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Size: 5122
Comment:
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Size: 5220
Comment: added 's' to diffusion_recon directory in SUBJECTS_DIR environmental variable set in subjects.csh. diffusion_recon doesn't exist
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| Deletions are marked like this. | Additions are marked like this. |
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| ||Return to [[FsTutorial/Diffusion|Diffusion]] || | ##||Return to [[FsTutorial/Diffusion|Diffusion]] || ||Return to [[FsTutorial/Diffusion_DtiIntegration|Diffusion and DTI Integration]] || |
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| Be sure to source FreeSurfer before trying to run any of the following scripts. | Be sure to source FreeSurfer before trying to run any of the following scripts. |
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| {{{ #!/bin/tcsh -ef |
{{{#!/bin/tcsh -ef |
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| setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_recon | setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_recons |
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| {{{ #!/bin/tcsh –ef |
{{{#!/bin/tcsh –ef |
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| {{{ #!/bin/tcsh -ef |
{{{#!/bin/tcsh -ef |
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| set cmd = (mri_vol2vol --mov $outdir/lowb.nii --targ $vol --inv --interp nearest\ | set cmd = (mri_vol2vol --mov $outdir/lowb.nii --targ $vol --inv --interp nearest \ |
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| {{{ #!/bin/tcsh -ef |
{{{#!/bin/tcsh -ef |
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| set cmd = (mri_mask $outdir/$vol.nii $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz\ | set cmd = (mri_mask $outdir/$vol.nii $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \ |
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| {{{ #!/bin/tcsh -ef |
{{{#!/bin/tcsh -ef |
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| set interp = trilin | set interp = trilin |
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| set cmd = (mri_vol2vol --targ $template --m3z $morph --noDefM3zPath --reg $outdir/register.dat --mov $vol\ --o $outvol --interp $interp --no-save-reg ) |
set cmd = (mri_vol2vol --targ $template --m3z $morph --noDefM3zPath \ --reg $outdir/register.dat --mov $vol \ --o $outvol --interp $interp --no-save-reg) |
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| {{{ #!/bin/tcsh -ef |
{{{#!/bin/tcsh -ef |
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| set type = CVS-to-avg35 # alternatively could be 'TAL-to-avg35' or 'MNI-to-avg35' | set type = CVS-to-avg35 # alternatively could be 'TAL' or 'MNI' |
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| 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) |
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) |
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Return to Diffusion and DTI Integration |
Be sure to source FreeSurfer before trying to run any of the following scripts.
subjects.csh
Use this script to set the 'SUBJECTS_DIR' and 'TUTORIAL_DIR' parameters, as well as assigning variouos subject data sub-sets (normal subjects, lesioned subjects, both groups). The 'TUTORIAL_DATA' represents the file path of where the tutorial data is being stored.
{{{#!/bin/tcsh -ef
setenv SUBJECTS_DIR $TUTORIAL_DATA/diffusion_recons setenv TUTORIAL_DIR $TUTORIAL_DATA/diffusion_tutorial
set SUBJECTS = (Diff001 Diff002 Diff003 Diff004 Diff005 Diff006 Diff007 Diff008 Diff009 Diff010) set LESION_SUBJECTS = (LDiff006 LDiff007 LDiff008 LDiff009 LDiff010) set SUBJECTS_AND_LESION_SUBJECTS = (Diff001 Diff002 Diff003 Diff004 Diff005 LDiff006 LDiff007 LDiff008 LDiff009 LDiff010) }}}
DiffPreproc.csh
{{{#!/bin/tcsh –ef
- #
source subjects.csh
# Run dt_recon on all subjects foreach subj ($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 $cmd
end }}} Output: dwi.nii, dwi.mghdti.bvecs, dwi.mghdti.bvals, dwi-ec.nii, lowb.nii, bvecs.dat, bvals.dat, eigvec[123].nii, eigvals.nii, tensor.nii, dwirvar.nii, ivc.nii, adc.nii, radialdiff.nii, vr.nii, ra.nii, fa.nii, fa-tal.nii, register.dat.
Return to Diffusion |
AlignAnat2Diff.csh
{{{#!/bin/tcsh -ef
- #
source subjects.csh
# Loop through each subject foreach subj ($SUBJECTS)
- echo $subj set outdir = $TUTORIAL_DIR/$subj/dtrecon # For each subject's wmparc and aparc+aseg volumes resample them to diffusion space 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)
- set vol = $SUBJECTS_DIR/$subj/mri/$vol.mgz set vol2diff = ${vol:r}2diff.mgz set cmd = (mri_vol2vol --mov $outdir/lowb.nii --targ $vol --inv --interp nearest \
end }}} Output: wmparc2diff.mgz, aparc+aseg2diff.mgz.
Return to Diffusion |
DiffMasking.csh
{{{#!/bin/tcsh -ef
- #
source subjects.csh
# Loop through each subject foreach subj ($SUBJECTS)
- echo $subj set outdir = $TUTORIAL_DIR/$subj/dtrecon # Use wmparc2diff.mgz to mask out noise in the fa.nii, adc.nii, and ivc.nii volumes foreach vol (fa adc ivc)
- set cmd = (mri_mask $outdir/$vol.nii $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \
- $outdir/${vol}-masked.mgz)
- set cmd = (mri_mask $outdir/$vol.nii $SUBJECTS_DIR/$subj/mri/wmparc2diff.mgz \
end }}} Output: fa-masked.mgz, adc-masked.mgz, ivc-masked.mgz.
Return to Diffusion |
AlignAnatCVSToAvg.csh
{{{#!/bin/tcsh -ef
- #
source subjects.csh
set interp = trilin set template = $SUBJECTS_DIR/cvs_avg35/mri/norm.mgz
# Loop through each subject foreach subj ($SUBJECTS)
- echo $subj set outdir = $TUTORIAL_DIR/$subj/dtrecon set morph = $SUBJECTS_DIR/$subj/cvs/fullCVSmorph-to-avg35template.m3z
# Resample the fa-masked.mgz, adc-masked.mgz, and ivc-masked.mgz to common CVS space
- foreach vol (fa adc ivc)
- set vol = $outdir/${vol}-masked.mgz 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)
- set vol = $outdir/${vol}-masked.mgz echo $vol set outvol = ${vol:r}.ANAT+CVS-to-avg35.mgz echo $outvol set cmd = (mri_vol2vol --targ $template --m3z $morph --noDefM3zPath \
end }}} Output: fa-masked.ANAT+CVS-to-avg35.v2v.mgz, adc-masked.ANAT+CVS-to-avg35.v2v.mgz, ivc-masked.ANAT+CVS-to-avg35.v2v.mgz.
Return to Diffusion |
GroupAnalysis.csh
{{{#!/bin/tcsh -ef
source subjects.csh
set outdir = $TUTORIAL_DIR/GLM mkdir -p $outdir
# Assemble input for group analysis set type = CVS-to-avg35 # alternatively could be 'TAL' or 'MNI' set prefix = fa-masked # alternatively could be adc-masked or ivc-masked set inputfiles = ()
foreach subj ($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 }}} Output: 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.
Return to Diffusion |