102113.v4 orig.mgz -aux brain.mgz -seg wmparc.mgz -reg register.dat -overlay fa.nii -fthresh 0.2 -fmax 1

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

#------------------------------
#Testing tksurfer, tkmedit and qdec
#------------------------------

cd $SUBJECTS_DIR

tkmedit good_output brainmask.mgz lh.white \
        -aux T1.mgz -aux-surface rh.white \
        -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt

tksurfer good_output lh inflated

qdec

Group Analysis

setenv SUBJECTS_DIR $TUTORIAL_DATA/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_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 \
  --overwrite

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

cat 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/group_analysis_tutorial
cd $SUBJECTS_DIR

setenv SUBJECTS_DIR $TUTORIAL_DATA/group_analysis_tutorial
cd $SUBJECTS_DIR

#qdec &

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

#tkmedit 004 brainmask.mgz -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

tkmedit -f f.nii.gz -t 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

tkmedit -f template.nii.gz -overlay masks/brain.nii.gz -fthresh 0.5

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

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

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
tkmedit 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 --cwpvalthresh .0166

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

tkmedit 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.anat.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

tkmedit fsaverage orig.mgz -aparc+aseg -ov encode.merged.nii.gz -fminmax 1.3 5 -surfs

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

mkdir $TUTORIAL_DIR/GLM
set inputfiles = ($TUTORIAL_DIR/Diff???/dtrecon/fa-masked.ANAT+CVS-to-avg35.mgz)
echo $inputfiles
mri_concat --i $inputfiles --o $TUTORIAL_DIR/GLM/GroupAnalysis.fa-masked.CVS-to-avg35.Input.mgz

mri_average $inputfiles $TUTORIAL_DIR/GLM/Average.fa-masked.CVS-to-avg35.Input.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

#TRACULA OUTPUT

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='yellow' \
            $TUTORIAL_DATA/diffusion_tutorial/Diff001/dpath/rh.ilf_AS_avg32_mni_flt/path.pd.nii.gz:colormap=jet:isosurface=0,0:color='yellow'

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

#TRACT STATS

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

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/pathstats.byvoxel.txt

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

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