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neuroimagen:dcm2bids [2019/06/04 08:08]
osotolongo [Know your data]
neuroimagen:dcm2bids [2020/08/04 10:58] (current)
Line 15: Line 15:
 <code bash> <code bash>
 [osotolongo@detritus tmp]$ dcm2bids_helper -d /nas/corachan/MOPEAD/24N223T4/ [osotolongo@detritus tmp]$ dcm2bids_helper -d /nas/corachan/MOPEAD/24N223T4/
 +Example in:
 +/nas/data/mopead/tmp/tmp_dcm2bids/helper
 +[osotolongo@detritus tmp]$ ls tmp_dcm2bids/helper/
 +10001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008.json     23001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008.json
 +10001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008.nii.gz     23001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008.nii.gz
 +1001_24N223T4_AAhead_scout_20181205124008.json     24001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008.json
 +1001_24N223T4_AAhead_scout_20181205124008.nii.gz     24001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008.nii.gz
 +11001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008.json     25001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008.json
 +11001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008.nii.gz     25001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008.nii.gz
 +12001_24N223T4_ep2d_bold_p2_resting_state_20181205124008.json     27001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008.json
 +12001_24N223T4_ep2d_bold_p2_resting_state_20181205124008.nii.gz     27001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008.nii.gz
 +14001_24N223T4_ep2d_fid_basic_bold_p2_AP_20181205124008.json     28001_24N223T4_DTIep2d_diff_mddw_4b0_PA_20181205124008.json
 +14001_24N223T4_ep2d_fid_basic_bold_p2_AP_20181205124008.nii.gz     28001_24N223T4_DTIep2d_diff_mddw_4b0_PA_20181205124008.nii.gz
 +15001_24N223T4_ep2d_fid_basic_bold_p2_PA_20181205124008.json     5001_24N223T4_t1_mprage_sag_p2_iso_20181205124008.json
 +15001_24N223T4_ep2d_fid_basic_bold_p2_PA_20181205124008.nii.gz     5001_24N223T4_t1_mprage_sag_p2_iso_20181205124008.nii.gz
 +16001_24N223T4_asl_3d_tra_iso_3.0_highres_20181205124008.json     6001_24N223T4_t2_space_dark-fluid_sag_p2_iso_20181205124008.json
 +16001_24N223T4_asl_3d_tra_iso_3.0_highres_20181205124008.nii.gz     6001_24N223T4_t2_space_dark-fluid_sag_p2_iso_20181205124008.nii.gz
 +18001_24N223T4_asl_3d_tra_iso_3.0_highres_20181205124008_e1.json    7001_24N223T4_pd+t2_tse_tra_p2_3mm_20181205124008_e1a.json
 +18001_24N223T4_asl_3d_tra_iso_3.0_highres_20181205124008_e1.nii.gz  7001_24N223T4_pd+t2_tse_tra_p2_3mm_20181205124008_e1a.nii.gz
 +18001_24N223T4_asl_3d_tra_iso_3.0_highres_20181205124008.json     7001_24N223T4_pd+t2_tse_tra_p2_3mm_20181205124008_e1.json
 +18001_24N223T4_asl_3d_tra_iso_3.0_highres_20181205124008.nii.gz     7001_24N223T4_pd+t2_tse_tra_p2_3mm_20181205124008_e1.nii.gz
 +20001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008.json    8001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008.json
 +20001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008.nii.gz  8001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008.nii.gz
 +22001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008.json    9001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008_ph.json
 +22001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008.nii.gz  9001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008_ph.nii.gz
 </code> </code>
 +
 +Esto genera los archivos NIfTI y //.json// con el contenido del DCM. De aqui debemos generar el archivo de configuracion.
