From 6098f9e66e94b47ba75dfbc81345f2cc32abc713 Mon Sep 17 00:00:00 2001
From: Tashrif Billah <35086881+tashrifbillah@users.noreply.github.com>
Date: Sat, 6 Apr 2024 16:20:53 -0400
Subject: [PATCH] remove obsolete script workflows/synb0_eddy.sh

---
 workflows/synb0_eddy.sh | 155 ----------------------------------------
 1 file changed, 155 deletions(-)
 delete mode 100755 workflows/synb0_eddy.sh

diff --git a/workflows/synb0_eddy.sh b/workflows/synb0_eddy.sh
deleted file mode 100755
index a4bf611..0000000
--- a/workflows/synb0_eddy.sh
+++ /dev/null
@@ -1,155 +0,0 @@
-#!/bin/bash
-
-# for time profiling
-date
-START_TIME=$(date +%s)
-
-# User will edit only this block =========================================================
-caselist=$1
-s=01
-dir=80
-acq=AP
-BIDS_DATA_DIR=/data/pnl/Collaborators/CMA/mtsintou/Emotion/rawdata
-DWI_TEMPLATE=sub-*/ses-*/dwi/sub-*_ses-*_acq-${acq}_dir-${dir}_dwi.nii.gz
-INDEX=/data/pnl/Collaborators/CMA/mtsintou/Emotion/derivatives/index.txt
-ACQPARAMS=/data/pnl/Collaborators/CMA/mtsintou/Emotion/derivatives/acqparams.txt
-LUIGI_CONFIG_PATH=/data/pnl/soft/pnlpipe3/luigi-pnlpipe/params/cte/cnn_dwi_mask_params.cfg
-# ========================================================================================
-
-
-source /rfanfs/pnl-zorro/software/pnlpipe3/bashrc3-gpu
-NEW_SOFT_DIR=/rfanfs/pnl-zorro/software/pnlpipe3/
-
-
-# for a caselist, this script must be run in a for loop
-# https://github.com/pnlbwh/luigi-pnlpipe/wiki/Run-HCP-pipeline-on-PNL-GPU-machines-in-a-parallel-manner
-if [ -f $caselist ]
-then
-    c=`head -${LSB_JOBINDEX} $caselist | tail -1`
-
-    NUM_GPUS=`nvidia-smi -L | wc -l`
-    export CUDA_VISIBLE_DEVICES=$(( ${LSB_JOBINDEX}%${NUM_GPUS} ))
-else
-    c=$caselist
-fi
-
-
-echo "1. run Luigi pipeline and prepare DWI for synb0 container"
-export LUIGI_CONFIG_PATH
-/rfanfs/pnl-zorro/software/pnlpipe3/luigi-pnlpipe/exec/ExecuteTask --task CnnMask \
---bids-data-dir $BIDS_DATA_DIR \
---dwi-template "$DWI_TEMPLATE" \
--c ${c} -s ${s}
-# double quotes around $DWI_TEMPLATE are mandatory
-
-
-
-DERIVATIVES=$(dirname $BIDS_DATA_DIR)/derivatives/pnlpipe/
-SES_FOLDER=$DERIVATIVES/sub-${c}/ses-${s}
-pushd .
