MRtrix pipeline_3

#! /bin/bash

# mrtrix_roi.sh 

# usage: mrtrix_roi.sh foldername

f=${1}

echo FOLDER IS $f

cd ${f}

pwd

echo # CURRENT WORKING DIRECTORY IS $f

echo # -------------------------<T2 imaging process>------------------------------

echo # Step 1. dwidenoising of T2 images 

dwidenoise dwi.nii.gz dwi_denoised.nii.gz -nthread 4 -force

echo # step 2. dwipreproc 

dwipreproc -rpe_none -fslgrad bvecs bvals PA dwi_denoised.nii.gz dti_preproc.nii.gz -force

echo # Step 2. dwi2mask mr_mask.mif

dwi2mask -fslgrad bvecs bvals dti_preproc.nii.gz mask.nii.gz -force  

echo # Step 3. dwibiascorrect 

dwibiascorrect dti_preproc.nii.gz dwi_denoised_biascorr.nii.gz -fsl -mask mask.nii.gz -fslgrad bvecs bvals -force 

echo # Step 4. b0 image generation

dwiextract -fslgrad bvecs bvals dwi_denoised_biascorr.nii.gz b0.nii.gz -bzero  

echo # Step 5. bet2 b0 image 

bet2 b0 b0_bet2 -o -m -f 0.3

# echo # Step 10. # Brain registration

fslmaths b0_bet2_mask.nii.gz -dilM b0_brain_mask_dil

cp b0_brain_mask_dil.nii.gz ${f}/recon_all/mri

echo # Step 6. Response function estimation 

dwi2response tournier -fslgrad bvecs bvals -mask mask.nii.gz -voxels mr_voxels.nii.gz dwi_denoised_biascorr.nii.gz response_tournier.txt -force

# echo # Step 7. Fixel-Based Analysis (FBA) %% upsampling

# mrresize dwi_denoised_biascorr.nii.gz -scale 2.0 dwi_denoised_biascorr_upsampled.nii.gz -force

# dwi2mask -fslgrad bvecs bvals dwi_denoised_biascorr_upsampled.nii.gz upsampled_mask.nii.gz -force

echo # -------------------------<T1 imaging process>------------------------------

cd ${f}/recon_all/mri

echo # Step 8. # mri_convert brain.mgz and aparc+aseg.mgz

mri_convert brain.mgz brain.nii.gz && mri_convert aparc+aseg.mgz aparc+aseg.nii.gz

echo # Step 9. # flip4fsl brain.nii.gz and aparc+aseg.nii.gz

flip4fsl brain.nii.gz brain_flip.nii.gz && flip4fsl aparc+aseg.nii.gz aparc+aseg_flip.nii.gz

flip4fsl ../../b0_bet2.nii.gz b0_brain_flip.nii.gz

echo # Step 10. # fsl_reg.

fsl_reg brain_flip.nii.gz b0_brain_flip.nii.gz str2diff -e -fnirt "--refmask=b0_brain_mask_dil.nii.gz"

applywarp -i aparc+aseg_flip.nii.gz -r b0_brain_flip.nii.gz -o aparc+aseg_flip_warped2diff.nii.gz -w str2diff_warp --interp=nn

echo # Step 11. # Generation of tissue-segmented image for "anatomically constrained tractography"

5ttgen fsl brain_flip.nii.gz ../../mr_5TT.nii.gz -premasked -force

echo # Step 12. # labelconvert mr_5TT.nii.gz $FREESURFER_HOME/FreeSurferColorLUT.txt ~/mrtrix3/src/connectome/tables/fs_default.txt mr_parcels.nii.gz

labelconvert aparc+aseg_flip_warped2diff.nii.gz $FREESURFER_HOME/FreeSurferColorLUT.txt ~/mrtrix3/src/connectome/tables/fs_default.txt ../../mr_parcels.nii.gz -force

echo # ------------------------<ROI imaging process>------------------------------

cd ../../

echo # Step 13. dwi2fod

dwi2fod csd -fslgrad bvecs bvals dwi_denoised_biascorr.nii.gz response_tournier.txt dwi_denoised_biascorr_fod.nii.gz -force

if [ ! -e ${f}/dir ]; then

mkdir ${f}/roi

fi

echo # Step 14. Make_ROI roi 36 43 ; # 36-Left thalamus, 43-Right Thalamus

echo MAKING ROI FOR ${roi}

for roi in 36 43

do

fslmaths mr_parcels.nii.gz -thr ${roi} -uthr ${roi} -bin ${f}/roi/${roi} && fslmaths ${f}/roi/${roi} -dilM ${f}/roi/${roi}_dil

# fslmaths mr_parcels.nii.gz -thr 36 -uthr 36 -bin ./roi/36 && fslmaths ./roi/36 -dilM ./roi/36_dil

# fslmaths mr_parcels.nii.gz -thr 43 -uthr 43 -bin ./roi/43 && fslmaths ./roi/43 -dilM ./roi/43_dil

done

fslmaths ./roi/36.nii.gz -add ./roi/43.nii.gz ./roi/36_43.nii.gz && fslmaths ./roi/36_dil.nii.gz -add ./roi/43_dil.nii.gz ./roi/36_43.dil.nii.gz

echo # Step 15. Tckgen

tckgen dwi_denoised_biascorr_fod.nii.gz dwi_denoised_biascorr_upsampled_fod_80000.tck -seed_image ./roi/36_43.dil.nii.gz -mask mask.nii.gz -number 80000 -maxlength 250 -nthreads 4 -force

# tckgen dwi_denoised_biascorr_fod.nii.gz dwi_denoised_biascorr_upsampled_fod_80000_Lt_thalamus.tck -seed_image $f/roi/36.dil.nii.gz -mask mask.nii.gz -number 80000 -maxlength 250 -nthreads 4

# tckgen dwi_denoised_biascorr_fod.nii.gz dwi_denoised_biascorr_upsampled_fod_80000_Rt_thalamus.tck -seed_image $f/roi/43.dil.nii.gz -mask mask.nii.gz -number 80000 -maxlength 250 -nthreads 4

# tckgen dti_preproc_FOD.nii tracks_100M_iFOD2.tck -seed_image dti_preproc.nii -mask dilate_mask.nii -fslgrad bvec bval -algorithm iFOD2 -number 1000000000 -nthreads 4