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Update config files #10

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c16c4c6
Move unused config files to not_used folder
Mar 31, 2022
ea0d681
Update config_philips_cimaq.json
Mar 31, 2022
ab22033
Update config_philips_cimaq_qc.json
Mar 31, 2022
1ad43b1
Update config_siemens_cimaq.json
Mar 31, 2022
a0b4387
Update config_siemens_cimaq_iugm.json
Mar 31, 2022
51f17e8
Update config_siemens_cimaq_mc_connell_brain_imaging_centre.json
Mar 31, 2022
50304bf
Aligned config settings with revomal of unused config files
Mar 31, 2022
e84b967
Update README.md
PierreEMorin Aug 2, 2023
439316d
Update README.md
PierreEMorin Sep 1, 2023
c66bef5
Update - this is the final working version before dcm2bids 3.x
PierreEMorin Sep 15, 2023
5a55bd1
Update config_siemens_cimaq_iugm.json
PierreEMorin Sep 15, 2023
54ab9ef
Update
PierreEMorin Sep 15, 2023
3becd0a
Update config files to dcm2bids 3.x standards
PierreEMorin Sep 15, 2023
e8fe9a6
Merge branch 'master' into update_config_files_to_dcm2bids_standards
PierreEMorin Sep 15, 2023
3906d26
Merge pull request #1 from PierreEMorin/update_config_files_to_dcm2bi…
PierreEMorin Sep 15, 2023
b0bbcba
Update all configs files to dcm2bids 3.0 standards
PierreEMorin Sep 22, 2023
0e70659
Merge pull request #2 from PierreEMorin/update_config_files_to_dcm2bi…
PierreEMorin Sep 22, 2023
640c0d3
Update master
PierreEMorin Oct 4, 2023
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18 changes: 17 additions & 1 deletion README.md
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Original file line number Diff line number Diff line change
@@ -1,2 +1,18 @@
# bids_conversion
Scripts to convert data from CCNA and CIMAQ using dcm2bids
Script to help convert dicom to bids from CCNA or CIMAQ using dcm2bids
Code originaly provided by Arnaud Boré
Modified by Pierre-Emmanuel Morin

Requirements
* dcm2bids (https://github.com/UNFmontreal/Dcm2Bids)
* dcm2niix (https://github.com/rordenlab/dcm2niix)

Run (two steps)
* python3 convert_bids_ccna_cimaq.py /input_directory /output_directory mode (ccna or cimaq) > file
* bash ./file

