From c16c4c67a5586a899bfa96a4dc6dc1e11b2bc8d5 Mon Sep 17 00:00:00 2001 From: Pierre-Emmanuel Morin Date: Thu, 31 Mar 2022 13:25:22 -0400 Subject: [PATCH 01/15] Move unused config files to not_used folder --- configs/{ => not_used}/config_philips_cimaq_ubc.json | 0 .../config_siemens_cimaq_the_ottawa_hospital_civic.json | 0 .../config_siemens_cimaq_the_ottawa_hospital_civic_campus.json | 0 3 files changed, 0 insertions(+), 0 deletions(-) rename configs/{ => not_used}/config_philips_cimaq_ubc.json (100%) rename configs/{ => not_used}/config_siemens_cimaq_the_ottawa_hospital_civic.json (100%) rename configs/{ => not_used}/config_siemens_cimaq_the_ottawa_hospital_civic_campus.json (100%) diff --git a/configs/config_philips_cimaq_ubc.json b/configs/not_used/config_philips_cimaq_ubc.json similarity index 100% rename from configs/config_philips_cimaq_ubc.json rename to configs/not_used/config_philips_cimaq_ubc.json diff --git a/configs/config_siemens_cimaq_the_ottawa_hospital_civic.json b/configs/not_used/config_siemens_cimaq_the_ottawa_hospital_civic.json similarity index 100% rename from configs/config_siemens_cimaq_the_ottawa_hospital_civic.json rename to configs/not_used/config_siemens_cimaq_the_ottawa_hospital_civic.json diff --git a/configs/config_siemens_cimaq_the_ottawa_hospital_civic_campus.json b/configs/not_used/config_siemens_cimaq_the_ottawa_hospital_civic_campus.json similarity index 100% rename from configs/config_siemens_cimaq_the_ottawa_hospital_civic_campus.json rename to configs/not_used/config_siemens_cimaq_the_ottawa_hospital_civic_campus.json From ea0d6811575e524695447d1f528eecf9dabaa545 Mon Sep 17 00:00:00 2001 From: Pierre-Emmanuel Morin Date: Thu, 31 Mar 2022 13:37:56 -0400 Subject: [PATCH 02/15] Update config_philips_cimaq.json Added some missing configs --- configs/config_philips_cimaq.json | 48 ++++++++++++++++++++++++++++++- 1 file changed, 47 insertions(+), 1 deletion(-) diff --git a/configs/config_philips_cimaq.json b/configs/config_philips_cimaq.json index 99fab9b..634dda2 100644 --- a/configs/config_philips_cimaq.json +++ b/configs/config_philips_cimaq.json @@ -1,6 +1,21 @@ { "lowerCase": "True", "descriptions": [ + { + "dataType": "anat", + "modalityLabel": "T1w", + "criteria": { + "SeriesDescription": "T1*", + "ProtocolName": "T1*" + } + }, + { + "dataType": "anat", + "modalityLabel": "T1w", + "criteria": { + "ProtocolName": "3D*MPR*" + } + }, { "dataType": "anat", "modalityLabel": "T2star", @@ -47,6 +62,13 @@ "EchoTime": 0.0125 } }, + { + "dataType": "anat", + "modalityLabel": "FLAIR", + "criteria": { + "SeriesDescription": "*FLAIR*" + } + }, { "dataType": "func", "modalityLabel": "bold", @@ -124,7 +146,31 @@ "intendedFor": 7, "criteria": { "SeriesDescription": "B0_map", - "ImageType": ["ORIGINAL", "PRIMARY", "B0", "MAP", "B0", "UNSPECIFIED"] + "ImageType": ["ORIGINAL", "PRIMARY", "B0", "MAP", "B0", "UNSPECIFIED"] + }, + "sidecarChanges": { + "Units": "Hz" + } + }, + { + "dataType": "fmap", + "modalityLabel": "fieldmap", + "intendedFor": 7, + "criteria": { + "SeriesDescription": "B0 map", + "ImageType": ["ORIGINAL", "PRIMARY", "B0 MAP", "B0", "UNSPECIFIED", "FIELDMAPHZ"] + }, + "sidecarChanges": { + "Units": "Hz" + } + }, + { + "dataType": "fmap", + "modalityLabel": "fieldmap", + "intendedFor": 7, + "criteria": { + "SeriesDescription": "B0 map", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"] }, "sidecarChanges": { "Units": "Hz" From ab22033acaa80a14aaae43847eefa9894e510194 Mon Sep 17 00:00:00 2001 From: Pierre-Emmanuel Morin Date: Thu, 31 Mar 2022 13:40:42 -0400 Subject: [PATCH 03/15] Update config_philips_cimaq_qc.json Added some missing configs --- configs/config_philips_cimaq_qc.json | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/configs/config_philips_cimaq_qc.json b/configs/config_philips_cimaq_qc.json index 8a424eb..c162e5f 100644 --- a/configs/config_philips_cimaq_qc.json +++ b/configs/config_philips_cimaq_qc.json @@ -1,6 +1,14 @@ { "lowerCase": "True", "descriptions": [ + { + "dataType": "anat", + "modalityLabel": "T1w", + "criteria": { + "SeriesDescription": "T1*", + "ProtocolName": "T1*" + } + }, { "dataType": "anat", "modalityLabel": "T2star", From 1ad43b1d52128b7d826133c2fc27a1604193db51 Mon Sep 17 00:00:00 2001 From: Pierre-Emmanuel Morin Date: Thu, 31 Mar 2022 13:44:42 -0400 Subject: [PATCH 04/15] Update config_siemens_cimaq.json Added missing configs and corrected some tabulation --- configs/config_siemens_cimaq.json | 25 +++++++++++++++++-------- 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/configs/config_siemens_cimaq.json b/configs/config_siemens_cimaq.json index 3f78e0d..6857390 100644 --- a/configs/config_siemens_cimaq.json +++ b/configs/config_siemens_cimaq.json @@ -6,7 +6,7 @@ "modalityLabel": "T2star", "criteria": { "SeriesDescription": "T2*star*", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"] + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"] } }, { @@ -14,7 +14,7 @@ "modalityLabel": "T2star", "criteria": { "SeriesDescription": "*T2*STAR*", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"] + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"] } }, { @@ -22,7 +22,7 @@ "modalityLabel": "T2star", "criteria": { "SeriesDescription": "*T2*STAR*", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS2D"] + "ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS2D"] } }, { @@ -58,8 +58,8 @@ "intendedFor": 5, "criteria": { "SeriesDescription": "gre_field_mapping", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], - "EchoTime": 0.00492 + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], + "EchoTime": 0.00492 } }, { @@ -156,12 +156,21 @@ "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"] } }, + { + "dataType": "fmap", + "modalityLabel": "phasediff", + "intendedFor": 12, + "criteria": { + "SeriesDescription": "fmri_fieldmap_gre_field_mapping", + "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND", "PHASE"] + } + }, { "dataType": "anat", "modalityLabel": "T2w", "criteria": { "SeriesDescription": "*PD*T2*", - "EchoTime": 0.091 + "EchoTime": 0.091 } }, { @@ -169,7 +178,7 @@ "modalityLabel": "T2w", "criteria": { "SeriesDescription": "*PD*T2*", - "EchoTime": 0.093 + "EchoTime": 0.093 } }, { @@ -177,7 +186,7 @@ "modalityLabel": "PD", "criteria": { "SeriesDescription": "*PD*T2*", - "EchoTime": 0.01 + "EchoTime": 0.01 } }, { From a0b438723edb2a902cfeba44445a80442985c288 Mon Sep 17 00:00:00 2001 From: Pierre-Emmanuel Morin Date: Thu, 31 Mar 2022 13:50:45 -0400 Subject: [PATCH 05/15] Update config_siemens_cimaq_iugm.json Added missing config --- configs/config_siemens_cimaq_iugm.json | 35 ++++++++++++++++++++++++-- 1 file changed, 33 insertions(+), 2 deletions(-) diff --git a/configs/config_siemens_cimaq_iugm.json b/configs/config_siemens_cimaq_iugm.json index 2febeee..43a0ee5 100644 --- a/configs/config_siemens_cimaq_iugm.json +++ b/configs/config_siemens_cimaq_iugm.json @@ -1,6 +1,13 @@ { "lowerCase": "True", "descriptions": [ + { + "dataType": "anat", + "modalityLabel": "T1w", + "criteria": { + "ProtocolName": "MPRAGE*" + } + }, { "dataType": "anat", "modalityLabel": "T2star", @@ -9,6 +16,22 @@ "ImageType": ["*", "*", "M", "*"] } }, + { + "dataType": "anat", + "modalityLabel": "T2*star", + "criteria": { + "SeriesDescription": "*T2*star*", + "ImageType": ["*", "*", "M", "*"] + } + }, + { + "dataType": "anat", + "modalityLabel": "T2*star", + "criteria": { + "SeriesDescription": "*T2*star*", + "ImageType": ["*", "*", "P", "*", "*"] + } + }, { "dataType": "func", "modalityLabel": "bold", @@ -112,15 +135,23 @@ "dataType": "anat", "modalityLabel": "T2w", "criteria": { - "SeriesDescription": "*PD*T2*", + "SeriesDescription": "PD*T2*", "EchoTime": 0.091 } }, + { + "dataType": "anat", + "modalityLabel": "T2w", + "criteria": { + "SeriesDescription": "PD*T2*", + "EchoTime": 0.093 + } + }, { "dataType": "anat", "modalityLabel": "PD", "criteria": { - "SeriesDescription": "*PD*T2*", + "SeriesDescription": "PD*T2*", "EchoTime": 0.01 } }, From 51f17e88a3767be64744e04607dfccd2680b494e Mon Sep 17 00:00:00 2001 From: Pierre-Emmanuel Morin Date: Thu, 31 Mar 2022 13:52:32 -0400 Subject: [PATCH 06/15] Update config_siemens_cimaq_mc_connell_brain_imaging_centre.json Added missing configs --- ...nfig_siemens_cimaq_mc_connell_brain_imaging_centre.json | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/configs/config_siemens_cimaq_mc_connell_brain_imaging_centre.json b/configs/config_siemens_cimaq_mc_connell_brain_imaging_centre.json index 759ba01..b6f4a57 100644 --- a/configs/config_siemens_cimaq_mc_connell_brain_imaging_centre.json +++ b/configs/config_siemens_cimaq_mc_connell_brain_imaging_centre.json @@ -1,6 +1,13 @@ { "lowerCase": "True", "descriptions": [ + { + "dataType": "anat", + "modalityLabel": "T1w", + "criteria": { + "ProtocolName": "MPRAGE*" + } + }, { "dataType": "anat", "modalityLabel": "T2star", From 50304bfcfc4e90d9ae875703dfd76174c41b5d8f Mon Sep 17 00:00:00 2001 From: Pierre-Emmanuel Morin Date: Thu, 31 Mar 2022 14:11:05 -0400 Subject: [PATCH 07/15] Aligned config settings with revomal of unused config files --- convert_bids_ccna_cimaq.py | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/convert_bids_ccna_cimaq.py