trac_2_tckgen

#!/bin/bash

list=$1
threads=128
#threadsX2=$((${threads}*2))

adni=/lus/theta-fs0/projects/AD_Brain_Imaging/anal/adni

CMD_batch=/lus/theta-fs0/projects/AD_Brain_Imaging/anal/adni/adni_on_alcf/job/cmd2.batch.trac.${list}
rm -rf $CMD_batch

#######################################################################################################
cat<<EOC >$CMD_batch
#!/bin/bash
#COBALT -t 360
#COBALT -n 250
#COBALT --attrs mcdram=cache:numa=quad
#COBALT -A AD_Brain_Imaging
echo start............................................
#export n_nodes=$COBALT_JOBSIZE
#export n_mpi_ranks_per_node=202
#export n_mpi_ranks=202
#export n_openmp_threads_per_rank=64
#export n_hyperthreads_per_core=4
EOC

#######################################################################################################

i=1

for s in `cat /lus/theta-fs0/projects/AD_Brain_Imaging/anal/adni/fs/\$list`
do
#s=`echo $SUBJECT | egrep -o '[0-9]{8}'`
CMD=/lus/theta-fs0/projects/AD_Brain_Imaging/anal/adni/adni_on_alcf/job/cmd2.trac.${s}
rm -rf $CMD

SUBJECT=${s}
rm ./job/log.tckgen.${SUBJECT}

#echo ${SUBJECT}

cat<<EOC >$CMD
#!/bin/bash
source ~/.bashrc
workingdir=/lus/theta-fs0/projects/AD_Brain_Imaging/anal/adni/fs/${SUBJECT}/dmri2
echo \$workingdir
mkdir \$workingdir
cd \$workingdir
pwd
ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=128
echo beginning of the code \`date +"%Y-%m-%d/%H:%M:%S"\`

#############################################################MRTRIX########################
FREESURFER_HOME=/lus/theta-fs0/projects/AD_Brain_Imaging/app/freesurfer
source /lus/theta-fs0/projects/AD_Brain_Imaging/app/freesurfer/FreeSurferEnv.sh


##############################PREPROCESSING####################################
#    mrconvert dti.nii.gz -force mr_dwi.mif.gz -fslgrad dti.bvec dti.bval -datatype float32 -stride 0,0,0,1 -nthreads 128
#    sleep 0.2
    
#    dwidenoise mr_dwi.mif.gz -force mr_dwi_denoised.mif.gz -nthreads 128
#    sleep 0.2
    
#    dwipreproc -rpe_none -pe_dir PA mr_dwi_denoised.mif.gz -force mr_dwi_denoised_preproc.mif.gz -rpe_none -nthreads 128
#    sleep 0.2
    
#    dwi2mask mr_dwi_denoised_preproc.mif.gz - -nthreads 128 | maskfilter - erode -npass 7 -force mr_eroded_mask.mif.gz -nthreads 128
#    sleep 0.2
    
#    dwibiascorrect mr_dwi_denoised_preproc.mif.gz -force mr_dwi_denoised_preproc_biasCorr.mif.gz -ants -mask mr_eroded_mask.mif.gz -fslgrad dti.bvec dti.bval -nthreads 128
#    sleep 0.2
    
#    dwiextract mr_dwi_denoised_preproc_biasCorr.mif.gz - -bzero -nthreads 128 | mrmath - mean -force mr_meanb0.mif.gz -axis 3 -nthreads 128
#    sleep 0.2
    
#    mrresize mr_dwi_denoised_preproc_biasCorr.mif.gz -scale 2.0 -force mr_dwi_denoised_preproc_biasCorr_upsample.mif.gz -nthreads 128
#	   sleep 0.2
    
#    dwi2response dhollander -mask mr_eroded_mask.mif.gz -voxels mr_voxels_eroded.mif.gz mr_dwi_denoised_preproc_biasCorr.mif.gz response_wm.txt response_gm.txt response_csf.txt -force -nthreads 128
#    sleep 0.2
    