 +
 +Lo que nos interesa es T1, T2, DTI y fMRI. Vamos a empezar por el T1, 
 +<code bash>
 +[osotolongo@detritus tmp]$ ls tmp_dcm2bids/helper/ | grep t1
 +5001_24N223T4_t1_mprage_sag_p2_iso_20181205124008.json
 +5001_24N223T4_t1_mprage_sag_p2_iso_20181205124008.nii.gz
 +[osotolongo@detritus tmp]$ cat tmp_dcm2bids/helper/5001_24N223T4_t1_mprage_sag_p2_iso_20181205124008.json
 +{
 + "Modality": "MR",
 + "MagneticFieldStrength": 3,
 + "Manufacturer": "Siemens",
 + "ManufacturersModelName": "MAGNETOM_Vida",
 + "InstitutionName": "Clinica_Corachan",
 + "InstitutionAddress": "Calle_Buigas_19_Barcelona_ES_08007",
 + "DeviceSerialNumber": "175609",
 + "StationName": "AWP175609",
 + "BodyPartExamined": "BRAIN",
 + "PatientPosition": "HFS",
 + "ProcedureStepDescription": "RM_CRANEO_PROT_MOPEAD",
 + "SoftwareVersions": "syngo_MR_XA10",
 + "MRAcquisitionType": "3D",
 + "SeriesDescription": "t1_mprage_sag_p2_iso",
 + "ProtocolName": "t1_mprage_sag_p2_iso",
 + "ScanningSequence": "GR",
 + "SequenceVariant": "SK",
 + "ScanOptions": "PFP_PER",
 + "SequenceName": "_tfl3d1_16ns",
 + "ImageType": ["ORIGINAL", "PRIMARY", "M", "NORM", "DIS2D", "MFSPLIT"],
 + "SeriesNumber": 5001,
 + "AcquisitionTime": "12:41:26.122500",
 + "AcquisitionNumber": 1,
 + "SliceThickness": 1.2,
 + "SAR": 0.0822361,
 + "EchoTime": 0.00223,
 + "RepetitionTime": 2.2,
 + "InversionTime": 0.968,
 + "FlipAngle": 8,
 + "PercentPhaseFOV": 93.75,
 + "PhaseEncodingSteps": 240,
 + "AcquisitionMatrixPE": 240,
 + "ReconMatrixPE": 256,
 + "PixelBandwidth": 199,
 + "ImageOrientationPatientDICOM": [
 + 0,
 + 0.99916,
 + -0.0409808,
 + 0,
 + -0.0409808,
 + -0.99916 ],
 + "InPlanePhaseEncodingDirectionDICOM": "ROW",
 + "ConversionSoftware": "dcm2niix",
 + "ConversionSoftwareVersion": "v1.0.20180622 (JP2:OpenJPEG) (JP-LS:CharLS) GCC5.5.0"
 +}
 +
 +</code>
 +
 +Tenemos que hacer un archivo que diga el criterio de busqueda para dcm2bids y como etiquetar la salida,
 +<code JSON>
 +{
 + "descriptions": [
 + {
 + "dataType": "anat",
 + "modalityLabel": "T1w",
 + "criteria": {
 + "SeriesDescription": "t1_mprage_sag_p2_iso"
 + }
 + }
 + ]
 +}
 +
 +</code>
 +
 +Vamos a probarlo ahora, segun nuestra DB, este sujeto es el //0024//, asi que,
 +
 +<code bash>
 +[osotolongo@detritus tmp]$ dcm2bids -d /nas/corachan/MOPEAD/24N223T4/ -p 0024 -c conv_config.json 
 +INFO:dcm2bids.dcm2bids:--- dcm2bids start ---
 +INFO:dcm2bids.dcm2bids:OS:version: Linux-2.6.32-431.17.1.el6.centos.plus.x86_64-x86_64-with-centos-6.10-Final
 +INFO:dcm2bids.dcm2bids:python:version: 3.4.8 (default, Apr  9 2018, 11:43:18) [GCC 4.4.7 20120313 (Red Hat 4.4.7-18)]
 +INFO:dcm2bids.dcm2bids:dcm2bids:version: 2.1.4
 +INFO:dcm2bids.dcm2bids:dcm2niix:version: v1.0.20180622
 +INFO:dcm2bids.dcm2bids:participant: sub-0024
 +INFO:dcm2bids.dcm2bids:session: 
 +INFO:dcm2bids.dcm2bids:config: /nas/data/mopead/tmp/conv_config.json
 +INFO:dcm2bids.dcm2bids:BIDS directory: /nas/data/mopead/tmp
 +INFO:dcm2bids.utils:Running dcm2niix -b y -ba y -z y -f '%3s_%f_%p_%t' -o /nas/data/mopead/tmp/tmp_dcm2bids/sub-0024 /nas/corachan/MOPEAD/24N223T4/
 +INFO:dcm2bids.dcm2niix:Check log file for dcm2niix output
 +INFO:dcm2bids.sidecar:Sidecars pairing:
 +INFO:dcm2bids.sidecar:No Pairing  <-  1001_24N223T4_AAhead_scout_20181205124008