b/convert_bids_ccna_cimaq.py index ec709fe..2bf10ef 100755 --- a/convert_bids_ccna_cimaq.py +++ b/convert_bids_ccna_cimaq.py @@ -20,9 +20,7 @@ PHILIPS_CONFIG = os.path.join(CONFIG_FOLDER, 'config_philips_cimaq.json') QUEBEC_CONFIG = os.path.join(CONFIG_FOLDER, 'config_philips_cimaq_QC.json') CIMAQ_SIEMENS_CONFIG = ['IUGM', 'hospital_douglas', - 'Mc_Connell_Brain_Imaging_Centre', - 'THE_OTTAWA_HOSPITAL_CIVIC', - 'the_ottawa_hospital_civic_campus'] + 'Mc_Connell_Brain_Imaging_Centre'] TIME_SLEEP = 1 From e84b967a3f8a92f91722d6907b5b014dc8ba1928 Mon Sep 17 00:00:00 2001 From: Pierre-Emmanuel Morin Date: Wed, 2 Aug 2023 11:07:48 -0400 Subject: [PATCH 08/15] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 74baf8f..a276a92 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,2 @@ # 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 From 439316d8c4d394652022ac2826bd72b7bb9a03cc Mon Sep 17 00:00:00 2001 From: Pierre-Emmanuel Morin Date: Fri, 1 Sep 2023 09:25:08 -0400 Subject: [PATCH 09/15] Update README.md --- README.md | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/README.md b/README.md index a276a92..75a8893 100644 --- a/README.md +++ b/README.md @@ -1,2 +1,17 @@ # bids_conversion Script to help convert dicom to bids from CCNA or CIMAQ using dcm2bids + +Requirements +* requirements.txt (pip install -r requirements.txt) +* dcm2bids (https://github.com/UNFmontreal/Dcm2Bids) +* dcm2niix (https://github.com/rordenlab/dcm2niix) + +Run (two steps) +* python3 convert_bids_ccna_cimaq.py /dicom_directory /output_directory mode (ccna or cimaq) > file +* bash ./file + +Tips +* dicom_directory must contain the tarchive files (usually found in /data/$PROJECT/data/tarchive) +* the output file 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 bundle into smaller ones, make sure all of a participant's files are grouped together. If not, you will have to reorganize the tree manually From c66bef5395035922eb4013b47b18275a0011571b Mon Sep 17 00:00:00 2001 From: Pierre-Emmanuel Morin Date: Fri, 15 Sep 2023 11:54:21 -0400 Subject: [PATCH 10/15] Update - this is the final working version before dcm2bids 3.x --- convert_bids_ccna_cimaq.py | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/convert_bids_ccna_cimaq.py b/convert_bids_ccna_cimaq.py index 2bf10ef..c275b5b 100755 --- a/convert_bids_ccna_cimaq.py +++ b/convert_bids_ccna_cimaq.py @@ -12,15 +12,16 @@ GE = ['DISCOVERY_MR750', 'SIGNA_Pioneer', 'DISCOVERY_MR750w', 'Signa_HDxt'] PHILIPS = ['Intera', 'Achieva', 'Ingenia', 'Achieva_dStream'] -CONFIG_FOLDER = '/home/bore/p/unf/s/bids_conversion/configs' +CONFIG_FOLDER = '/home/pemorin/bids_conversion-master/configs' MAIN_CONFIG = os.path.join(CONFIG_FOLDER, 'config.json') GE_CONFIG = os.path.join(CONFIG_FOLDER, 'config_ge_cimaq.json') SIEMENS_CONFIG = os.path.join(CONFIG_FOLDER, 'config_siemens_cimaq.json') PHILIPS_CONFIG = os.path.join(CONFIG_FOLDER, 'config_philips_cimaq.json') -QUEBEC_CONFIG = os.path.join(CONFIG_FOLDER, 'config_philips_cimaq_QC.json') -CIMAQ_SIEMENS_CONFIG = ['IUGM', 'hospital_douglas', - 'Mc_Connell_Brain_Imaging_Centre'] +QUEBEC_CONFIG = os.path.join(CONFIG_FOLDER, 'config_philips_cimaq_qc.json') +CIMAQ_SIEMENS_CONFIG = ['IUGM', 'iugm', 'hospital_douglas', + 'Mc_Connell_Brain_Imaging_Centre', + 'mc_connell_brain_imaging_centre'] TIME_SLEEP = 1 @@ -92,10 +93,13 @@ def __init__(self, filename, patient_name, patient_id, patient_date, self.run_command = run_command def get_session(self, session): - if session == 'Initial': - return 1 - else: - return 2 + if self.mode == 'ccna': + if session == 'Initial': + return 1 + else: + return 2 + elif self.mode == 'cimaq': + return session def getManufacturer(self): if self.scanner_model in SIEMENS: @@ -203,7 +207,7 @@ def convert(self, bidsOutput): cmd = 'dcm2bids -d {} -p {} -s {} '\ '-c {} -o {}'.format(self.filename, - self.candid, + self.pscid, self.session, curr_config, bidsOutput) @@ -332,7 +336,7 @@ def main(): # print(sub.candid, sub.pscid) sub.extract() sub.convert(args.oFolder) - sub.delete_filename() + #sub.delete_filename() if __name__ == '__main__': From 5a55bd18138aa28822707f5f8eabcc5b178e9974 Mon Sep 17 00:00:00 2001 From: Pierre-Emmanuel Morin Date: Fri, 15 Sep 2023 11:56:27 -0400 Subject: [PATCH 11/15] Update config_siemens_cimaq_iugm.json --- configs/config_siemens_cimaq_iugm.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/configs/config_siemens_cimaq_iugm.json b/configs/config_siemens_cimaq_iugm.json index 43a0ee5..e8c5502 100644 --- a/configs/config_siemens_cimaq_iugm.json +++ b/configs/config_siemens_cimaq_iugm.json @@ -18,7 +18,7 @@ }, { "dataType": "anat", - "modalityLabel": "T2*star", + "modalityLabel": "T2star", "criteria": { "SeriesDescription": "*T2*star*", "ImageType": ["*", "*", "M", "*"] @@ -26,7 +26,7 @@ }, { "dataType": "anat", - "modalityLabel": "T2*star", + "modalityLabel": "T2star", "criteria": { "SeriesDescription": "*T2*star*", "ImageType": ["*", "*", "P", "*", "*"] From 54ab9effe6e872d2081ac5b369cfd33ac4a712a8 Mon Sep 17 00:00:00 2001 From: Pierre-Emmanuel Morin Date: Fri, 15 Sep 2023 12:08:07 -0400 Subject: [PATCH 12/15] Update --- README.md | 1 + 1 file changed, 1 insertion(+) diff --git a/README.md b/README.md index 75a8893..e4282be 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,6 @@ # bids_conversion Script to help convert dicom to bids from CCNA or CIMAQ using dcm2bids +Code originaly provided by Arnaud Boré Requirements * requirements.txt (pip install -r requirements.txt) From 3becd0aff9eb7db0626529911ef20ba79f48894a Mon Sep 17 00:00:00 2001 From: Pierre-Emmanuel Morin Date: Fri, 15 Sep 2023 14:56:20 -0400 Subject: [PATCH 13/15] Update config files to dcm2bids 3.x standards --- configs/config.json | 12 +- configs/config_ge.json | 28 +-- configs/config_ge_ccna.json | 44 ++--- configs/config_ge_cimaq.json | 44 ++--- configs/config_lower.json | 6 +- configs/config_philips_ccna.json | 92 +++++----- configs/config_philips_cimaq.json | 130 +++++++++----- configs/config_philips_cimaq_qc.json | 76 +++++---- configs/config_siemens_ccna.json | 100 +++++------ configs/config_siemens_ccna_lower.json | 5 +- configs/config_siemens_cimaq.json | 159 +++++++++++------- ...config_siemens_cimaq_hospital_douglas.json | 140 ++++++++------- configs/config_siemens_cimaq_iugm.json | 139 +++++++++------ ...cimaq_mc_connell_brain_imaging_centre.json | 105 +++++++----- .../config_philips_cimaq_ubc.json | 0 ...emens_cimaq_the_ottawa_hospital_civic.json | 0 ...imaq_the_ottawa_hospital_civic_campus.json | 0 17 files changed, 624 insertions(+), 456 deletions(-) rename configs/{ => not_used}/config_philips_cimaq_ubc.json (100%) rename configs/{ => not_used}/config_siemens_cimaq_the_ottawa_hospital_civic.json (100%) rename configs/{ => not_used}/config_siemens_cimaq_the_ottawa_hospital_civic_campus.json (100%) diff --git a/configs/config.json b/configs/config.json index 88e1a61..962db95 100644 --- a/configs/config.json +++ b/configs/config.json @@ -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*" } diff --git a/configs/config_ge.json b/configs/config_ge.json index 63968a8..c33a889 100644 --- a/configs/config_ge.json +++ b/configs/config_ge.json @@ -2,54 +2,54 @@ "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", + "datatype": "func", + "suffix": "bold", "customLabels": "task-rest", "criteria": { "SeriesDescription": "*Connectivity*" } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-rest", "criteria": { "SeriesDescription": "*CONNECTIVITY*" } }, { - "dataType": "anat", - "modalityLabel": "T2", + "datatype": "anat", + "suffix": "T2", "criteria": { "SeriesDescription": "*PD*T2*", "EchoNumber": 2 } }, { - "dataType": "anat", - "modalityLabel": "PD", + "datatype": "anat", + "suffix": "PD", "criteria": { "SeriesDescription": "*PD*T2*", "EchoNumber": 1 } }, { - "dataType": "dwi", - "modalityLabel": "dwi", + "datatype": "dwi", + "suffix": "dwi", "criteria": { "SeriesDescription": "*DTI*" } diff --git a/configs/config_ge_ccna.json b/configs/config_ge_ccna.json index 863bcf7..29073df 100644 --- a/configs/config_ge_ccna.json +++ b/configs/config_ge_ccna.json @@ -2,60 +2,60 @@ "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", + "datatype": "func", + "suffix": "bold", "customLabels": "task-rest", - "sidecarChanges": { - "TaskName": "rest" - }, "criteria": { "SeriesDescription": "*Connectivity*" + }, + "sidecar_changes": { + "TaskName": "rest" } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-rest", - "sidecarChanges": { - "TaskName": "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*" } diff --git a/configs/config_ge_cimaq.json b/configs/config_ge_cimaq.json index 3b13380..52d81a4 100644 --- a/configs/config_ge_cimaq.json +++ b/configs/config_ge_cimaq.json @@ -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", + "datatype": "func", + "suffix": "bold", "customLabels": "task-rest", "criteria": { "SeriesDescription": "*Connectivity*" } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "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*" } diff --git a/configs/config_lower.json b/configs/config_lower.json index a052f5d..fbbb7ca 100644 --- a/configs/config_lower.json +++ b/configs/config_lower.json @@ -3,11 +3,11 @@ "lowerCase": "True", "descriptions": [ { - "dataType": "anat", - "modalityLabel": "T2star", + "datatype": "anat", + "suffix": "T2star", "criteria": { "SeriesDescription": "*T2*STAR*", - "ImageType": ["M"] + "ImageType": ["M"] } } ] diff --git a/configs/config_philips_ccna.json b/configs/config_philips_ccna.json index a945dce..a58664a 100644 --- a/configs/config_philips_ccna.json +++ b/configs/config_philips_ccna.json @@ -3,129 +3,129 @@ "caseSensitive": false, "descriptions": [ { - "dataType": "anat", - "modalityLabel": "T2star", + "datatype": "anat", + "suffix": "T2star", "criteria": { "SeriesDescription": "T2_STAR" } }, { - "dataType": "anat", - "modalityLabel": "T2star", + "datatype": "anat", + "suffix": "T2star", "criteria": { "SeriesDescription": "T2_FFE*" } }, { - "dataType": "anat", - "modalityLabel": "T2w", + "datatype": "anat", + "suffix": "T2w", "criteria": { "SeriesDescription": "DUAL_*", "EchoTime": 0.1 } }, { - "dataType": "anat", - "modalityLabel": "PD", + "datatype": "anat", + "suffix": "PD", "criteria": { "SeriesDescription": "DUAL_*", "EchoTime": 0.0125 } }, { - "dataType": "anat", - "modalityLabel": "T2w", + "datatype": "anat", + "suffix": "T2w", "criteria": { "SeriesDescription": "*PD_T2*", "EchoTime": 0.1 } }, { - "dataType": "anat", - "modalityLabel": "PD", + "datatype": "anat", + "suffix": "PD", "criteria": { "SeriesDescription": "*PD_T2*", "EchoTime": 0.0125 } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-rest", - "sidecarChanges": { - "TaskName": "rest" - }, "criteria": { "SeriesDescription": "*fMRI" - } + }, + "sidecar_changes": { + "TaskName": "rest" + }, }, { - "dataType": "dwi", - "modalityLabel": "dwi", + "datatype": "dwi", + "suffix": "dwi", "criteria": { "SeriesDescription": "DTI_32_iso" }, - "sidecarChanges": { - "PhaseEncodingDirection": "j-" + "sidecar_changes": { + "PhaseEncodingDirection": "j-" } }, { - "dataType": "fmap", - "modalityLabel": "epi", + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "DTI_b0_AP" }, - "intendedFor": 7, - "sidecarChanges": { + "sidecar_changes": { "PhaseEncodingDirection": "j", + "intendedFor": 7, "TotalReadoutTime": 0.062 } }, { - "dataType": "dwi", - "modalityLabel": "dwi", + "datatype": "dwi", + "suffix": "dwi", "criteria": { "SeriesDescription": "DTI_32" }, - "sidecarChanges": { - "PhaseEncodingDirection": "j-" + "sidecar_changes": { + "PhaseEncodingDirection": "j-" } }, { - "dataType": "dwi", - "modalityLabel": "dwi", + "datatype": "dwi", + "suffix": "dwi", "criteria": { "SeriesDescription": "DTI" }, - "sidecarChanges": { - "PhaseEncodingDirection": "j" + "sidecar_changes": { + "PhaseEncodingDirection": "j" } }, { - "dataType": "fmap", - "modalityLabel": "epi", + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "DTI_b0", "InstitutionName": "UBC" }, - "sidecarChanges": { - "PhaseEncodingDirection": "j-", - "TotalReadoutTime": 0.062 + "sidecar_changes": { + "PhaseEncodingDirection": "j-", + "intendedFor": 9, + "TotalReadoutTime": 0.062 }, - "intendedFor": 9 }, { - "dataType": "fmap", - "modalityLabel": "epi", + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "DTI_b0", "InstitutionName": "UBC_MRI_Research_Centre" }, - "sidecarChanges": { - "PhaseEncodingDirection": "j", - "TotalReadoutTime": 0.062 + "sidecar_changes": { + "PhaseEncodingDirection": "j", + "intendedFor": 10, + "TotalReadoutTime": 0.062 }, - "intendedFor": 10 } ] } diff --git a/configs/config_philips_cimaq.json b/configs/config_philips_cimaq.json index 99fab9b..bd058a8 100644 --- a/configs/config_philips_cimaq.json +++ b/configs/config_philips_cimaq.json @@ -2,141 +2,189 @@ "lowerCase": "True", "descriptions": [ { - "dataType": "anat", - "modalityLabel": "T2star", + "datatype": "anat", + "suffix": "T1w", + "criteria": { + "SeriesDescription": "T1*", + "ProtocolName": "T1*" + } + }, + { + "datatype": "anat", + "suffix": "T1w", + "criteria": { + "ProtocolName": "3D*MPR*" + } + }, + { + "datatype": "anat", + "suffix": "T2star", "criteria": { "SeriesDescription": "T2_STAR" } }, { - "dataType": "anat", - "modalityLabel": "T2star", + "datatype": "anat", + "suffix": "T2star", "criteria": { "SeriesDescription": "*T2_FFE*" } }, { - "dataType": "anat", - "modalityLabel": "T2w", + "datatype": "anat", + "suffix": "T2w", "criteria": { "SeriesDescription": "DUAL_*", "EchoTime": 0.1 } }, { - "dataType": "anat", - "modalityLabel": "PD", + "datatype": "anat", + "suffix": "PD", "criteria": { "SeriesDescription": "DUAL_*", "EchoTime": 0.0125 } }, { - "dataType": "anat", - "modalityLabel": "T2w", + "datatype": "anat", + "suffix": "T2w", "criteria": { "SeriesDescription": "*PD_T2*", "EchoTime": 0.1 } }, { - "dataType": "anat", - "modalityLabel": "PD", + "datatype": "anat", + "suffix": "PD", "criteria": { "SeriesDescription": "*PD_T2*", "EchoTime": 0.0125 } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "anat", + "suffix": "FLAIR", + "criteria": { + "SeriesDescription": "*FLAIR*" + } + }, + { + "datatype": "func", + "suffix": "bold", "customLabels": "task-rest", "criteria": { "SeriesDescription": "*fMRI" }, - "sidecarChanges": { + "sidecar_changes": { "TaskName": "rest", "TotalReadoutTime": 1 } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-memory", "criteria": { "SeriesDescription": "*MemoryTask" }, - "sidecarChanges": { + "sidecar_changes": { "TaskName": "memory", "TotalReadoutTime": 1 } }, { - "dataType": "fmap", - "modalityLabel": "epi", - "intendedFor": 7, + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "fMRI*MemoryTask_*PA*" }, - "sidecarChanges": { + "sidecar_changes": { "PhaseEncodingDirection": "j", + "intendedFor": 7, "TotalReadoutTime": 1 } }, { - "dataType": "dwi", - "modalityLabel": "dwi", + "datatype": "dwi", + "suffix": "dwi", "criteria": { "SeriesDescription": "DTI_32*" }, - "sidecarChanges": { + "sidecar_changes": { "PhaseEncodingDirection": "j-", "TotalReadoutTime": 1 } }, { - "dataType": "fmap", - "modalityLabel": "epi", - "intendedFor": 9, + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "*b0*_AP*" }, - "sidecarChanges": { + "sidecar_changes": { "PhaseEncodingDirection": "j-", + "intendedFor": 9, "TotalReadoutTime": 1 } }, { - "dataType": "fmap", - "modalityLabel": "epi", - "intendedFor": 7, + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "fMRI*MemoryTask_*AP*" }, - "sidecarChanges": { + "sidecar_changes": { "PhaseEncodingDirection": "j-", + "intendedFor": 7, "TotalReadoutTime": 1 } }, { - "dataType": "fmap", - "modalityLabel": "fieldmap", - "intendedFor": 7, + "datatype": "fmap", + "suffix": "fieldmap", "criteria": { "SeriesDescription": "B0_map", - "ImageType": ["ORIGINAL", "PRIMARY", "B0", "MAP", "B0", "UNSPECIFIED"] + "ImageType": ["ORIGINAL", "PRIMARY", "B0", "MAP", "B0", "UNSPECIFIED"] }, - "sidecarChanges": { + "sidecar_changes": { + "intendedFor": 7, "Units": "Hz" } }, { - "dataType": "fmap", - "modalityLabel": "magnitude", - "intendedFor": 7, + "datatype": "fmap", + "suffix": "fieldmap", + "criteria": { + "SeriesDescription": "B0 map", + "ImageType": ["ORIGINAL", "PRIMARY", "B0 MAP", "B0", "UNSPECIFIED", "FIELDMAPHZ"] + }, + "sidecar_changes": { + "intendedFor": 7, + "Units": "Hz" + } + }, + { + "datatype": "fmap", + "suffix": "fieldmap", + "criteria": { + "SeriesDescription": "B0 map", + "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"] + }, + "sidecar_changes": { + "intendedFor": 7, + "Units": "Hz" + } + }, + { + "datatype": "fmap", + "suffix": "magnitude", "criteria": { "SeriesDescription": "B0_map", "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"] + }, + "sidecar_changes": { + "intendedFor": 7 } } ] diff --git a/configs/config_philips_cimaq_qc.json b/configs/config_philips_cimaq_qc.json index 8a424eb..8611171 100644 --- a/configs/config_philips_cimaq_qc.json +++ b/configs/config_philips_cimaq_qc.json @@ -2,117 +2,125 @@ "lowerCase": "True", "descriptions": [ { - "dataType": "anat", - "modalityLabel": "T2star", + "datatype": "anat", + "suffix": "T1w", + "criteria": { + "SeriesDescription": "T1*", + "ProtocolName": "T1*" + } + }, + { + "datatype": "anat", + "suffix": "T2star", "criteria": { "SeriesDescription": "T2_FFE*" } }, { - "dataType": "anat", - "modalityLabel": "T2w", + "datatype": "anat", + "suffix": "T2w", "criteria": { "SeriesDescription": "DUAL_*", "EchoTime": 0.1 } }, { - "dataType": "anat", - "modalityLabel": "PD", + "datatype": "anat", + "suffix": "PD", "criteria": { "SeriesDescription": "DUAL_*", "EchoTime": 0.0125 } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-rest", "criteria": { "SeriesDescription": "*fMRI" }, - "sidecarChanges": { + "sidecar_changes": { "TaskName": "rest", "TotalReadoutTime": 1 } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-memory", "criteria": { "SeriesDescription": "*MemoryTask" }, - "sidecarChanges": { + "sidecar_changes": { "TaskName": "memory", "TotalReadoutTime": 1 } }, { - "dataType": "fmap", - "modalityLabel": "epi", - "intendedFor": 4, + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "fMRI*MemoryTask_*PA*" }, - "sidecarChanges": { + "sidecar_changes": { "PhaseEncodingDirection": "j", + "intendedFor": 4, "TotalReadoutTime": 1 } }, { - "dataType": "dwi", - "modalityLabel": "dwi", + "datatype": "dwi", + "suffix": "dwi", "criteria": { "SeriesDescription": "DTI_32*" }, - "sidecarChanges": { + "sidecar_changes": { "PhaseEncodingDirection": "j-", "TotalReadoutTime": 