Tips
* input_directory must contain the tarchive files (usually found in /data/$PROJECT/data/tarchive)
* the output directory will contain the untar tarchive files, the bids files (sub-PSCID/CandID) and a sub-folder containing the log and failed conversion
* tweaking of the config files will be required
* if you're splitting your input_directory into smaller ones, make sure all of a participant's files are grouped together. If not, you will have to reorganize the tree manually
12 changes: 6 additions & 6 deletions configs/config.json
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Expand Up @@ -3,23 +3,23 @@
"lowerCase": "True",
"descriptions": [
{
"dataType": "anat",
"modalityLabel": "T1w",
"datatype": "anat",
"suffix": "T1w",
"criteria": {
"SeriesDescription": "*T1*",
"ProtocolName": "*T1*"
}
},
{
"dataType": "anat",
"modalityLabel": "T1w",
"datatype": "anat",
"suffix": "T1w",
"criteria": {
"ProtocolName": "MPRAGE*"
}
},
{
"dataType": "anat",
"modalityLabel": "FLAIR",
"datatype": "anat",
"suffix": "FLAIR",
"criteria": {
"SeriesDescription": "*FLAIR*"
}
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38 changes: 20 additions & 18 deletions configs/config_ge.json
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Expand Up @@ -2,54 +2,56 @@
"lowerCase": "True",
"descriptions": [
{
"dataType": "anat",
"modalityLabel": "T2star",
"datatype": "anat",
"suffix": "T2star",
"criteria": {
"SeriesDescription": "OAx_T2star_GRE"
}
},
{
"dataType": "anat",
"modalityLabel": "T2star",
"datatype": "anat",
"suffix": "T2star",
"criteria": {
"SeriesDescription": "T2_STAR*"
}
},
{
"dataType": "func",
"modalityLabel": "bold",
"customLabels": "task-rest",
"id": "task_rest",
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-rest",
"criteria": {
"SeriesDescription": "*Connectivity*"
}
},
{
"dataType": "func",
"modalityLabel": "bold",
"customLabels": "task-rest",
"id": "task_rest",
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-rest",
"criteria": {
"SeriesDescription": "*CONNECTIVITY*"
}
},
{
"dataType": "anat",
"modalityLabel": "T2",
"datatype": "anat",
"suffix": "T2",
"criteria": {
"SeriesDescription": "*PD*T2*",
"EchoNumber": 2
"EchoNumber": 2
}
},
{
"dataType": "anat",
"modalityLabel": "PD",
"datatype": "anat",
"suffix": "PD",
"criteria": {
"SeriesDescription": "*PD*T2*",
"EchoNumber": 1
"EchoNumber": 1
}
},
{
"dataType": "dwi",
"modalityLabel": "dwi",
"datatype": "dwi",
"suffix": "dwi",
"criteria": {
"SeriesDescription": "*DTI*"
}
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50 changes: 26 additions & 24 deletions configs/config_ge_ccna.json
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Expand Up @@ -2,60 +2,62 @@
"lowerCase": "True",
"descriptions": [
{
"dataType": "anat",
"modalityLabel": "T2star",
"datatype": "anat",
"suffix": "T2star",
"criteria": {
"SeriesDescription": "OAx_T2star_GRE"
}
},
{
"dataType": "anat",
"modalityLabel": "T2star",
"datatype": "anat",
"suffix": "T2star",
"criteria": {
"SeriesDescription": "*T2_STAR*"
}
},
{
"dataType": "func",
"modalityLabel": "bold",
"customLabels": "task-rest",
"sidecarChanges": {
"TaskName": "rest"
},
"id": "task_rest",
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-rest",
"criteria": {
"SeriesDescription": "*Connectivity*"
},
"sidecar_changes": {
"TaskName": "rest"
}
},
{
"dataType": "func",
"modalityLabel": "bold",
"customLabels": "task-rest",
"sidecarChanges": {
"TaskName": "rest"
},
"id": "task_rest",
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-rest",
"criteria": {
"SeriesDescription": "*CONNECTIVITY*"
},
"sidecar_changes": {
"TaskName": "rest"
}
},
{
"dataType": "anat",
"modalityLabel": "T2w",
"datatype": "anat",
"suffix": "T2w",
"criteria": {
"SeriesDescription": "*PD*T2*",
"EchoNumber": 2
"EchoNumber": 2
}
},
{
"dataType": "anat",
"modalityLabel": "PD",
"datatype": "anat",
"suffix": "PD",
"criteria": {
"SeriesDescription": "*PD*T2*",
"EchoNumber": 1
"EchoNumber": 1
}
},
{
"dataType": "dwi",
"modalityLabel": "dwi",
"datatype": "dwi",
"suffix": "dwi",
"criteria": {
"SeriesDescription": "*DTI*"
}
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48 changes: 24 additions & 24 deletions configs/config_ge_cimaq.json
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@@ -1,70 +1,70 @@
{
"descriptions": [
{
"dataType": "anat",
"modalityLabel": "T2star",
"datatype": "anat",
"suffix": "T2star",
"criteria": {
"SeriesDescription": "OAx_T2star_GRE"
}
},
{
"dataType": "anat",
"modalityLabel": "T2star",
"datatype": "anat",
"suffix": "T2star",
"criteria": {
"SeriesDescription": "T2_STAR-RPT"
}
},
{
"dataType": "func",
"modalityLabel": "bold",
"customLabels": "task-rest",
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-rest",
"criteria": {
"SeriesDescription": "*Connectivity*"
}
},
{
"dataType": "func",
"modalityLabel": "bold",
"customLabels": "task-rest",
"datatype": "func",
"suffix": "bold",
"custom_entities": "task-rest",
"criteria": {
"SeriesDescription": "*CONNECTIVITY*"
}
},
{
"dataType": "anat",
"modalityLabel": "T2",
"datatype": "anat",
"suffix": "T2",
"criteria": {
"SeriesDescription": "*PD*T2*",
"EchoTime": 0.089792
"EchoTime": 0.089792
}
},
{
"dataType": "anat",
"modalityLabel": "T2",
"datatype": "anat",
"suffix": "T2",
"criteria": {
"SeriesDescription": "*PD*T2*",
"EchoTime": 0.086328
"EchoTime": 0.086328
}
},
{
"dataType": "anat",
"modalityLabel": "PD",
"datatype": "anat",
"suffix": "PD",
"criteria": {
"SeriesDescription": "*PD*T2*",
"EchoTime": 0.011224
"EchoTime": 0.011224
}
},
{
"dataType": "anat",
"modalityLabel": "PD",
"datatype": "anat",
"suffix": "PD",
"criteria": {
"SeriesDescription": "*PD*T2*",
"EchoTime": 0.009592
"EchoTime": 0.009592
}
},
{
"dataType": "dwi",
"modalityLabel": "dwi",
"datatype": "dwi",
"suffix": "dwi",
"criteria": {
"SeriesDescription": "*DTI*"
}
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6 changes: 3 additions & 3 deletions configs/config_lower.json
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Expand Up @@ -3,11 +3,11 @@
"lowerCase": "True",
"descriptions": [
{
"dataType": "anat",
"modalityLabel": "T2star",
"datatype": "anat",
"suffix": "T2star",
"criteria": {
"SeriesDescription": "*T2*STAR*",
"ImageType": ["M"]
"ImageType": ["M"]
}
}
]
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