 +INFO:dcm2bids.sidecar:_T1w  <-  5001_24N223T4_t1_mprage_sag_p2_iso_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  6001_24N223T4_t2_space_dark-fluid_sag_p2_iso_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  7001_24N223T4_pd+t2_tse_tra_p2_3mm_20181205124008_e1
 +INFO:dcm2bids.sidecar:No Pairing  <-  7001_24N223T4_pd+t2_tse_tra_p2_3mm_20181205124008_e1a
 +INFO:dcm2bids.sidecar:No Pairing  <-  8001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  9001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008_ph
 +INFO:dcm2bids.sidecar:No Pairing  <-  10001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  11001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  12001_24N223T4_ep2d_bold_p2_resting_state_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  14001_24N223T4_ep2d_fid_basic_bold_p2_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  15001_24N223T4_ep2d_fid_basic_bold_p2_PA_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  16001_24N223T4_asl_3d_tra_iso_3.0_highres_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  18001_24N223T4_asl_3d_tra_iso_3.0_highres_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  18001_24N223T4_asl_3d_tra_iso_3.0_highres_20181205124008_e1
 +INFO:dcm2bids.sidecar:No Pairing  <-  20001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  22001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  23001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  24001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  25001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  27001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  28001_24N223T4_DTIep2d_diff_mddw_4b0_PA_20181205124008
 +INFO:dcm2bids.dcm2bids:moving acquisitions into BIDS folder
 +WARNING:dcm2bids.version:Your using dcm2niix version v1.0.20180622
 +WARNING:dcm2bids.version:A new version exists : v1.0.20190410
 +WARNING:dcm2bids.version:Check https://github.com/rordenlab/dcm2niix
 +
 +</code>
 +y nos deja el T1 en su sitio,
 +
 +<code>
 +[osotolongo@detritus tmp]$ tree sub-0024
 +sub-0024
 +└── anat
 +    ├── sub-0024_T1w.json
 +    └── sub-0024_T1w.nii.gz
 +
 +1 directory, 2 files
 +</code>
 +
 +Vamos a intentar añadir ahora el fMRI que se ve menos complicado,
 +
 +<code>
 +[osotolongo@detritus tmp]$ cat conv_config.json
 +{
 + "descriptions": [
 + {
 + "dataType": "anat",
 + "modalityLabel": "T1w",
 + "criteria": {
 + "SeriesDescription": "t1_mprage_sag_p2_iso"
 + }
 + },
 + {
 + "dataType": "func",
 + "modalityLabel": "bold",
 + "customLabels": "task-rest",
 + "criteria": {
 + "SeriesDescription": "*resting_state",
 + }
 + }
 + ]
 +}
 +[osotolongo@detritus tmp]$ dcm2bids -d /nas/corachan/MOPEAD/24N223T4/ -p 0024 -c conv_config.json 
 +INFO:dcm2bids.dcm2bids:--- dcm2bids start ---
 +INFO:dcm2bids.dcm2bids:OS:version: Linux-2.6.32-431.17.1.el6.centos.plus.x86_64-x86_64-with-centos-6.10-Final
 +INFO:dcm2bids.dcm2bids:python:version: 3.4.8 (default, Apr  9 2018, 11:43:18) [GCC 4.4.7 20120313 (Red Hat 4.4.7-18)]
 +INFO:dcm2bids.dcm2bids:dcm2bids:version: 2.1.4
 +INFO:dcm2bids.dcm2bids:dcm2niix:version: v1.0.20180622
 +INFO:dcm2bids.dcm2bids:participant: sub-0024
 +INFO:dcm2bids.dcm2bids:session: 
 +INFO:dcm2bids.dcm2bids:config: /nas/data/mopead/tmp/conv_config.json
 +INFO:dcm2bids.dcm2bids:BIDS directory: /nas/data/mopead/tmp
 +WARNING:dcm2bids.dcm2niix:Previous dcm2niix directory output found:
 +WARNING:dcm2bids.dcm2niix:/nas/data/mopead/tmp/tmp_dcm2bids/sub-0024