1 } }, { - "dataType": "fmap", - "modalityLabel": "epi", - "intendedFor": 6, + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "*b0*AP*" }, - "sidecarChanges": { + "sidecar_changes": { "PhaseEncodingDirection": "j-", + "intendedFor": 6, "TotalReadoutTime": 1 } }, { - "dataType": "fmap", - "modalityLabel": "epi", - "intendedFor": 4, + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "fMRI*MemoryTask_*AP*" }, - "sidecarChanges": { + "sidecar_changes": { "PhaseEncodingDirection": "j-", + "intendedFor": 4, "TotalReadoutTime": 1 } }, { - "dataType": "fmap", - "modalityLabel": "fieldmap", - "intendedFor": 4, + "datatype": "fmap", + "suffix": "fieldmap", "criteria": { "SeriesDescription": "B0_map", "ImageType": ["ORIGINAL", "PRIMARY", "B0", "MAP", "B0", "UNSPECIFIED"] }, - "sidecarChanges": { + "sidecar_changes": { + "intendedFor": 4, "Units": "Hz" } }, { - "dataType": "fmap", - "modalityLabel": "magnitude", - "intendedFor": 4, + "datatype": "fmap", + "suffix": "magnitude", "criteria": { "SeriesDescription": "B0_map", + "intendedFor": 4, "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"] } } diff --git a/configs/config_siemens_ccna.json b/configs/config_siemens_ccna.json index 232daae..932b6ef 100644 --- a/configs/config_siemens_ccna.json +++ b/configs/config_siemens_ccna.json @@ -2,8 +2,8 @@ "caseSensitive": false, "descriptions": [ { - "dataType": "anat", - "modalityLabel": "T2star", + "datatype": "anat", + "suffix": "T2star", "customLabels": "part-mag", "criteria": { "SeriesDescription": "T2*star*", @@ -11,8 +11,8 @@ } }, { - "dataType": "anat", - "modalityLabel": "T2star", + "datatype": "anat", + "suffix": "T2star", "customLabels": "part-phase", "criteria": { "SeriesDescription": "T2*star*", @@ -20,104 +20,110 @@ } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-rest", - "sidecarChanges": { - "TaskName": "rest" - }, "criteria": { "SeriesDescription": "*Connectivity*" + }, + "sidecar_changes": { + "TaskName": "rest" } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-rest", - "sidecarChanges": { - "TaskName": "rest" - }, "criteria": { "SeriesDescription": "*R*S*fMRI*" + }, + "sidecar_changes": { + "TaskName": "rest" } }, { - "dataType": "anat", - "modalityLabel": "T2w", + "datatype": "anat", + "suffix": "T2w", "criteria": { "SeriesDescription": "*PD*T2*", - "EchoTime": 0.091 + "EchoTime": 0.091 } }, { - "dataType": "anat", - "modalityLabel": "T2w", + "datatype": "anat", + "suffix": "T2w", "criteria": { "SeriesDescription": "*PD*T2*", - "EchoTime": 0.093 + "EchoTime": 0.093 } }, { - "dataType": "anat", - "modalityLabel": "PD", + "datatype": "anat", + "suffix": "PD", "criteria": { "SeriesDescription": "*PD*T2*", - "EchoTime": 0.01 + "EchoTime": 0.01 } }, { - "dataType": "dwi", - "modalityLabel": "dwi", + "datatype": "dwi", + "suffix": "dwi", "criteria": { "SeriesDescription": "DTI-EDM" } }, { - "dataType": "dwi", - "modalityLabel": "dwi", + "datatype": "dwi", + "suffix": "dwi", "criteria": { "SeriesDescription": "DTI" } }, { - "dataType": "fmap", - "modalityLabel": "epi", + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "D*0*" }, - "intendedFor": [7, 8] + "sidecar_changes": { + "intendedFor": [7, 8] + } }, { - "dataType": "fmap", - "modalityLabel": "magnitude1", - "intendedFor": [2, 3], + "datatype": "fmap", + "suffix": "magnitude1", "criteria": { "SeriesDescription": "*gre_field_mapping*", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], - "EchoTime": 0.00492 + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], + "EchoTime": 0.00492 + }, + "sidecar_changes": { + "intendedFor": [2, 3] } }, { - "dataType": "fmap", - "modalityLabel": "magnitude2", - "intendedFor": [2, 3], + "datatype": "fmap", + "suffix": "magnitude2", "criteria": { "SeriesDescription": "*gre_field_mapping*", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], - "EchoTime": 0.00738 + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], + "EchoTime": 0.00738 + }, + "sidecar_changes": { + "intendedFor": [2, 3] } }, { - "dataType": "fmap", - "modalityLabel": "phasediff", - "intendedFor": [2, 3], + "datatype": "fmap", + "suffix": "phasediff", "criteria": { "SeriesDescription": "*gre_field_mapping*", - "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"], - "EchoTime": 0.00738 + "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"], + "EchoTime": 0.00738 }, - "sidecarChanges": { - "EchoTime1": 0.00492, + "sidecar_changes": { + "intendedFor": [2, 3], + "EchoTime1": 0.00492, "EchoTime2": 0.00738 } } diff --git a/configs/config_siemens_ccna_lower.json b/configs/config_siemens_ccna_lower.json index 467e734..68d2087 100644 --- a/configs/config_siemens_ccna_lower.json +++ b/configs/config_siemens_ccna_lower.json @@ -2,12 +2,11 @@ "caseSensitive": false, "descriptions": [ { - "dataType": "anat", - "modalityLabel": "T2star", + "datatype": "anat", + "suffix": "T2star", "criteria": { "SeriesDescription": "T2*STAR", "ImageType": ["M"] - } } ] diff --git a/configs/config_siemens_cimaq.json b/configs/config_siemens_cimaq.json index 3f78e0d..8823998 100644 --- a/configs/config_siemens_cimaq.json +++ b/configs/config_siemens_cimaq.json @@ -2,32 +2,32 @@ "lowerCase": "True", "descriptions": [ { - "dataType": "anat", - "modalityLabel": "T2star", + "datatype": "anat", + "suffix": "T2star", "criteria": { "SeriesDescription": "T2*star*", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"] + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"] } }, { - "dataType": "anat", - "modalityLabel": "T2star", + "datatype": "anat", + "suffix": "T2star", "criteria": { "SeriesDescription": "*T2*STAR*", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"] + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"] } }, { - "dataType": "anat", - "modalityLabel": "T2star", + "datatype": "anat", + "suffix": "T2star", "criteria": { "SeriesDescription": "*T2*STAR*", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS2D"] + "ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS2D"] } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-rest", "criteria": { "SeriesDescription": "*Connectivity*", @@ -35,8 +35,8 @@ } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-rest", "criteria": { "SeriesDescription": "*R*fMRI*", @@ -44,8 +44,8 @@ } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-rest", "criteria": { "SeriesDescription": "*Resting*State*", @@ -53,66 +53,78 @@ } }, { - "dataType": "fmap", - "modalityLabel": "magnitude1", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "magnitude1", "criteria": { "SeriesDescription": "gre_field_mapping", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], - "EchoTime": 0.00492 + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], + "EchoTime": 0.00492 + }, + "sidecar_changes": { + "intendedFor": 5 } }, { - "dataType": "fmap", - "modalityLabel": "magnitude2", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "magnitude2", "criteria": { "SeriesDescription": "gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], "EchoTime": 0.00738 } + "sidecar_changes": { + "intendedFor": 5 + } }, { - "dataType": "fmap", - "modalityLabel": "phasediff", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "phasediff", "criteria": { "SeriesDescription": "gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"] + }, + "sidecar_changes": { + "intendedFor": 5 } }, { - "dataType": "fmap", - "modalityLabel": "phasediff", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "phasediff", "criteria": { "SeriesDescription": "BOLD_RS_fieldmap_gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"] + }, + "sidecar_changes": { + "intendedFor": 5 } }, { - "dataType": "fmap", - "modalityLabel": "magnitude1", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "magnitude1", "criteria": { "SeriesDescription": "BOLD_RS_fieldmap_gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], "EchoTime": 0.00492 + }, + "sidecar_changes": { + "intendedFor": 5 } }, { - "dataType": "fmap", - "modalityLabel": "magnitude2", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "magnitude2", "criteria": { "SeriesDescription": "BOLD_RS_fieldmap_gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], "EchoTime": 0.00738 + }, + "sidecar_changes": { + "intendedFor": 5 } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-memory", "criteria": { "SeriesDescription": "*MemoryTask", @@ -120,79 +132,100 @@ } }, { - "dataType": "fmap", - "modalityLabel": "epi", - "intendedFor": 12, + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "fmri*MemoryTask_*" + }, + "sidecar_changes": { + "intendedFor": 12 } }, { - "dataType": "fmap", - "modalityLabel": "magnitude1", - "intendedFor": 12, + "datatype": "fmap", + "suffix": "magnitude1", "criteria": { "SeriesDescription": "fmri_fieldmap_gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], "EchoTime": 0.00492 + }, + "sidecar_changes": { + "intendedFor": 12 } }, { - "dataType": "fmap", - "modalityLabel": "magnitude2", - "intendedFor": 12, + "datatype": "fmap", + "suffix": "magnitude2", "criteria": { "SeriesDescription": "fmri_fieldmap_gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], "EchoTime": 