#% make sure to use "DILATED MASK" for FOD generation
#    dwi2mask mr_dwi_denoised_preproc_biasCorr.mif.gz - -nthreads 128 | maskfilter - dilate -npass 5 -force mr_dilate_mask.mif.gz -nthreads 128
#   	sleep 0.2
    
#    dwi2fod msmt_csd mr_dwi_denoised_preproc_biasCorr.mif.gz response_wm.txt WM_FODs.mif.gz response_gm.txt gm.mif.gz response_csf.txt csf.mif.gz -mask mr_dilate_mask.mif.gz -force -nthreads 128
#   	sleep 0.2
    
#    mrconvert WM_FODs.mif.gz - -coord 3 0 -nthreads 128 | mrcat csf.mif.gz gm.mif.gz - tissueRGB.mif.gz -axis 3 -nthreads 128
#    sleep 0.2
#################################################################################
echo preprocessing is done \`date +"%Y-%m-%d/%H:%M:%S"\`

SUBJECT=${s}
cd /lus/theta-fs0/projects/AD_Brain_Imaging/anal/adni/fs/\${SUBJECT}/dmri2
mkdir xfm
### flirt 
echo *****NOW GENERATING ANAT2DIFF.FLT.MAT *****
mri_convert ../mri/brain.mgz brain_anat_orig.nii.gz
sleep 0.2
orientLAS brain_anat_orig.nii.gz brain_anat.nii.gz
sleep 0.2
mrconvert mr_meanb0.mif.gz mr_meanb0.nii.gz -force
sleep 0.2
bet2 mr_meanb0.nii.gz mr_meanb0_brain.nii.gz
sleep 0.2
flirt -in brain_anat.nii.gz -ref mr_meanb0_brain.nii.gz -out brain_anat2diff -omat anat2diff.flt.mat -v
sleep 0.2
### 5TTGEN#########################################
echo ***** NOW 5TTGEN *****
mri_convert ../mri/T1.mgz T1.nii.gz
sleep 0.2
orientLAS T1.nii.gz T1_flip.nii.gz
sleep 0.2
flirt -in T1_flip.nii.gz -out T1_2diff_flt.nii.gz -ref mr_meanb0.nii.gz -applyxfm -init anat2diff.flt.mat -v
sleep 0.2
 
#5ttgen fsl brain_anat.nii.gz 5tt_from_brain_anat_test.nii.gz -nocrop 
5ttgen freesurfer aparc+aseg_flip.nii.gz 5tt_freesurfer.nii.gz -nocrop -sgm_amyg_hipp -force -nthreads 128
sleep 0.2

flirt -in 5tt_freesurfer.nii.gz -ref mr_meanb0_brain.nii.gz -out 5tt_freesurfer2diff -applyxfm -init anat2diff.flt.mat -v
sleep 0.2

mrconvert 5tt_freesurfer2diff.nii.gz 5tt_freesurfer2diff.mif.gz -force
sleep 0.2

cp 5tt_freesurfer2diff.nii.gz 5tt2.nii.gz
sleep 0.2

cp 5tt_freesurfer2diff.mif.gz 5tt2.mif.gz
sleep 0.2

5tt2gmwmi 5tt2.mif.gz -force 5tt2_gmwmi_mask.mif.gz -force -nthreads 128
sleep 0.2

dwi2fod msmt_csd mr_dwi_denoised_preproc_biasCorr.mif.gz response_wm.txt WM_FODs.mif.gz response_gm.txt gm.mif.gz response_csf.txt csf.mif.gz -mask mr_dilate_mask.mif.gz -force -nthreads 128
sleep 0.2

