├── README.md
└── BIDS_single_ses.sh


/README.md:
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 1 | # BIDS-Auto-Organization
 2 | 
 3 | Automatical organization bash script for your MRI images into BIDS format, temporarily available for T1, dwi and restfmri single session modalities.
 4 | 
 5 | ## Raw DICOM file structure
 6 | 
 7 | * Dataset/<br>
 8 |   * Dicom/<br>
 9 |     * anat/<br>
10 |       * 001/<br>
11 |       * 002/<br> 
12 |       * ...
13 |     * dwi/<br>
14 |       * 001/<br>
15 |       * 002/<br>
16 |       * ...<br>
17 |     * rest/<br>
18 |       * 001/<br>
19 |       * 002/<br>
20 |       * ...<br>
21 | 
22 | ## Dependencies
23 | 
24 | The bash script requires *dcm2niix* and *jo* to be installed in Ubuntu as follows:
25 | 
26 | ```Bash
27 | apt-get install dcm2niix
28 | apt-get install jo
29 | 


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/BIDS_single_ses.sh:
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 1 | #!/bin/bash
 2 | 
 3 | set -e
 4 | 
 5 | # setting your dataset path here
 6 | homedir=~/Desktop/BIDS_test
 7 | 
 8 | dcmdir=${homedir}/Dicom
 9 | niidir=${homedir}/Nifti
10 | 
11 | if [ -d ${niidir} ];then
12 | 	rm -r ${niidir}
13 | fi
14 | 
15 | mkdir ${niidir}
16 | 
17 | 
18 | jo -p "Name"="KCL Multi-site schizophrenia dataset - Graph Convolutional Network" "BIDSVersion"="1.0.2" >> ${niidir}/dataset_description.json
19 | 
20 | if [ -d ${dcmdir}/anat ];then
21 | 	for subj in `ls ${dcmdir}/anat/`
22 | 		do
23 | 		echo "processing anatomical images of $subj"
24 | 		mkdir -p ${niidir}/sub-${subj}/anat
25 | 		dcm2niix -z n -b y -o ${niidir}/sub-${subj}/anat -f ${subj}_%f_%p ${dcmdir}/anat/${subj}
26 | 		cd ${niidir}/sub-${subj}/anat
27 | 		mv *.json sub-${subj}_T1w.json
28 | 		mv *.nii sub-${subj}_T1w.nii
29 | 		done
30 | fi
31 | 
32 | if [ -d ${dcmdir}/dwi ];then
33 | 	for subj in `ls ${dcmdir}/dwi/`
34 | 		do
35 | 		echo "processing diffusion images of $subj"
36 | 		mkdir -p ${niidir}/sub-${subj}/dwi
37 | 		dcm2niix -z n -b y -o ${niidir}/sub-${subj}/dwi -f ${subj}_%f_%p ${dcmdir}/dwi/${subj}
38 | 		cd ${niidir}/sub-${subj}/dwi
39 | 		mv *.json sub-${subj}_dwi.json
40 | 		mv *.nii sub-${subj}_dwi.nii
41 | 		mv *.bval sub-${subj}_dwi.bval
42 | 		mv *.bvec sub-${subj}_dwi.bvec
43 | 		done
44 | fi
45 | 
46 | if [ -d ${dcmdir}/rest ];then 
47 | 	for subj in `ls ${dcmdir}/rest/`
48 | 		do
49 | 		echo "processing resting-state functional images of $subj"
50 | 		mkdir -p ${niidir}/sub-${subj}/func
51 | 		dcm2niix -z n -b y -o ${niidir}/sub-${subj}/func -f ${subj}_%f_%p ${dcmdir}/rest/${subj}
52 | 		cd ${niidir}/sub-${subj}/func
53 | 		mv *.json sub-${subj}_task-rest_bold.json
54 | 		mv *.nii sub-${subj}_task-rest_bold.nii
55 | 		for funcjson in `ls *.json`
56 | 			do
57 | 			taskexist=`cat ${funcjson} | jq '.TaskName'`
58 | 			if [ "$taskexist" == "null" ]; then
59 | 				jsonname="${funcjson%.*}"
60 | 				taskfield=$(echo $jsonname | cut -d '_' -f2 | cut -d '-' -f2)
61 | 				jq '. |= . + {"TaskName":"'${taskfield}'"}' ${funcjson} > tasknameadd.json
62 | 				rm ${funcjson}
63 | 				mv tasknameadd.json ${funcjson}
64 | 				echo "TaskName was added to ${jsonname} and matches the tasklabel in the filename"
65 | 			else
66 | 				Taskquotevalue=$(jq '.TaskName' ${funcjson})
67 | 				Taskvalue=$(echo $Taskquotevalue | cut -d '"' -f2)	
68 | 				jsonname="${funcjson%.*}"
69 | 				taskfield=$(echo $jsonname | cut -d '_' -f2 | cut -d '-' -f2)
70 | 				if [ $Taskvalue == $taskfield ]; then
71 | 					echo "TaskName is present and matches the tasklabel in the filename"
72 | 				else
73 | 					echo "TaskName and tasklabel do not match"
74 | 				fi
75 | 			fi
76 | 			done
77 | 		done
78 | fi
79 | 
80 | 
81 | 
82 | 
83 | 
84 | 


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