 +WARNING:dcm2bids.dcm2niix:Use --forceDcm2niix to rerun dcm2niix
 +INFO:dcm2bids.sidecar:Sidecars pairing:
 +INFO:dcm2bids.sidecar:No Pairing  <-  1001_24N223T4_AAhead_scout_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  6001_24N223T4_t2_space_dark-fluid_sag_p2_iso_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  7001_24N223T4_pd+t2_tse_tra_p2_3mm_20181205124008_e1
 +INFO:dcm2bids.sidecar:No Pairing  <-  7001_24N223T4_pd+t2_tse_tra_p2_3mm_20181205124008_e1a
 +INFO:dcm2bids.sidecar:No Pairing  <-  8001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  9001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008_ph
 +INFO:dcm2bids.sidecar:No Pairing  <-  10001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  11001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008
 +INFO:dcm2bids.sidecar:_task-rest_bold  <-  12001_24N223T4_ep2d_bold_p2_resting_state_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  14001_24N223T4_ep2d_fid_basic_bold_p2_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  15001_24N223T4_ep2d_fid_basic_bold_p2_PA_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  16001_24N223T4_asl_3d_tra_iso_3.0_highres_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  18001_24N223T4_asl_3d_tra_iso_3.0_highres_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  18001_24N223T4_asl_3d_tra_iso_3.0_highres_20181205124008_e1
 +INFO:dcm2bids.sidecar:No Pairing  <-  20001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  22001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  23001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  24001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  25001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  27001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  28001_24N223T4_DTIep2d_diff_mddw_4b0_PA_20181205124008
 +INFO:dcm2bids.dcm2bids:moving acquisitions into BIDS folder
 +WARNING:dcm2bids.version:Your using dcm2niix version v1.0.20180622
 +WARNING:dcm2bids.version:A new version exists : v1.0.20190410
 +WARNING:dcm2bids.version:Check https://github.com/rordenlab/dcm2niix
 +[osotolongo@detritus tmp]$ tree sub-0024
 +sub-0024
 +├── anat
 +│   ├── sub-0024_T1w.json
 +│   └── sub-0024_T1w.nii.gz
 +└── func
 +    ├── sub-0024_task-rest_bold.json
 +    └── sub-0024_task-rest_bold.nii.gz
 +
 +2 directories, 4 files
 +
 +</code>
 +
 +Voy a cambiar las reglas y asegurarme que se sobreescriba todo,
 +
 +<code>
 +[osotolongo@detritus tmp]$ cat conv_config.json
 +{
 + "descriptions": [
 + {
 + "dataType": "anat",
 + "modalityLabel": "T1w",
 + "criteria": {
 + "SeriesDescription": "t1_mprage_sag_p2_iso"
 + }
 + },
 + {
 + "dataType": "func",
 + "modalityLabel": "bold",
 + "customLabels": "task-rest",
 + "criteria": {
 + "SeriesDescription": "*resting_state+"
 + }
 + },
 + {
 + "dataType": "func",
 +                        "modalityLabel": "bold",
 +                        "customLabels": "task-rest_dir-PA_sbref",
 + "criteria": {
 + "SeriesDescription": "ep2d_fid_basic_bold_p2_PA"
 + }
 + },
 +                {
 +                        "dataType": "func",
 +                        "modalityLabel": "bold",
 +                        "customLabels": "task-rest_dir-AP_sbref",
 +                        "criteria": {
 +                                "SeriesDescription": "ep2d_fid_basic_bold_p2_AP"
