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neuroimagen:dcm2bids [2019/06/04 08:07]
osotolongo created
neuroimagen:dcm2bids [2020/08/04 10:58] (current)
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 Dada la creciente aparicion de software de analisis que utiliza el formato [[http://bids.neuroimaging.io/|BIDS]] necesitamos implementar un procedimiento para convertir las imagenes DICOM directamente. Ya hemos implementado un [[neuroimagen:bids|esquema para convertir los NIfTI]] deberiamos quitar el paso intermedio y asegurarnos que no haya perdida de datos por el camino. Voy a empezar mirando [[https://cbedetti.github.io/Dcm2Bids/|dmc2bids]] que parece prometedor. Dada la creciente aparicion de software de analisis que utiliza el formato [[http://bids.neuroimaging.io/|BIDS]] necesitamos implementar un procedimiento para convertir las imagenes DICOM directamente. Ya hemos implementado un [[neuroimagen:bids|esquema para convertir los NIfTI]] deberiamos quitar el paso intermedio y asegurarnos que no haya perdida de datos por el camino. Voy a empezar mirando [[https://cbedetti.github.io/Dcm2Bids/|dmc2bids]] que parece prometedor.
  
-===== Know your data =====+===== Know your data ;-)=====
 Lo mas complicado es que tenemos que escribir un archivo de configuracion para el proceso.  Lo mas complicado es que tenemos que escribir un archivo de configuracion para el proceso. 
  
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.1559635667.txt.gz · Last modified: 2020/08/04 10:46 (external edit)