0.00738 + }, + "sidecar_changes": { + "intendedFor": 12 } }, { - "dataType": "fmap", - "modalityLabel": "phasediff", - "intendedFor": 12, + "datatype": "fmap", + "suffix": "phasediff", "criteria": { "SeriesDescription": "fmri_fieldmap_gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"] + }, + "sidecar_changes": { + "intendedFor": 12 + } + }, + { + "datatype": "fmap", + "suffix": "phasediff", + "criteria": { + "SeriesDescription": "fmri_fieldmap_gre_field_mapping", + "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND", "PHASE"] + }, + "sidecar_changes": { + "intendedFor": 12 } }, { - "dataType": "anat", - "modalityLabel": "T2w", + "datatype": "anat", + "suffix": "T2w", "criteria": { "SeriesDescription": "*PD*T2*", - "EchoTime": 0.091 + "EchoTime": 0.091 } }, { - "dataType": "anat", - "modalityLabel": "T2w", + "datatype": "anat", + "suffix": "T2w", "criteria": { "SeriesDescription": "*PD*T2*", - "EchoTime": 0.093 + "EchoTime": 0.093 } }, { - "dataType": "anat", - "modalityLabel": "PD", + "datatype": "anat", + "suffix": "PD", "criteria": { "SeriesDescription": "*PD*T2*", - "EchoTime": 0.01 + "EchoTime": 0.01 } }, { - "dataType": "dwi", - "modalityLabel": "dwi", + "datatype": "dwi", + "suffix": "dwi", "criteria": { "SeriesDescription": "DWI" } }, { - "dataType": "fmap", - "modalityLabel": "epi", - "intendedFor": 20, + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "D*0*" + }, + "sidecar_changes": { + "intendedFor": 20 } } ] diff --git a/configs/config_siemens_cimaq_hospital_douglas.json b/configs/config_siemens_cimaq_hospital_douglas.json index a1015b2..6ff0ae2 100644 --- a/configs/config_siemens_cimaq_hospital_douglas.json +++ b/configs/config_siemens_cimaq_hospital_douglas.json @@ -2,140 +2,154 @@ "lowerCase": "True", "descriptions": [ { - "dataType": "anat", - "modalityLabel": "T2star", + "datatype": "anat", + "suffix": "T2star", "criteria": { "SeriesDescription": "*T2*STAR*", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS2D"] + "ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS2D"] } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-rest", "criteria": { "ProtocolName": "Resting*State*" }, - "sidecarChanges": { + "sidecar_changes": { "TaskName": "rest" - } + } }, { - "dataType": "fmap", - "modalityLabel": "magnitude1", - "intendedFor": 1, + "datatype": "fmap", + "suffix": "magnitude1", "criteria": { "SeriesDescription": "gre_field_mapping", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], - "EchoTime": 0.00492 - } + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], + "EchoTime": 0.00492 + }, + "sidecar_changes": { + "intendedFor": 1, + "TaskName": "rest" + } }, { - "dataType": "fmap", - "modalityLabel": "magnitude2", - "intendedFor": 1, + "datatype": "fmap", + "suffix": "magnitude2", "criteria": { "SeriesDescription": "gre_field_mapping", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], - "EchoTime": 0.00738 - } + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], + "EchoTime": 0.00738 + }, + "sidecar_changes": { + "intendedFor": 1, + "TaskName": "rest" + } }, { - "dataType": "fmap", - "modalityLabel": "phasediff", - "intendedFor": 1, + "datatype": "fmap", + "suffix": "phasediff", "criteria": { "SeriesDescription": "gre_field_mapping", - "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"], - "EchoTime": 0.00738 + "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"], + "EchoTime": 0.00738 }, - "sidecarChanges": { - "EchoTime1": 0.00492, + "sidecar_changes": { + "intendedFor": 1, + "EchoTime1": 0.00492, "EchoTime2": 0.00738 } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-memory", "criteria": { "SeriesDescription": "*MemoryTask" }, - "sidecarChanges": { + "sidecar_changes": { "TaskName": "memory" - } + } }, { - "dataType": "fmap", - "modalityLabel": "magnitude1", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "magnitude1", "criteria": { "SeriesDescription": "fmri_fieldmap_gre_field_mapping", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], - "EchoTime": 0.00492 - } + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], + "EchoTime": 0.00492 + }, + "sidecar_changes": { + "intendedFor": 5, + } }, { - "dataType": "fmap", - "modalityLabel": "magnitude2", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "magnitude2", "criteria": { "SeriesDescription": "fmri_fieldmap_gre_field_mapping", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], - "EchoTime": 0.00738 - } + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], + "EchoTime": 0.00738 + }, + "sidecar_changes": { + "intendedFor": 5, + } }, { - "dataType": "fmap", - "modalityLabel": "phasediff", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "phasediff", "criteria": { "SeriesDescription": "fmri_fieldmap_gre_field_mapping", - "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"], - "EchoTime": 0.00738 + "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"], + "EchoTime": 0.00738 }, - "sidecarChanges": { - "EchoTime1": 0.00492, + "sidecar_changes": { + "intendedFor": 5, + "EchoTime1": 0.00492, "EchoTime2": 0.00738 } }, { - "dataType": "fmap", - "modalityLabel": "epi", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "fmri*MemoryTask_*" + }, + "sidecar_changes": { + "intendedFor": 5 } }, { - "dataType": "anat", - "modalityLabel": "T2w", + "datatype": "anat", + "suffix": "T2w", "criteria": { "SeriesDescription": "*PD*T2*", - "EchoTime": 0.091 + "EchoTime": 0.091 } }, { - "dataType": "anat", - "modalityLabel": "PD", + "datatype": "anat", + "suffix": "PD", "criteria": { "SeriesDescription": "*PD*T2*", - "EchoTime": 0.01 + "EchoTime": 0.01 } }, { - "dataType": "dwi", - "modalityLabel": "dwi", + "datatype": "dwi", + "suffix": "dwi", "criteria": { "ImageType": ["ORIGINAL", "PRIMARY", "DIFFUSION", "NONE", "ND", "NORM", "MOSAIC"] } }, { - "dataType": "fmap", - "modalityLabel": "epi", - "intendedFor": 12, + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "D*B0*" + }, + "sidecar_changes": { + "intendedFor": 12 } } ] diff --git a/configs/config_siemens_cimaq_iugm.json b/configs/config_siemens_cimaq_iugm.json index 2febeee..17bb00c 100644 --- a/configs/config_siemens_cimaq_iugm.json +++ b/configs/config_siemens_cimaq_iugm.json @@ -2,146 +2,189 @@ "lowerCase": "True", "descriptions": [ { - "dataType": "anat", - "modalityLabel": "T2star", + "datatype": "anat", + "suffix": "T1w", + "criteria": { + "ProtocolName": "MPRAGE*" + } + }, + { + "datatype": "anat", + "suffix": "T2star", "criteria": { "SeriesDescription": "*T2*STAR*", - "ImageType": ["*", "*", "M", "*"] + "ImageType": ["*", "*", "M", "*"] } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "anat", + "suffix": "T2star", + "criteria": { + "SeriesDescription": "*T2*star*", + "ImageType": ["*", "*", "M", "*"] + } + }, + { + "datatype": "anat", + "suffix": "T2star", + "criteria": { + "SeriesDescription": "*T2*star*", + "ImageType": ["*", "*", "P", "*", "*"] + } + }, + { + "datatype": "func", + "suffix": "bold", "customLabels": "task-rest", "criteria": { "EchoTime": 0.03, "SliceThickness": 3.5 }, - "sidecarChanges": { + "sidecar_changes": { "TaskName": "rest" - } + } }, { - "dataType": "fmap", - "modalityLabel": "magnitude1", - "intendedFor": 1, + "datatype": "fmap", + "suffix": "magnitude1", "criteria": { "SeriesDescription": "gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], "EchoTime": 0.00492 - } + }, + "sidecar_changes": { + "intendedFor": 1, + } }, { - "dataType": "fmap", - "modalityLabel": "magnitude2", - "intendedFor": 1, + "datatype": "fmap", + "suffix": "magnitude2", "criteria": { "SeriesDescription": "gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], "EchoTime": 0.00738 - } + }, + "sidecar_changes": { + "intendedFor": 1, + } }, { - "dataType": "fmap", - "modalityLabel": "phasediff", - "intendedFor": 1, + "datatype": "fmap", + "suffix": "phasediff", "criteria": { "SeriesDescription": "gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"], "EchoTime": 0.00738 }, - "sidecarChanges": { + "sidecar_changes": { + "intendedFor": 1, "EchoTime1": 0.00492, "EchoTime2": 0.00738 } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-memory", "criteria": { "SeriesDescription": "*MemoryTask" }, - "sidecarChanges": { + "sidecar_changes": { "TaskName": "memory" } }, { - "dataType": "fmap", - "modalityLabel": "magnitude1", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "magnitude1", "criteria": { "SeriesDescription": "fmri_fieldmap_gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], "EchoTime": 0.00492 + }, + "sidecar_changes": { + "intendedFor": 5 } }, { - "dataType": "fmap", - "modalityLabel": "magnitude2", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "magnitude2", "criteria": { "SeriesDescription": "fmri_fieldmap_gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], "EchoTime": 0.00738 + }, + "sidecar_changes": { + "intendedFor": 5 } }, { - "dataType": "fmap", - "modalityLabel": "phasediff", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "phasediff", "criteria": { "SeriesDescription": "fmri_fieldmap_gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"], "EchoTime": 0.00738 }, - "sidecarChanges": { + "sidecar_changes": { + "intendedFor": 5, "EchoTime1": 0.00492, "EchoTime2": 0.00738 } }, { - "dataType": "fmap", - "modalityLabel": "epi", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "fmri*MemoryTask_*" + }, + "sidecar_changes": { + "intendedFor": 5 } }, { - "dataType": "anat", - "modalityLabel": "T2w", + "datatype": "anat", + "suffix": "T2w", "criteria": { - "SeriesDescription": "*PD*T2*", + "SeriesDescription": "PD*T2*", "EchoTime": 0.091 } }, { - "dataType": "anat", - "modalityLabel": "PD", + "datatype": "anat", + "suffix": "T2w", + "criteria": { + "SeriesDescription": "PD*T2*", + "EchoTime": 0.093 + } + }, + { + "datatype": "anat", + "suffix": "PD", "criteria": { - "SeriesDescription": "*PD*T2*", + "SeriesDescription": "PD*T2*", "EchoTime": 0.01 } }, { - "dataType": "dwi", - "modalityLabel": "dwi", + "datatype": "dwi", + "suffix": "dwi", "criteria": { "SeriesDescription": "D*I" } }, { - "dataType": "fmap", - "modalityLabel": "epi", - "intendedFor": 12, + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "D*0*" + }, + "sidecar_changes": { + "intendedFor": 12 } }, { - "dataType": "anat", - "modalityLabel": "T2star", + "datatype": "anat", + "suffix": "T2star", "criteria": { "SeriesDescription": "*T2*STAR*", "ImageType": ["*", "*", "M", "*", "*"] diff --git a/configs/config_siemens_cimaq_mc_connell_brain_imaging_centre.json b/configs/config_siemens_cimaq_mc_connell_brain_imaging_centre.json index 759ba01..d1c24f1 100644 --- a/configs/config_siemens_cimaq_mc_connell_brain_imaging_centre.json +++ b/configs/config_siemens_cimaq_mc_connell_brain_imaging_centre.json @@ -2,72 +2,83 @@ "lowerCase": "True", "descriptions": [ { - "dataType": "anat", - "modalityLabel": "T2star", + "datatype": "anat", + "suffix": "T1w", + "criteria": { + "ProtocolName": "MPRAGE*" + } + }, + { + "datatype": "anat", + "suffix": "T2star", "criteria": { "SeriesDescription": "*T2*STAR*", "ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS2D"] } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-rest", "criteria": { "ProtocolName": "*Resting*State*" }, - "sidecarChanges": { + "sidecar_changes": { "TaskName": "rest" - } + } }, { - "dataType": "fmap", - "modalityLabel": "magnitude1", - "intendedFor": 1, + "datatype": "fmap", + "suffix": "magnitude1", "criteria": { "SeriesDescription": "BOLD_RS_fieldmap_gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], "EchoTime": 0.00492 - } + }, + "sidecar_changes": { + "intendedFor": 1 + } }, { - "dataType": "fmap", - "modalityLabel": "magnitude2", - "intendedFor": 1, + "datatype": "fmap", + "suffix": "magnitude2", "criteria": { "SeriesDescription": "BOLD_RS_fieldmap_gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], "EchoTime": 0.00738 - } + }, + "sidecar_changes": { + "intendedFor": 1 + } }, { - "dataType": "fmap", - "modalityLabel": "phasediff", - "intendedFor": 1, + "datatype": "fmap", + "suffix": "phasediff", "criteria": { "SeriesDescription": "BOLD_RS_fieldmap_gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"], "EchoTime": 0.00738 }, - "sidecarChanges": { + "sidecar_changes": { + "intendedFor": 1, "EchoTime1": 0.00492, "EchoTime2": 0.00738 } }, { - "dataType": "func", - "modalityLabel": "bold", + "datatype": "func", + "suffix": "bold", "customLabels": "task-memory", "criteria": { "SeriesDescription": "*MemoryTask" }, - "sidecarChanges": { + "sidecar_changes": { "TaskName": "memory" - } + } }, { - "dataType": "fmap", - "modalityLabel": "magnitude1", + "datatype": "fmap", + "suffix": "magnitude1", "intendedFor": 5, "criteria": { "SeriesDescription": "fmri_fieldmap_gre_field_mapping", @@ -76,66 +87,72 @@ } }, { - "dataType": "fmap", - "modalityLabel": "magnitude2", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "magnitude2", "criteria": { "SeriesDescription": "fmri_fieldmap_gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], "EchoTime": 0.00738 - } + }, + "sidecar_changes": { + "intendedFor": 5 + } }, { - "dataType": "fmap", - "modalityLabel": "phasediff", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "phasediff", "criteria": { "SeriesDescription": "fmri_fieldmap_gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"], "EchoTime": 0.00738 }, - "sidecarChanges": { + "sidecar_changes": { + "intendedFor": 5, "EchoTime1": 0.00492, "EchoTime2": 0.00738 } }, { - "dataType": "fmap", - "modalityLabel": "epi", - "intendedFor": 5, + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "fmri*MemoryTask_*" + }, + "sidecar_changes": { + "intendedFor": 5 } }, { - "dataType": "anat", - "modalityLabel": "T2w", + "datatype": "anat", + "suffix": "T2w", "criteria": { "SeriesDescription": "*PD*T2*", "EchoTime": 0.091 } }, { - "dataType": "anat", - "modalityLabel": "PD", + "datatype": "anat", + "suffix": "PD", "criteria": { "SeriesDescription": "*PD*T2*", "EchoTime": 0.01 } }, { - "dataType": "dwi", - "modalityLabel": "dwi", + "datatype": "dwi", + "suffix": "dwi", "criteria": { "SeriesDescription": "DWI" } }, { - "dataType": "fmap", - "modalityLabel": "epi", - "intendedFor": 12, + "datatype": "fmap", + "suffix": "epi", "criteria": { "SeriesDescription": "D*B0*" + }, + "sidecar_changes": { + "intendedFor": 12 } } ] diff --git a/configs/config_philips_cimaq_ubc.json b/configs/not_used/config_philips_cimaq_ubc.json similarity index 100% rename from configs/config_philips_cimaq_ubc.json rename to configs/not_used/config_philips_cimaq_ubc.json diff --git a/configs/config_siemens_cimaq_the_ottawa_hospital_civic.json b/configs/not_used/config_siemens_cimaq_the_ottawa_hospital_civic.json similarity index 100% rename from configs/config_siemens_cimaq_the_ottawa_hospital_civic.json rename to configs/not_used/config_siemens_cimaq_the_ottawa_hospital_civic.json diff --git a/configs/config_siemens_cimaq_the_ottawa_hospital_civic_campus.json b/configs/not_used/config_siemens_cimaq_the_ottawa_hospital_civic_campus.json similarity index 100% rename from configs/config_siemens_cimaq_the_ottawa_hospital_civic_campus.json rename to configs/not_used/config_siemens_cimaq_the_ottawa_hospital_civic_campus.json From b0bbcbacce0230065d5ae1c888ad33cefda39c8d Mon Sep 17 00:00:00 2001 From: Pierre-Emmanuel Morin Date: Fri, 22 Sep 2023 15:38:31 -0400 Subject: [PATCH 14/15] Update all configs files to dcm2bids 3.0 standards --- configs/config_ge.json | 10 +-- configs/config_ge_ccna.json | 6 +- configs/config_ge_cimaq.json | 4 +- configs/config_philips_ccna.json | 19 +++--- configs/config_philips_cimaq.json | 62 ++++++------------- configs/config_philips_cimaq_qc.json | 27 ++++---- configs/config_siemens_ccna.json | 21 ++++--- configs/config_siemens_cimaq.json | 57 +++++++---------- ...config_siemens_cimaq_hospital_douglas.json | 23 ++++--- configs/config_siemens_cimaq_iugm.json | 53 +++++++++------- ...cimaq_mc_connell_brain_imaging_centre.json | 31 ++++++---- 11 files changed, 157 insertions(+), 156 deletions(-) diff --git a/configs/config_ge.json b/configs/config_ge.json index c33a889..5f5c6ef 100644 --- a/configs/config_ge.json +++ b/configs/config_ge.json @@ -16,17 +16,19 @@ } }, { + "id": "task_rest", "datatype": "func", "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "SeriesDescription": "*Connectivity*" } }, { + "id": "task_rest", "datatype": "func", "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "SeriesDescription": "*CONNECTIVITY*" } @@ -36,7 +38,7 @@ "suffix": "T2", "criteria": { "SeriesDescription": "*PD*T2*", - "EchoNumber": 2 + "EchoNumber": 2 } }, { @@ -44,7 +46,7 @@ "suffix": "PD", "criteria": { "SeriesDescription": "*PD*T2*", - "EchoNumber": 1 + "EchoNumber": 1 } }, { diff --git a/configs/config_ge_ccna.json b/configs/config_ge_ccna.json index 29073df..e409404 100644 --- a/configs/config_ge_ccna.json +++ b/configs/config_ge_ccna.json @@ -16,9 +16,10 @@ } }, { + "id": "task_rest", "datatype": "func", "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "SeriesDescription": "*Connectivity*" }, @@ -27,9 +28,10 @@ } }, { + "id": "task_rest", "datatype": "func", "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "SeriesDescription": "*CONNECTIVITY*" }, diff --git a/configs/config_ge_cimaq.json b/configs/config_ge_cimaq.json index 52d81a4..061dc3a 100644 --- a/configs/config_ge_cimaq.json +++ b/configs/config_ge_cimaq.json @@ -17,7 +17,7 @@ { "datatype": "func", "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "SeriesDescription": "*Connectivity*" } @@ -25,7 +25,7 @@ { "datatype": "func", "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "SeriesDescription": "*CONNECTIVITY*" } diff --git a/configs/config_philips_ccna.json b/configs/config_philips_ccna.json index a58664a..d492e37 100644 --- a/configs/config_philips_ccna.json +++ b/configs/config_philips_ccna.json @@ -49,9 +49,10 @@ } }, { + "id": "task_rest", "datatype": "func", "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "SeriesDescription": "*fMRI" }, @@ -76,12 +77,13 @@ "SeriesDescription": "DTI_b0_AP" }, "sidecar_changes": { - "PhaseEncodingDirection": "j", - "intendedFor": 7, - "TotalReadoutTime": 0.062 + "PhaseEncodingDirection": "j", + "TotalReadoutTime": 0.062, + "IntendedFor": "dwi" } }, { + "id": "dwi", "datatype": "dwi", "suffix": "dwi", "criteria": { @@ -92,6 +94,7 @@ } }, { + "id": "dwi", "datatype": "dwi", "suffix": "dwi", "criteria": { @@ -110,8 +113,8 @@ }, "sidecar_changes": { "PhaseEncodingDirection": "j-", - "intendedFor": 9, - "TotalReadoutTime": 0.062 + "TotalReadoutTime": 0.062, + "IntendedFor": "dwi" }, }, { @@ -123,8 +126,8 @@ }, "sidecar_changes": { "PhaseEncodingDirection": "j", - "intendedFor": 10, - "TotalReadoutTime": 0.062 + "TotalReadoutTime": 0.062, + "IntendedFor": "dwi" }, } ] diff --git a/configs/config_philips_cimaq.json b/configs/config_philips_cimaq.json index 32345bd..6c5d9e4 100644 --- a/configs/config_philips_cimaq.json +++ b/configs/config_philips_cimaq.json @@ -70,9 +70,10 @@ } }, { + "id": "task_rest", "datatype": "func", "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "SeriesDescription": "*fMRI" }, @@ -82,9 +83,10 @@ } }, { + "id": "task_memory", "datatype": "func", "suffix": "bold", - "customLabels": "task-memory", + "custom_entities": "task-memory", "criteria": { "SeriesDescription": "*MemoryTask" }, @@ -101,8 +103,8 @@ }, "sidecar_changes": { "PhaseEncodingDirection": "j", - "intendedFor": 7, - "TotalReadoutTime": 1 + "TotalReadoutTime": 1, + "IntendedFor": "task_memory" } }, { @@ -124,8 +126,8 @@ }, "sidecar_changes": { "PhaseEncodingDirection": "j-", - "intendedFor": 9, - "TotalReadoutTime": 1 + "TotalReadoutTime": 1, + "IntendedFor": "task_memory" } }, { @@ -136,8 +138,8 @@ }, "sidecar_changes": { "PhaseEncodingDirection": "j-", - "intendedFor": 7, - "TotalReadoutTime": 1 + "TotalReadoutTime": 1, + "IntendedFor": "task_memory" } }, { @@ -145,35 +147,11 @@ "suffix": "fieldmap", "criteria": { "SeriesDescription": "B0_map", - "ImageType": ["ORIGINAL", "PRIMARY", "B0", "MAP", "B0", "UNSPECIFIED"] - }, - "sidecarChanges": { - "Units": "Hz" - } - }, - { - "dataType": "fmap", - "modalityLabel": "fieldmap", - "intendedFor": 7, - "criteria": { - "SeriesDescription": "B0 map", - "ImageType": ["ORIGINAL", "PRIMARY", "B0 MAP", "B0", "UNSPECIFIED", "FIELDMAPHZ"] - }, - "sidecarChanges": { - "Units": "Hz" - } - }, - { - "dataType": "fmap", - "modalityLabel": "fieldmap", - "intendedFor": 7, - "criteria": { - "SeriesDescription": "B0 map", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"] + "ImageType": ["ORIGINAL", "PRIMARY", "B0", "MAP", "B0", "UNSPECIFIED"] }, "sidecar_changes": { - "intendedFor": 7, - "Units": "Hz" + "Units": "Hz", + "IntendedFor": "task_rest" } }, { @@ -181,11 +159,11 @@ "suffix": "fieldmap", "criteria": { "SeriesDescription": "B0 map", - "ImageType": ["ORIGINAL", "PRIMARY", "B0 MAP", "B0", "UNSPECIFIED", "FIELDMAPHZ"] + "ImageType": ["ORIGINAL", "PRIMARY", "B0 MAP", "B0", "UNSPECIFIED", "FIELDMAPHZ"] }, "sidecar_changes": { - "intendedFor": 7, - "Units": "Hz" + "Units": "Hz", + "IntendedFor": "task_rest" } }, { @@ -193,11 +171,11 @@ "suffix": "fieldmap", "criteria": { "SeriesDescription": "B0 map", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"] + "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"] }, "sidecar_changes": { - "intendedFor": 7, - "Units": "Hz" + "Units": "Hz", + "IntendedFor": "task_rest" } }, { @@ -208,7 +186,7 @@ "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"] }, "sidecar_changes": { - "intendedFor": 7 + "IntendedFor": "task_rest" } } ] diff --git a/configs/config_philips_cimaq_qc.json b/configs/config_philips_cimaq_qc.json index 8611171..6610b46 100644 --- a/configs/config_philips_cimaq_qc.json +++ b/configs/config_philips_cimaq_qc.json @@ -33,9 +33,10 @@ } }, { + "id": "task_rest", "datatype": "func", "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "SeriesDescription": "*fMRI" }, @@ -45,9 +46,10 @@ } }, { + "id": "task_memory", "datatype": "func", "suffix": "bold", - "customLabels": "task-memory", + "custom_entities": "task-memory", "criteria": { "SeriesDescription": "*MemoryTask" }, @@ -64,8 +66,8 @@ }, "sidecar_changes": { "PhaseEncodingDirection": "j", - "intendedFor": 4, - "TotalReadoutTime": 1 + "TotalReadoutTime": 1, + "IntendedFor": "task_rest" } }, { @@ -87,8 +89,8 @@ }, "sidecar_changes": { "PhaseEncodingDirection": "j-", - "intendedFor": 6, - "TotalReadoutTime": 1 + "TotalReadoutTime": 1, + "IntendedFor": "task_memory" } }, { @@ -99,8 +101,8 @@ }, "sidecar_changes": { "PhaseEncodingDirection": "j-", - "intendedFor": 4, - "TotalReadoutTime": 1 + "TotalReadoutTime": 1, + "IntendedFor": "task_rest" } }, { @@ -111,8 +113,8 @@ "ImageType": ["ORIGINAL", "PRIMARY", "B0", "MAP", "B0", "UNSPECIFIED"] }, "sidecar_changes": { - "intendedFor": 4, - "Units": "Hz" + "Units": "Hz", + "IntendedFor": "task_rest" } }, { @@ -120,8 +122,11 @@ "suffix": "magnitude", "criteria": { "SeriesDescription": "B0_map", - "intendedFor": 4, "ImageType": ["ORIGINAL", "PRIMARY", "M", "FFE", "M", "FFE"] + }, + "sidecar_changes": { + "Units": "Hz", + "IntendedFor": "task_rest" } } ] diff --git a/configs/config_siemens_ccna.json b/configs/config_siemens_ccna.json index 932b6ef..56498ee 100644 --- a/configs/config_siemens_ccna.json +++ b/configs/config_siemens_ccna.json @@ -4,7 +4,7 @@ { "datatype": "anat", "suffix": "T2star", - "customLabels": "part-mag", + "custom_entities": "part-mag", "criteria": { "SeriesDescription": "T2*star*", "ImageType": ["M"] @@ -13,16 +13,17 @@ { "datatype": "anat", "suffix": "T2star", - "customLabels": "part-phase", + "custom_entities": "part-phase", "criteria": { "SeriesDescription": "T2*star*", "ImageType": ["P"] } }, { + "id": "taks_rest", "datatype": "func", "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "SeriesDescription": "*Connectivity*" }, @@ -31,9 +32,10 @@ } }, { + "id": "taks_rest", "datatype": "func", "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "SeriesDescription": "*R*S*fMRI*" }, @@ -73,6 +75,7 @@ } }, { + "id": "dwi", "datatype": "dwi", "suffix": "dwi", "criteria": { @@ -86,7 +89,7 @@ "SeriesDescription": "D*0*" }, "sidecar_changes": { - "intendedFor": [7, 8] + "IntendedFor": "dwi" } }, { @@ -98,7 +101,7 @@ "EchoTime": 0.00492 }, "sidecar_changes": { - "intendedFor": [2, 3] + "IntendedFor": "taks_rest" } }, { @@ -110,7 +113,7 @@ "EchoTime": 0.00738 }, "sidecar_changes": { - "intendedFor": [2, 3] + "IntendedFor": "taks_rest" } }, { @@ -122,9 +125,9 @@ "EchoTime": 0.00738 }, "sidecar_changes": { - "intendedFor": [2, 3], "EchoTime1": 0.00492, - "EchoTime2": 0.00738 + "EchoTime2": 0.00738, + "IntendedFor": "taks_rest" } } ] diff --git a/configs/config_siemens_cimaq.json b/configs/config_siemens_cimaq.json index a2f09c8..63329be 100644 --- a/configs/config_siemens_cimaq.json +++ b/configs/config_siemens_cimaq.json @@ -26,9 +26,10 @@ } }, { + "id": "task_memory", "datatype": "func", "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "SeriesDescription": "*Connectivity*", "TaskName": "rest" @@ -37,7 +38,7 @@ { "datatype": "func", "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "SeriesDescription": "*R*fMRI*", "TaskName": "rest" @@ -46,7 +47,7 @@ { "datatype": "func", "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "SeriesDescription": "*Resting*State*", "TaskName": "rest" @@ -57,11 +58,11 @@ "suffix": "magnitude1", "criteria": { "SeriesDescription": "gre_field_mapping", - "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], - "EchoTime": 0.00492 + "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], + "EchoTime": 0.00492 }, "sidecar_changes": { - "intendedFor": 5 + "IntendedFor": "task_memory" } }, { @@ -73,7 +74,7 @@ "EchoTime": 0.00738 } "sidecar_changes": { - "intendedFor": 5 + "IntendedFor": "task_memory" } }, { @@ -84,7 +85,7 @@ "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"] }, "sidecar_changes": { - "intendedFor": 5 + "IntendedFor": "task_memory" } }, { @@ -95,7 +96,7 @@ "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"] }, "sidecar_changes": { - "intendedFor": 5 + "IntendedFor": "task_memory" } }, { @@ -107,7 +108,7 @@ "EchoTime": 0.00492 }, "sidecar_changes": { - "intendedFor": 5 + "IntendedFor": "task_memory" } }, { @@ -119,13 +120,14 @@ "EchoTime": 0.00738 }, "sidecar_changes": { - "intendedFor": 5 + "IntendedFor": "task_memory" } }, { + "id": "task_memory", "datatype": "func", "suffix": "bold", - "customLabels": "task-memory", + "custom_entities": "task-memory", "criteria": { "SeriesDescription": "*MemoryTask", "TaskName": "memory" @@ -138,7 +140,7 @@ "SeriesDescription": "fmri*MemoryTask_*" }, "sidecar_changes": { - "intendedFor": 12 + "IntendedFor": "task_memory" } }, { @@ -150,7 +152,7 @@ "EchoTime": 0.00492 }, "sidecar_changes": { - "intendedFor": 12 + "IntendedFor": "task_memory" } }, { @@ -162,7 +164,7 @@ "EchoTime": 0.00738 }, "sidecar_changes": { - "intendedFor": 12 + "IntendedFor": "task_memory" } }, { @@ -173,7 +175,7 @@ "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND"] }, "sidecar_changes": { - "intendedFor": 12 + "IntendedFor": "task_memory" } }, { @@ -184,27 +186,15 @@ "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND", "PHASE"] }, "sidecar_changes": { - "intendedFor": 12 + "IntendedFor": "task_memory" } }, { - "datatype": "anat", "suffix": "T2w", - "criteria": { - "SeriesDescription": "fmri_fieldmap_gre_field_mapping", - "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND", "PHASE"] - }, - "sidecar_changes": { - "intendedFor": 12 - } - }, - { - "dataType": "anat", - "modalityLabel": "T2w", "criteria": { "SeriesDescription": "*PD*T2*", - "EchoTime": 0.091 + "EchoTime": 0.091 } }, { @@ -212,7 +202,7 @@ "suffix": "T2w", "criteria": { "SeriesDescription": "*PD*T2*", - "EchoTime": 0.093 + "EchoTime": 0.093 } }, { @@ -220,10 +210,11 @@ "suffix": "PD", "criteria": { "SeriesDescription": "*PD*T2*", - "EchoTime": 0.01 + "EchoTime": 0.01 } }, { + "id": "dwi", "datatype": "dwi", "suffix": "dwi", "criteria": { @@ -237,7 +228,7 @@ "SeriesDescription": "D*0*" }, "sidecar_changes": { - "intendedFor": 20 + "IntendedFor": "dwi" } } ] diff --git a/configs/config_siemens_cimaq_hospital_douglas.json b/configs/config_siemens_cimaq_hospital_douglas.json index 6ff0ae2..4a2bb30 100644 --- a/configs/config_siemens_cimaq_hospital_douglas.json +++ b/configs/config_siemens_cimaq_hospital_douglas.json @@ -10,9 +10,10 @@ } }, { + "id": "task_rest", "datatype": "func", "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "ProtocolName": "Resting*State*" }, @@ -29,7 +30,7 @@ "EchoTime": 0.00492 }, "sidecar_changes": { - "intendedFor": 1, + "IntendedFor": "task_rest", "TaskName": "rest" } }, @@ -42,7 +43,7 @@ "EchoTime": 0.00738 }, "sidecar_changes": { - "intendedFor": 1, + "IntendedFor": "task_rest", "TaskName": "rest" } }, @@ -55,15 +56,16 @@ "EchoTime": 0.00738 }, "sidecar_changes": { - "intendedFor": 1, + "IntendedFor": "task_rest", "EchoTime1": 0.00492, "EchoTime2": 0.00738 } }, { + "id": "task_memory", "datatype": "func", "suffix": "bold", - "customLabels": "task-memory", + "custom_entities": "task-memory", "criteria": { "SeriesDescription": "*MemoryTask" }, @@ -80,7 +82,7 @@ "EchoTime": 0.00492 }, "sidecar_changes": { - "intendedFor": 5, + "IntendedFor": "task_memory" } }, { @@ -92,7 +94,7 @@ "EchoTime": 0.00738 }, "sidecar_changes": { - "intendedFor": 5, + "IntendedFor": "task_memory" } }, { @@ -104,7 +106,7 @@ "EchoTime": 0.00738 }, "sidecar_changes": { - "intendedFor": 5, + "IntendedFor": "task_memory", "EchoTime1": 0.00492, "EchoTime2": 0.00738 } @@ -116,7 +118,7 @@ "SeriesDescription": "fmri*MemoryTask_*" }, "sidecar_changes": { - "intendedFor": 5 + "IntendedFor": "task_memory" } }, { @@ -136,6 +138,7 @@ } }, { + "id": "dwi", "datatype": "dwi", "suffix": "dwi", "criteria": { @@ -149,7 +152,7 @@ "SeriesDescription": "D*B0*" }, "sidecar_changes": { - "intendedFor": 12 + "IntendedFor": "dwi" } } ] diff --git a/configs/config_siemens_cimaq_iugm.json b/configs/config_siemens_cimaq_iugm.json index 6d8a245..9a0e398 100644 --- a/configs/config_siemens_cimaq_iugm.json +++ b/configs/config_siemens_cimaq_iugm.json @@ -21,7 +21,7 @@ "suffix": "T2star", "criteria": { "SeriesDescription": "*T2*star*", - "ImageType": ["*", "*", "M", "*"] + "ImageType": ["*", "*", "M", "*"] } }, { @@ -29,21 +29,14 @@ "suffix": "T2star", "criteria": { "SeriesDescription": "*T2*star*", - "ImageType": ["*", "*", "P", "*", "*"] + "ImageType": ["*", "*", "P", "*", "*"] } }, { + "id": "task_rest", "datatype": "func", "suffix": "bold", - "criteria": { - "SeriesDescription": "*T2*star*", - "ImageType": ["*", "*", "P", "*", "*"] - } - }, - { - "datatype": "func", - "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "EchoTime": 0.03, "SliceThickness": 3.5 @@ -61,7 +54,7 @@ "EchoTime": 0.00492 }, "sidecar_changes": { - "intendedFor": 1, + "IntendedFor": "task_rest" } }, { @@ -73,7 +66,7 @@ "EchoTime": 0.00738 }, "sidecar_changes": { - "intendedFor": 1, + "IntendedFor": "task_rest" } }, { @@ -85,15 +78,16 @@ "EchoTime": 0.00738 }, "sidecar_changes": { - "intendedFor": 1, "EchoTime1": 0.00492, - "EchoTime2": 0.00738 + "EchoTime2": 0.00738, + "IntendedFor": "task_rest" } }, { + "id": "task_memory", "datatype": "func", "suffix": "bold", - "customLabels": "task-memory", + "custom_entities": "task-memory", "criteria": { "SeriesDescription": "*MemoryTask" }, @@ -110,7 +104,7 @@ "EchoTime": 0.00492 }, "sidecar_changes": { - "intendedFor": 5 + "IntendedFor": "task_memory" } }, { @@ -122,7 +116,7 @@ "EchoTime": 0.00738 }, "sidecar_changes": { - "intendedFor": 5 + "IntendedFor": "task_memory" } }, { @@ -134,9 +128,23 @@ "EchoTime": 0.00738 }, "sidecar_changes": { - "intendedFor": 5, "EchoTime1": 0.00492, - "EchoTime2": 0.00738 + "EchoTime2": 0.00738, + "IntendedFor": "task_memory" + } + }, + { + "datatype": "fmap", + "suffix": "phasediff", + "criteria": { + "SeriesDescription": "*gre_field_mapping", + "ImageType": ["ORIGINAL", "PRIMARY", "P", "ND", "PHASE"], + "EchoTime": 0.00738 + }, + "sidecar_changes": { + "EchoTime1": 0.00492, + "EchoTime2": 0.00738, + "IntendedFor": "task_memory" } }, { @@ -146,7 +154,7 @@ "SeriesDescription": "fmri*MemoryTask_*" }, "sidecar_changes": { - "intendedFor": 5 + "IntendedFor": "task_memory" } }, { @@ -174,6 +182,7 @@ } }, { + "id": "dwi", "datatype": "dwi", "suffix": "dwi", "criteria": { @@ -187,7 +196,7 @@ "SeriesDescription": "D*0*" }, "sidecar_changes": { - "intendedFor": 12 + "IntendedFor": "dwi" } }, { diff --git a/configs/config_siemens_cimaq_mc_connell_brain_imaging_centre.json b/configs/config_siemens_cimaq_mc_connell_brain_imaging_centre.json index 40f609f..5734a9b 100644 --- a/configs/config_siemens_cimaq_mc_connell_brain_imaging_centre.json +++ b/configs/config_siemens_cimaq_mc_connell_brain_imaging_centre.json @@ -17,9 +17,10 @@ } }, { + "id": "task_rest", "datatype": "func", "suffix": "bold", - "customLabels": "task-rest", + "custom_entities": "task-rest", "criteria": { "ProtocolName": "*Resting*State*" }, @@ -36,7 +37,7 @@ "EchoTime": 0.00492 }, "sidecar_changes": { - "intendedFor": 1 + "IntendedFor": "task_rest" } }, { @@ -48,7 +49,7 @@ "EchoTime": 0.00738 }, "sidecar_changes": { - "intendedFor": 1 + "IntendedFor": "task_rest" } }, { @@ -60,15 +61,16 @@ "EchoTime": 0.00738 }, "sidecar_changes": { - "intendedFor": 1, "EchoTime1": 0.00492, - "EchoTime2": 0.00738 + "EchoTime2": 0.00738, + "IntendedFor": "task_rest" } }, { + "id": "task_memory", "datatype": "func", "suffix": "bold", - "customLabels": "task-memory", + "custom_entities": "task-memory", "criteria": { "SeriesDescription": "*MemoryTask" }, @@ -79,12 +81,14 @@ { "datatype": "fmap", "suffix": "magnitude1", - "intendedFor": 5, "criteria": { "SeriesDescription": "fmri_fieldmap_gre_field_mapping", "ImageType": ["ORIGINAL", "PRIMARY", "M", "ND"], "EchoTime": 0.00492 - } + }, + "sidecar_changes": { + "IntendedFor": "task_memory" + } }, { "datatype": "fmap", @@ -95,7 +99,7 @@ "EchoTime": 0.00738 }, "sidecar_changes": { - "intendedFor": 5 + "IntendedFor": "task_memory" } }, { @@ -107,9 +111,9 @@ "EchoTime": 0.00738 }, "sidecar_changes": { - "intendedFor": 5, "EchoTime1": 0.00492, - "EchoTime2": 0.00738 + "EchoTime2": 0.00738, + "IntendedFor": "task_memory" } }, { @@ -119,7 +123,7 @@ "SeriesDescription": "fmri*MemoryTask_*" }, "sidecar_changes": { - "intendedFor": 5 + "IntendedFor": "task_memory" } }, { @@ -139,6 +143,7 @@ } }, { + "id": "dwi", "datatype": "dwi", "suffix": "dwi", "criteria": { @@ -152,7 +157,7 @@ "SeriesDescription": "D*B0*" }, "sidecar_changes": { - "intendedFor": 12 + "IntendedFor": "dwi" } } ] From 640c0d3e86670c9ae5e33601ce3a98d2c9ae7296 Mon Sep 17 00:00:00 2001 From: Pierre-Emmanuel Morin Date: Wed, 4 Oct 2023 15:52:50 -0400 Subject: [PATCH 15/15] Update master requirement.txt no longer necessary README.txt changed accordingly --- README.md | 10 +++++----- requirements.txt | 39 --------------------------------------- 2 files changed, 5 insertions(+), 44 deletions(-) delete mode 100644 requirements.txt diff --git a/README.md b/README.md index e4282be..49b595d 100644 --- a/README.md +++ b/README.md @@ -1,18 +1,18 @@ # bids_conversion 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 -* requirements.txt (pip install -r requirements.txt) * dcm2bids (https://github.com/UNFmontreal/Dcm2Bids) * dcm2niix (https://github.com/rordenlab/dcm2niix) Run (two steps) -* python3 convert_bids_ccna_cimaq.py /dicom_directory /output_directory mode (ccna or cimaq) > file +* python3 convert_bids_ccna_cimaq.py /input_directory /output_directory mode (ccna or cimaq) > file * bash ./file Tips -* dicom_directory must contain the tarchive files (usually found in /data/$PROJECT/data/tarchive) -* the output file will contain the untar tarchive files, the bids files (sub-PSCID/CandID) and a sub-folder containing the log and failed conversion +* 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 bundle into smaller ones, make sure all of a participant's files are grouped together. If not, you will have to reorganize the tree manually +* 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 diff --git a/requirements.txt b/requirements.txt deleted file mode 100644 index 2675b91..0000000 --- a/requirements.txt +++ /dev/null @@ -1,39 +0,0 @@ -backcall==0.1.0 -bids-validator==1.2.4 -bz2file==0.98 -coloredlogs==10.0 -cycler==0.10.0 -decorator==4.4.0 -dipy==1.0.0 -docopt==0.6.2 -fury==0.2.0 -future==0.17.1 -h5py==2.9.0 -humanfriendly==4.18 -ipython==7.8.0 -ipython-genutils==0.2.0 -jedi==0.15.1 -kiwisolver==1.0.1 -matplotlib==2.2.2 -nibabel==2.4.0 -num2words==0.5.10 -numpy==1.16.2 -pandas==0.25.1 -parso==0.5.1 -patsy==0.5.1 -pexpect==4.7.0 -pickleshare==0.7.5 -Pillow==7.1.0 -prompt-toolkit==2.0.9 -ptyprocess==0.6.0 -pybids==0.9.1 -Pygments==2.4.2 -pyparsing==2.2.0 -python-dateutil==2.7.2 -pytz==2018.4 -scipy==1.0.1 -six==1.11.0 -SQLAlchemy==1.3.8 -traitlets==4.3.2 -vtk==8.1.0 -wcwidth==0.1.7