 +                        }
 +                }
 + ]
 +}
 +
 +[osotolongo@detritus tmp]$ dcm2bids -d /nas/corachan/MOPEAD/24N223T4/ -p 0024 -c conv_config.json --clobber --forceDcm2niix
 +INFO:dcm2bids.dcm2bids:--- dcm2bids start ---
 +INFO:dcm2bids.dcm2bids:OS:version: Linux-2.6.32-431.17.1.el6.centos.plus.x86_64-x86_64-with-centos-6.10-Final
 +INFO:dcm2bids.dcm2bids:python:version: 3.4.8 (default, Apr  9 2018, 11:43:18) [GCC 4.4.7 20120313 (Red Hat 4.4.7-18)]
 +INFO:dcm2bids.dcm2bids:dcm2bids:version: 2.1.4
 +INFO:dcm2bids.dcm2bids:dcm2niix:version: v1.0.20180622
 +INFO:dcm2bids.dcm2bids:participant: sub-0024
 +INFO:dcm2bids.dcm2bids:session: 
 +INFO:dcm2bids.dcm2bids:config: /nas/data/mopead/tmp/conv_config.json
 +INFO:dcm2bids.dcm2bids:BIDS directory: /nas/data/mopead/tmp
 +WARNING:dcm2bids.dcm2niix:Previous dcm2niix directory output found:
 +WARNING:dcm2bids.dcm2niix:/nas/data/mopead/tmp/tmp_dcm2bids/sub-0024
 +WARNING:dcm2bids.dcm2niix:'force' argument is set to True
 +WARNING:dcm2bids.dcm2niix:Cleaning the previous directory and running dcm2niix
 +INFO:dcm2bids.utils:Running dcm2niix -b y -ba y -z y -f '%3s_%f_%p_%t' -o /nas/data/mopead/tmp/tmp_dcm2bids/sub-0024 /nas/corachan/MOPEAD/24N223T4/
 +INFO:dcm2bids.dcm2niix:Check log file for dcm2niix output
 +INFO:dcm2bids.sidecar:Sidecars pairing:
 +INFO:dcm2bids.sidecar:No Pairing  <-  1001_24N223T4_AAhead_scout_20181205124008
 +INFO:dcm2bids.sidecar:_T1w  <-  5001_24N223T4_t1_mprage_sag_p2_iso_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  6001_24N223T4_t2_space_dark-fluid_sag_p2_iso_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  7001_24N223T4_pd+t2_tse_tra_p2_3mm_20181205124008_e1
 +INFO:dcm2bids.sidecar:No Pairing  <-  7001_24N223T4_pd+t2_tse_tra_p2_3mm_20181205124008_e1a
 +INFO:dcm2bids.sidecar:No Pairing  <-  8001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  9001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008_ph
 +INFO:dcm2bids.sidecar:No Pairing  <-  10001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  11001_24N223T4_t2_swi_tra_p2_384_2mm_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  12001_24N223T4_ep2d_bold_p2_resting_state_20181205124008
 +INFO:dcm2bids.sidecar:_task-rest_dir-AP_sbref_bold  <-  14001_24N223T4_ep2d_fid_basic_bold_p2_AP_20181205124008
 +INFO:dcm2bids.sidecar:_task-rest_dir-PA_sbref_bold  <-  15001_24N223T4_ep2d_fid_basic_bold_p2_PA_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  16001_24N223T4_asl_3d_tra_iso_3.0_highres_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  18001_24N223T4_asl_3d_tra_iso_3.0_highres_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  18001_24N223T4_asl_3d_tra_iso_3.0_highres_20181205124008_e1
 +INFO:dcm2bids.sidecar:No Pairing  <-  20001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  22001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  23001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  24001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  25001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  27001_24N223T4_DTIep2d_diff_mddw_48dir_p3_AP_20181205124008
 +INFO:dcm2bids.sidecar:No Pairing  <-  28001_24N223T4_DTIep2d_diff_mddw_4b0_PA_20181205124008
 +INFO:dcm2bids.dcm2bids:moving acquisitions into BIDS folder
 +INFO:dcm2bids.dcm2bids:'/nas/data/mopead/tmp/sub-0024/anat/sub-0024_T1w.json' already exists