### APARC+ASEG to diff
for im in aparc+aseg aparc.a2009s+aseg
do
   echo ****NOW CONVERTING MGZ TO NII
   mri_convert ../mri/\${im}.mgz \${im}.nii.gz
   sleep 0.2
   
   echo ****FLIPING FOR FSL
   orientLAS \${im}.nii.gz \${im}_flip.nii.gz
   sleep 0.2
   
   echo ****NOW FLIRTING
   flirt -in \${im}_flip.nii.gz -out \${im}_2_diff_flt.nii.gz -ref mr_meanb0_brain.nii.gz -applyxfm -init anat2diff.flt.mat -interp nearestneighbour
   sleep 0.2
done
### labelconvert for aparc+aseg and aparc.a2009+aseg
labelconvert aparc+aseg_2_diff_flt.nii.gz $FREESURFER_HOME/FreeSurferColorLUT.txt /lus/theta-fs0/projects/AD_Brain_Imaging//app/mrtrix3/share/mrtrix3/labelconvert/fs_default.txt nodes_aparc+aseg2.mif.gz -force
sleep 0.2

labelconvert aparc.a2009s+aseg_2_diff_flt.nii.gz $FREESURFER_HOME/FreeSurferColorLUT.txt /lus/theta-fs0/projects/AD_Brain_Imaging//app/mrtrix3/share/mrtrix3/labelconvert/fs_a2009s.txt nodes_aparc.a2009s+aseg2.mif.gz -force
sleep 0.2

echo now ready for tckgen \`date +"%Y-%m-%d/%H:%M:%S"\`

### tckgen
if [ -e mr_track_10M_SIFT2_${s}.tck ]; then
tracknum=\`tckinfo mr_track_10M_SIFT2_${s}.tck | grep max_num_tracks | grep -o 10000000\`
  if [ \$tracknum != 10000000 ]; then
  tckgen WM_FODs.mif.gz /tmp/mr_track_20M2_${s}.tck -act 5tt2.mif.gz -backtrack -crop_at_gmwmi -seed_dynamic WM_FODs.mif.gz -maxlength 250 -minlength 30 -select 20M -force -nthreads 128
  sleep 0.2
  
  tcksift -act 5tt2.mif.gz /tmp/mr_track_20M2_${s}.tck WM_FODs.mif.gz mr_track_10M_SIFT2_${s}.tck -term_number 10M -force -nthreads 128 && echo 'sift done'*******
  sleep 0.2
  else 
  echo 'sift done'*******
  fi
else  
tckgen WM_FODs.mif.gz /tmp/mr_track_20M2_${s}.tck -act 5tt2.mif.gz -backtrack -crop_at_gmwmi -seed_dynamic WM_FODs.mif.gz -maxlength 250 -minlength 30 -select 20M -force -nthreads 128 
sleep 0.2

tcksift -act 5tt2.mif.gz /tmp/mr_track_20M2_${s}.tck WM_FODs.mif.gz mr_track_10M_SIFT2_${s}.tck -term_number 10M -force -nthreads 128 && echo 'sift done'*******
sleep 0.2
fi
#### tck2connectome
for im in aparc+aseg aparc.a2009s+aseg
do
tck2connectome -force -zero_diagonal mr_track_10M_SIFT2_${s}.tck nodes_\${im}2.mif.gz mr_sift_10M_connectome_\${im}_count.csv -nthreads 128
tck2connectome -force -zero_diagonal -scale_length -stat_edge mean mr_track_10M_SIFT2_${s}.tck nodes_\${im}2.mif.gz mr_sift_10M_connectome_\${im}_length.csv -nthreads 128 
tck2connectome -force -zero_diagonal -scale_invnodevol mr_track_10M_SIFT2_${s}.tck nodes_\${im}2.mif.gz mr_sift_10M_connectome_\${im}_volumeadj.csv -nthreads 128
done
#############################################################MRTRIX########################
EOC

chmod +x $CMD




echo "aprun -n 1 -N 1 -d 128 -j 2 -cc depth -e OMP_NUM_THREADS=128 $CMD > ./job/log.tckgen.${SUBJECT} 2>&1 &">>$CMD_batch 
echo "sleep 1">>$CMD_batch
i=$(($i+1))
echo $i
#echo "execute $CMD_sub"

done

echo "wait" >> $CMD_batch
### batch submission

echo $CMD_batch
chmod +x $CMD_batch
echo "qsub $CMD_batch"