Deletions are marked like this. | Additions are marked like this. |
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Output: dwi.nii, dwi.mghdti.bvecs, dwi.mghdti.bvals, dwi-ec.nii, lowb.nii, bvecs.dat, bvals.dat, eigvec[123].nii, eigvals.nii, tensor.nii, dwirvar.nii, ivc.nii, adc.nii, radialdiff.nii, vr.nii, ra.nii, fa.nii. | Output: dwi.nii, dwi.mghdti.bvecs, dwi.mghdti.bvals, dwi-ec.nii, lowb.nii, bvecs.dat, bvals.dat, eigvec[123].nii, eigvals.nii, tensor.nii, dwirvar.nii, ivc.nii, adc.nii, radialdiff.nii, vr.nii, ra.nii, fa.nii, fa-tal.nii, register.dat. |
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#!/bin/tcsh –ef source $SUBJECTS_DIR/scripts/subjects.csh |
#!/bin/tcsh –ef # |
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source subjects.csh # Run dt_recon on all subjects |
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set outdir = $SUBJECTS_DIR/$subj/LZDiff <-----!!*****!! | set outdir = $TUTORIAL_DIR/$subj/dtrecon |
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set dicomfile = $SUBEJCTS_DIR/$subj/orig/*-1.dcm | set dicomfile = $TUTORIAL_DIR/$subj/orig/*-1.dcm |
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#!/bin/tcsh -ef source $SUBJECTS_DIR/scripts/subjects.csh |
#!/bin/tcsh -ef # |
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source subjects.csh # Loop through each subject |
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set outdir = $SUBJECTS_DIR/$subj/LZDiff <-----!!*****!! | set outdir = $TUTORIAL_DIR/$subj/dtrecon |
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# For each subject's wmparc and aparc+aseg volumes do... | |
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#!/bin/tcsh -ef source $SUBJECTS_DIR/scripts/subjects.csh |
#!/bin/tcsh -ef # |
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source subjects.csh # Loop through each subject |
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set outdir = $SUBJECTS_DIR/$subj/LZDiff <-----!!*****!! | set outdir = $TUTORIAL_DIR/$subj/dtrecon |
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# Use wmparc2diff.mgz.... | |
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#!/bin/tcsh -ef source $SUBJECTS_DIR/scripts/subjects.csh |
#!/bin/tcsh -ef # source subjects.csh |
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set template = /autofs/cluster/con_001/users/lilla/CVS_atlas/buckner35rerun/avg35rerun/mri/norm.mgz <-----!!*****!! | set template = $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz |
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# Loop through each subject | |
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set outdir = $SUBJECTS_DIR/$subj/LZDiff <-----!!*****!! | set outdir = $TUTORIAL_DIR/$subj/dtrecon |
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foreach vol (fa adc ivc) |
# Uncomment '(fa adc ivc)' and remove '(fa)' to run all three volumes through... foreach vol (fa) # (fa adc ivc) |
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set outvol = ${vol:r}.ANAT+CVS-to-avg35.v2v.mgz | set outvol = ${vol:r}.ANAT+CVS-to-avg35.mgz |
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set cmd = ( mri_vol2vol --targ $template --m3z $morph --noDefM3zPath --reg $outdir/register.dat --mov $vol\ | set cmd = (mri_vol2vol --targ $template --m3z $morph --noDefM3zPath --reg $outdir/register.dat --mov $vol\ |
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set outdir = $SUBJECTS_DIR/diffusion_tutorial/GLM set type = CVS-to-avg35 # alternatively could be TAL-to-avg35 or MNI-to-avg35 set prefix = fa-masked #alternatively could be adc-masked or ivc-masked set inputfiles = ($outdir/../*/LZDiff/${prefix}.ANAT+${type}.v2v.mgz) <-----!!*****!! |
#!/bin/tcsh -ef |
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set cmd = (mri_concat --i $inputfiles --o $outdir/GroupAnalysis.{$prefix}.${type}.Input.mgz) |
source subjects.csh set outdir = $TUTORIAL_DIR/GLM mkdir -p $outdir # Assembling input for group analysis set type = CVS-to-avg35 # alternatively could be 'TAL-to-avg35' or 'MNI-to-avg35' set prefix = fa-masked #alternatively could be adc-masked or ivc-masked set inputfiles = () foreach subj ($SUBJECTS) set inputfiles=($inputfiles $TUTORIAL_DIR/$subj/dtrecon/${prefix}.ANAT+${type}.mgz) end set cmd = (mri_concat --i $inputfiles --o $outdir/GroupAnalysis.${prefix}.${type}.Input.mgz) |
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# Create average of the input images for visualization | |
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set cmd = ( mri_glmfit --y $outdir/GroupAnalysis.{$prefix}.${type}.Input.mgz --fsgd group_analysis.fsgd\ | set cmd = (mri_glmfit --y $outdir/GroupAnalysis.{$prefix}.${type}.Input.mgz --fsgd group_analysis.fsgd\ |
Return to Diffusion |
Be sure to source FreeSurfer before trying to run any of the following scripts.
subjects.csh
DiffPreproc.csh
Output: dwi.nii, dwi.mghdti.bvecs, dwi.mghdti.bvals, dwi-ec.nii, lowb.nii, bvecs.dat, bvals.dat, eigvec[123].nii, eigvals.nii, tensor.nii, dwirvar.nii, ivc.nii, adc.nii, radialdiff.nii, vr.nii, ra.nii, fa.nii, fa-tal.nii, register.dat.