-cd $SES_FOLDER
-mkdir -p INPUTS OUTPUTS
-
-
-if [ ! -z `ls $SES_FOLDER/dwi/*_desc-XcUnEdEp_dwi.nii.gz` ]
-then
-    echo $c was processed before
-    exit
-fi
-
-
-echo "2. prepare b0 and T1 for synb0 container"
-_unring_prefix=`ls dwi/sub-${c}_ses-${s}_*desc-XcUn_dwi.nii.gz`
-unring_prefix=${_unring_prefix//.nii.gz}
-unring_mask=`ls dwi/sub-${c}_ses-${s}_*desc-dwiXcUnCNN_mask.nii.gz`
-if [ ! -f INPUTS/b0.nii.gz ]
-then
-    fslmaths ${unring_prefix}.nii.gz -mul $unring_mask ${unring_prefix}.nii.gz && \
-    bse.py -i ${unring_prefix}.nii.gz -o INPUTS/b0.nii.gz
-fi
-
-T1=anat/sub-${c}_ses-${s}_desc-XcMaN4_T1w.nii.gz
-if [ -f $T1 ]
-then
-    cp $T1 INPUTS/T1.nii.gz
-else
-    echo "Run structural pipeline first:"
-    echo "https://github.com/pnlbwh/luigi-pnlpipe/blob/hcp/docs/Process_DIAGNOSE-CTE_data.md#structural-pipeline"
-fi
-
-cp $ACQPARAMS INPUTS/
-cp $INDEX INPUTS/
-
-
-echo "3. run synb0 container"
-TMPDIR=$HOME/tmp/
-mkdir -p $TMPDIR
-if [ ! -f OUTPUTS/b0_all_topup.nii.gz ]
-then
-    TMPDIR=$TMPDIR \
-    singularity run -B INPUTS/:/INPUTS -B OUTPUTS/:/OUTPUTS \
-    -B ${NEW_SOFT_DIR}/fs7.1.0/license.txt:/extra/freesurfer/license.txt \
-    ${NEW_SOFT_DIR}/containers/synb0-disco_v3.0.sif --stripped
-fi
-
-echo "4. create mask of topup (synb0) corrected b0"
-# CNN method
-_caselist=$(mktemp --suffix=.txt)
-realpath OUTPUTS/b0_all_topup.nii.gz > $_caselist
-echo "0 0" > OUTPUTS/b0_all_topup.bval
-dwi_masking.py -i $_caselist -f ${NEW_SOFT_DIR}/CNN-Diffusion-MRIBrain-Segmentation/model_folder
-mask=`ls OUTPUTS/*-multi_BrainMask.nii.gz`
-rm $_caselist
-
-if [ -z $mask ]
-then
-    echo topup mask creation failed
-    exit 1
-fi
-
-
-eddy_out=OUTPUTS/sub-${c}_ses-${s}_dir-${dir}_desc-XcUnEdEp_dwi
-# initial guess was masking the --imain would improve quality of eddy corrected DWI
-# however, the b0_all_topup_mask is underinclusive
-# so it only crops off the frontal distortion
-# so omit masking at this step
-# fslmaths ${unring_prefix}.nii.gz -mul $mask ${unring_prefix}.nii.gz
-echo "5. run eddy_cuda"
-eddy_cuda \
-  --imain=${unring_prefix}.nii.gz \
-  --bvecs=${unring_prefix}.bvec \
-  --bvals=${unring_prefix}.bval \
-  --mask=$mask \
-  --topup=OUTPUTS/topup \
-  --acqp=INPUTS/acqparams.txt \
-  --index=INPUTS/index.txt \
-  --repol --data_is_shelled --verbose \
-  --out=$eddy_out || { exit 1; }
-
-
-
-echo "6. organize outputs"
-# provide masked eddy_out for clarity, quality, and convenience
-fslmaths ${eddy_out}.nii.gz -mul $mask ${eddy_out}.nii.gz
-
-bids_prefix=dwi/sub-${c}_ses-${s}_dir-${dir}_desc-XcUnEdEp_dwi
-mv ${eddy_out}.nii.gz ${bids_prefix}.nii.gz
-mv ${eddy_out}.eddy_rotated_bvecs ${bids_prefix}.bvec
-cp ${unring_prefix}.bval ${bids_prefix}.bval
-
-mask_prefix=${bids_prefix//_dwi/}
-mask_prefix=${mask_prefix//XcUn/dwiXcUn}
-mv $mask ${mask_prefix}_mask.nii.gz
-mv OUTPUTS/b0_all_topup_bse.nii.gz ${mask_prefix}_bse.nii.gz
-
-
-
-echo "Luigi-SynB0-Eddy pipeline has completed"
-echo "See outputs at $PWD/dwi/"
-
-popd
-
-# for time profiling
-date
-ELAPSED_TIME=$(($(date +%s) - $START_TIME))
-echo "Elapsed time: $(($ELAPSED_TIME/60)) min $(($ELAPSED_TIME%60)) sec"