#!/bin/bash
## the goal of this script is to convert classic DICOM files into BIDS format using heudiconv
## Loic Daumail - 03232023
##Code adapted from tutorial https://reproducibility.stanford.edu/bids-tutorial-series-part-2a/
##requirements: Docker, heudiconv
##STEP 0: install the heudiconv image
docker pull nipy/heudiconv:latest

## STEP #1 This command will output a hidden .heudiconv folder within the Nifti folder that contains a 
## dicominfo .tsv file used to construct the heuristic file.

docker run --rm -it -v /Users/tong_processor/Desktop/Loic/phantom_mri/data:/base nipy/heudiconv:latest -d /base/gstudy_downloads/{subject}/DICOM-Classic/*.DCM -o /base/BIDS_conv/Nifti/ -f convertall -s M017 F019 -ss 001 -c none --overwrite

## Once you reached this stage, modify: 1) dicominfo.tsv file to add descriptions of the task 
## for each run 
## 2) the heuristic file to make specifications on
## the way you want to organize the data and which dicom file based on the info in dicominfo.tsv file 
## and run you want to convert
## follow this tutorial: http://nipy.org/workshops/2017-03-boston/lectures/bids-heudiconv/#21

## STEP #2 move the heuristic.py file to a Nifti/${subj}/code folder
SUB="M017" #we only need the heuristic file of one subject that we will use for all subjects
SES=(001)
unset subj
for subj in $SUB; do
for sess in $SES; do
mkdir /Users/tong_processor/Desktop/Loic/phantom_mri/data/BIDS_conv/Nifti/code
cp /Users/tong_processor/Desktop/Loic/phantom_mri/data/BIDS_conv/Nifti/.heudiconv/${subj}/${sess}/info/heuristic.py /Users/tong_processor/Desktop/Loic/phantom_mri/data/BIDS_conv/Nifti/code
done
done



## STEP #3 run heudiconv again, with dcm2niix

docker run --rm -it -v /Users/tong_processor/Desktop/Loic/phantom_mri/data/:/base nipy/heudiconv:latest -d /base/gstudy_downloads/{subject}/DICOM-Classic/*.DCM -o /base/BIDS_conv/Nifti -f /base/BIDS_conv/Nifti/code/heuristic.py -s M017 F019 -ss 001 -c dcm2niix -b --overwrite


### STEP 4: Test the validity of your dataset: http://bids-standard.github.io/bids-validator/