#!/bin/tcsh –ef # source subjects.csh # Run dt_recon on all subjects foreach subj ($SUBJECTS) echo $subj set outdir = $TUTORIAL_DIR/$subj/dtrecon mkdir -p $outdir set dicomfile = $TUTORIAL_DIR/$subj/orig/*-1.dcm set cmd = (dt_recon --i $dicomfile --s $subj --o $outdir) echo $cmd eval $cmd end
Return to Diffusion |
AlignAnat2Diff.csh
Outputs: wmparc2diff.mgz, aparc+aseg2diff.mgz
#!/bin/tcsh -ef # source subjects.csh # Loop through each subject foreach subj ($SUBJECTS) echo $subj set outdir = $TUTORIAL_DIR/$subj/dtrecon # For each subject's wmparc and aparc+aseg volumes do... foreach vol (wmparc aparc+aseg) set vol = $SUBJECTS_DIR/$subj/mri/$vol.mgz set vol2diff = ${vol:r}2diff.mgz set cmd = (mri_vol2vol --mov $outdir/lowb.nii --targ $vol --inv --interp nearest\ --o $vol2diff --reg $outdir/register.dat --no-save-reg) echo $cmd eval $cmd end end
Return to Diffusion |
DiffMasking.csh
Outputs: fa-masked.mgz, adc-masked.mgz, ivc-masked.mgz
#!/bin/tcsh -ef # source subjects.csh # Loop through each subject foreach subj ($SUBJECTS) echo $subj set outdir = $TUTORIAL_DIR/$subj/dtrecon # Use wmparc2diff.mgz.... foreach vol (fa adc ivc) set cmd = (mri_mask $outdir/$vol.nii $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz\ $outdir/${vol}-masked.mgz) echo $cmd eval $cmd end end
Return to Diffusion |
AlignAnatCVSToAvg.csh
Outputs: fa.ANAT+CVS-to-avg35.v2v.mgz, adc.ANAT+CVS-to-avg35.v2v.mgz, ivc.ANAT+CVS-to-avg35.v2v.mgz
#!/bin/tcsh -ef # source subjects.csh set interp = trilin set template = $FREESURFER_HOME/subjects/cvs_avg35/mri/norm.mgz # Loop through each subject foreach subj ($SUBJECTS) echo $subj set outdir = $TUTORIAL_DIR/$subj/dtrecon set morph = $SUBJECTS_DIR/$subj/cvs/fullCVSmorph-to-avg35template.m3z <-----!!*****!! # Uncomment '(fa adc ivc)' and remove '(fa)' to run all three volumes through... foreach vol (fa) # (fa adc ivc) set vol = $outdir/${vol}-masked.mgz # any volume in diffusion space (i.e. fa.nii or adc.nii) echo $vol set outvol = ${vol:r}.ANAT+CVS-to-avg35.mgz echo $outvol set cmd = (mri_vol2vol --targ $template --m3z $morph --noDefM3zPath --reg $outdir/register.dat --mov $vol\ --o $outvol --interp $interp --no-save-reg ) echo $cmd eval $cmd end end
Return to Diffusion |
GroupAnalysis.csh
Outputs: gender_age.fa-masked.CVS-to-avg35.glmdir, dof.dat, mri_glmfit.log, y.fsgd, X.mat, contrast/Xg.dat, contrast/rstd.mgz, contrast/rvar.mgz, contrast/beta.mgz, contrast/fwhm.dat, contrast/sar1.mgz, contrast/mask.mgz
#!/bin/tcsh -ef source subjects.csh set outdir = $TUTORIAL_DIR/GLM mkdir -p $outdir # Assembling input for group analysis set type = CVS-to-avg35 # alternatively could be 'TAL-to-avg35' or 'MNI-to-avg35' set prefix = fa-masked #alternatively could be adc-masked or ivc-masked set inputfiles = () foreach subj ($SUBJECTS) set inputfiles=($inputfiles $TUTORIAL_DIR/$subj/dtrecon/${prefix}.ANAT+${type}.mgz) end set cmd = (mri_concat --i $inputfiles --o $outdir/GroupAnalysis.${prefix}.${type}.Input.mgz) echo $cmd eval $cmd # Create average of the input images for visualization set cmd = (mri_average $inputfiles $outdir/Average.{$prefix}.${type}.Input.mgz) echo $cmd eval $cmd set cmd = (mri_glmfit --y $outdir/GroupAnalysis.{$prefix}.${type}.Input.mgz --fsgd group_analysis.fsgd\ dods --C contrast.mtx --glmdir $outdir/gender_age.{$prefix}.${type}.glmdir --mgz) echo $cmd eval $cmd