 +INFO:dcm2bids.dcm2bids:Overwriting because of 'clobber' option
 +INFO:dcm2bids.dcm2bids:'/nas/data/mopead/tmp/sub-0024/anat/sub-0024_T1w.nii.gz' already exists
 +INFO:dcm2bids.dcm2bids:Overwriting because of 'clobber' option
 +WARNING:dcm2bids.version:Your using dcm2niix version v1.0.20180622
 +WARNING:dcm2bids.version:A new version exists : v1.0.20190410
 +WARNING:dcm2bids.version:Check https://github.com/rordenlab/dcm2niix
 +[osotolongo@detritus tmp]$ tree sub-0024
 +sub-0024
 +├── anat
 +│   ├── sub-0024_T1w.json
 +│   └── sub-0024_T1w.nii.gz
 +└── func
 +    ├── sub-0024_task-rest_bold.json
 +    ├── sub-0024_task-rest_bold.nii.gz
 +    ├── sub-0024_task-rest_dir-AP_sbref_bold.json
 +    ├── sub-0024_task-rest_dir-AP_sbref_bold.nii.gz
 +    ├── sub-0024_task-rest_dir-PA_sbref_bold.json
 +    └── sub-0024_task-rest_dir-PA_sbref_bold.nii.gz
 +
 +2 directories, 8 files
 +</code>
 +y por ultimo el DTI,
 +<code>
 +[osotolongo@detritus tmp]$ cat conv_config.json 
 +{
 + "descriptions": [
 + {
 + "dataType": "anat",
 + "modalityLabel": "T1w",
 + "criteria": {
 + "SeriesDescription": "t1_mprage_sag_p2_iso"
 + }
 + },
 + {
 + "dataType": "func",
 + "modalityLabel": "bold",
 + "customLabels": "task-rest",
 + "criteria": {
 + "SeriesDescription": "*resting_state*"
 + }
 + },
 + {
 + "dataType": "func",
 +                        "modalityLabel": "bold",
 +                        "customLabels": "task-rest_dir-PA_sbref",
 + "criteria": {
 + "SeriesDescription": "ep2d_fid_basic_bold_p2_PA"
 + }
 + },
 +                {
 +                        "dataType": "func",
 +                        "modalityLabel": "bold",
 +                        "customLabels": "task-rest_dir-AP_sbref",
 +                        "criteria": {
 +                                "SeriesDescription": "ep2d_fid_basic_bold_p2_AP"
 +                        }
 +                },
 + {
 + "dataType": "dwi",
 + "modalityLabel": "dwi",
 + "criteria": {
 + "SeriesDescription": "DTIep2d_diff_mddw_48dir_p3_AP"
 + }
 + },
 + {
 +                        "dataType": "dwi",
 +                        "modalityLabel": "dwi",
 + "customLabels": "dir-PA_sbref",
 +                        "criteria": {
 +                                "SeriesDescription": "DTIep2d_diff_mddw_4b0_PA"
 +                        }
 +
 + }
 + ]
 +}
 +[osotolongo@detritus tmp]$ tree sub-0024/
 +sub-0024/
 +├── anat
 +│   ├── sub-0024_T1w.json
 +│   └── sub-0024_T1w.nii.gz
 +├── dwi
 +│   ├── sub-0024_dir-PA_sbref_dwi.json
 +│   ├── sub-0024_dir-PA_sbref_dwi.nii.gz
 +│   ├── sub-0024_dwi.json
 +│   └── sub-0024_dwi.nii.gz
 +└── func
 +    ├── sub-0024_task-rest_bold.json
 +    ├── sub-0024_task-rest_bold.nii.gz
 +    ├── sub-0024_task-rest_dir-AP_sbref_bold.json
 +    ├── sub-0024_task-rest_dir-AP_sbref_bold.nii.gz
 +    ├── sub-0024_task-rest_dir-PA_sbref_bold.json
 +    └── sub-0024_task-rest_dir-PA_sbref_bold.nii.gz
 +
 +3 directories, 12 files
 +</code>
 +
 +===== Convirtiendo =====
 +
 +Ya tengo la estructura de conversón hecha. Ahora debo intentar convertir los sujetos segun la base de datos del proyecto.
 +
 +Tengo la estructura de nombres y directorio almacenados en //ni_names.csv// y la configuracion en //tmpbids/conv_config.json//.
 +
 +Como siempre que se corre en un grupo grande empiezan a surgir problemas asi que he tenido que hacer algunos cambios en la configuracion.
 +
 +<code bash>
 +[osotolongo@detritus tmpbids]$ cat conv_config.json
 +{
 +        "descriptions": [
 +                {
 +                        "dataType": "anat",
 +                        "modalityLabel": "T1w",
 +                        "criteria": {
 +                                "SeriesDescription": "t1_mprage_sag_p2_iso"
 +                        }
 +                },
 +                {
 +                        "dataType": "anat",
 +                        "modalityLabel": "T2w",
 +                        "criteria": {
 +                                "SeriesDescription": "t2_space_dark-fluid_sag_p2_iso"
 +                        }
 +                },
 +                {
 +                        "dataType": "func",
 +                        "modalityLabel": "bold",
 +                        "customLabels": "task-rest",
 +                        "criteria": {
 +                                "SeriesDescription": "*resting_state*",
 +                                "RepetitionTime": 2.13
 +                        }
 +                },
 +                {
 +                        "dataType": "func",
 +                        "modalityLabel": "bold",
 +                        "customLabels": "task-rest_dir-PA_sbref",
 +                        "criteria": {
 +                                "SeriesDescription": "ep2d_fid_basic_bold_p2_PA"
 +                        }
 +                },
 +                {
 +                        "dataType": "func",
 +                        "modalityLabel": "bold",
 +                        "customLabels": "task-rest_dir-AP_sbref",
 +                        "criteria": {
 +                                "SeriesDescription": "ep2d_fid_basic_bold_p2_AP"
 +                        }
 +                },
 +                {
 +                        "dataType": "dwi",
 +                        "modalityLabel": "dwi",
 +                        "criteria": {
 +                                "SeriesDescription": "DTIep2d_diff_mddw_48dir_p3_AP"
 +                        }
 +                },
 +                {
 +                        "dataType": "dwi",
 +                        "modalityLabel": "dwi",
 +                        "customLabels": "dir-PA_sbref",
 +                        "criteria": {
 +                                "SeriesDescription": "DTIep2d_diff_mddw_4b0_PA"
 +                        }
 +
 +                }
 +        ]
 +}
 +</code>
 +
 +<code bash>
 +[osotolongo@detritus tmpbids]$ for x in `cat ../ni_names.csv`; do pname=$(echo ${x} | awk -F"," '{print $1}'); id=$(echo ${x} | awk -F"," '{print $2}'); dcm2bids -d /nas/corachan/MOPEAD/${pname}
 +/ -p ${id} -c conv_config.json; done
 +INFO:dcm2bids.dcm2bids:--- dcm2bids start ---
 +INFO:dcm2bids.dcm2bids:OS:version: Linux-2.6.32-431.17.1.el6.centos.plus.x86_64-x86_64-with-centos-6.10-Final
 +INFO:dcm2bids.dcm2bids:python:version: 3.4.8 (default, Apr  9 2018, 11:43:18) [GCC 4.4.7 20120313 (Red Hat 4.4.7-18)]
 +INFO:dcm2bids.dcm2bids:dcm2bids:version: 2.1.4
 +INFO:dcm2bids.dcm2bids:dcm2niix:version: v1.0.20191031
 +INFO:dcm2bids.dcm2bids:participant: sub-0001
 +INFO:dcm2bids.dcm2bids:session:
 +INFO:dcm2bids.dcm2bids:config: /nas/data/mopead/tmpbids/conv_config.json
 +INFO:dcm2bids.dcm2bids:BIDS directory: /nas/data/mopead/tmpbids
 +INFO:dcm2bids.utils:Running dcm2niix -b y -ba y -z y -f '%3s_%f_%p_%t' -o /nas/data/mopead/tmpbids/tmp_dcm2bids/sub-0001 /nas/corachan/MOPEAD/24A8DVSH/
 +INFO:dcm2bids.dcm2niix:Check log file for dcm2niix output
 +INFO:dcm2bids.sidecar:Sidecars pairing:
 +INFO:dcm2bids.sidecar:No Pairing  <-  013_24A8DVSH_ep2d_bold_p2_resting_state_20180714105659
 +INFO:dcm2bids.sidecar:No Pairing  <-  017_24A8DVSH_asl_3d_tra_iso_3.0_highres_20180714105659
 +INFO:dcm2bids.sidecar:No Pairing  <-  019_24A8DVSH_asl_3d_tra_iso_3.0_highres_20180714105659
 +INFO:dcm2bids.sidecar:No Pairing  <-  021_24A8DVSH_DTIep2d_diff_mddw_48dir_p3_AP_20180714105659
 +INFO:dcm2bids.sidecar:_T1w  <-  5001_24A8DVSH_t1_mprage_sag_p2_iso_20180714105659
 +INFO:dcm2bids.sidecar:_T2w  <-  6001_24A8DVSH_t2_space_dark-fluid_sag_p2_iso_20180714105659
 +INFO:dcm2bids.sidecar:No Pairing  <-  7001_24A8DVSH_pd+t2_tse_tra_p2_3mm_20180714105659_e1
 +INFO:dcm2bids.sidecar:No Pairing  <-  7001_24A8DVSH_pd+t2_tse_tra_p2_3mm_20180714105659_e1a
 +INFO:dcm2bids.sidecar:No Pairing  <-  8001_24A8DVSH_t2_swi_tra_p2_384_2mm_20180714105659
 +INFO:dcm2bids.sidecar:No Pairing  <-  9001_24A8DVSH_t2_swi_tra_p2_384_2mm_20180714105659_ph
 +INFO:dcm2bids.sidecar:No Pairing  <-  10001_24A8DVSH_t2_swi_tra_p2_384_2mm_20180714105659
 +INFO:dcm2bids.sidecar:No Pairing  <-  11001_24A8DVSH_t2_swi_tra_p2_384_2mm_20180714105659
 +INFO:dcm2bids.sidecar:_task-rest_bold  <-  12001_24A8DVSH_ep2d_bold_p2_resting_state_20180714105659
 +INFO:dcm2bids.sidecar:_task-rest_dir-AP_sbref_bold  <-  14001_24A8DVSH_ep2d_fid_basic_bold_p2_AP_20180714105659
 +INFO:dcm2bids.sidecar:_task-rest_dir-PA_sbref_bold  <-  15001_24A8DVSH_ep2d_fid_basic_bold_p2_PA_20180714105659
 +INFO:dcm2bids.sidecar:No Pairing  <-  16001_24A8DVSH_asl_3d_tra_iso_3.0_highres_20180714105659
 +INFO:dcm2bids.sidecar:No Pairing  <-  18001_24A8DVSH_asl_3d_tra_iso_3.0_highres_20180714105659
 +INFO:dcm2bids.sidecar:No Pairing  <-  18001_24A8DVSH_asl_3d_tra_iso_3.0_highres_20180714105659a
 +INFO:dcm2bids.sidecar:_dwi  <-  20001_24A8DVSH_DTIep2d_diff_mddw_48dir_p3_AP_20180714105659
 +INFO:dcm2bids.sidecar:No Pairing  <-  22001_24A8DVSH_DTIep2d_diff_mddw_48dir_p3_AP_20180714105659
 +INFO:dcm2bids.sidecar:No Pairing  <-  23001_24A8DVSH_DTIep2d_diff_mddw_48dir_p3_AP_20180714105659
 +INFO:dcm2bids.sidecar:No Pairing  <-  24001_24A8DVSH_DTIep2d_diff_mddw_48dir_p3_AP_20180714105659
 +INFO:dcm2bids.sidecar:No Pairing  <-  25001_24A8DVSH_DTIep2d_diff_mddw_48dir_p3_AP_20180714105659
 +INFO:dcm2bids.sidecar:No Pairing  <-  27001_24A8DVSH_DTIep2d_diff_mddw_48dir_p3_AP_20180714105659
 +INFO:dcm2bids.sidecar:_dir-PA_sbref_dwi  <-  28001_24A8DVSH_DTIep2d_diff_mddw_4b0_PA_20180714105659
 +INFO:dcm2bids.dcm2bids:moving acquisitions into BIDS folder
 +</code>
 +
 +<code bash>[osotolongo@detritus tmpbids]$ tree sub-0001/
 +sub-0001/
 +├── anat
 +│   ├── sub-0001_T1w.json
 +│   ├── sub-0001_T1w.nii.gz
 +│   ├── sub-0001_T2w.json
 +│   └── sub-0001_T2w.nii.gz
 +├── dwi
 +│   ├── sub-0001_dir-PA_sbref_dwi.json
 +│   ├── sub-0001_dir-PA_sbref_dwi.nii.gz
 +│   ├── sub-0001_dwi.bval
 +│   ├── sub-0001_dwi.bvec
 +│   ├── sub-0001_dwi.json
 +│   └── sub-0001_dwi.nii.gz
 +└── func
 +    ├── sub-0001_task-rest_bold.json
 +    ├── sub-0001_task-rest_bold.nii.gz
 +    ├── sub-0001_task-rest_dir-AP_sbref_bold.json
 +    ├── sub-0001_task-rest_dir-AP_sbref_bold.nii.gz
 +    ├── sub-0001_task-rest_dir-PA_sbref_bold.json
 +    └── sub-0001_task-rest_dir-PA_sbref_bold.nii.gz
 +
 +3 directories, 16 files
 +</code>
 +
 +
neuroimagen/dcm2bids.1559635708.txt.gz · Last modified: 2020/08/04 10:47 (external edit)