heuristic.py for heudiconv 0.10.0 incompatible with heudiconv 1.20 (or 1.1.6) ?

WilliamFCB commented 1 week ago

Summary

@yarikoptic

BIDS conversion with heudiconv 0.10.0 produces the expected output. However, no output is generated when using heudiconv 1.2.0. The anat, dwi, fmap, and func subdirectories are created, but empty Might this be related to the used heuristic fíle (created for heudiconv 0.10.0) not being compatible with heudiconv 1.2.0?

A minor issue, for both heudiconv version is that the fmri event files are not created

Any ideas?

Many thanks in advance William

Heudiconv call:

singularity exec --cleanenv --contain \
    -B /mnt/projects \
    ${heudiconv_sif} heudiconv \
    --files ${DICOM_FILES} \
    -s ${sourceid} \
    -ss ${session} \
    -f ${heuristic} \
    -c dcm2niix \
    -b \
    -g all \
    -o ${RAWBIDS_DIR} \
    --overwrite \
    --minmeta

heuristic file:

````python import os def create_key(template, outtype=('nii.gz'), annotation_classes=None): if template is None or not template: raise ValueError('template must be a valid format string') return template, outtype, annotation_classes def infotodict(seqinfo): t23d = create_key('sub-{subject}/{session}/anat/sub-{subject}_{session}_acq-{acq}_run-01_T2w') # use run-0{item:01d} to import multiple scans with same name unit = create_key('sub-{subject}/{session}/anat/sub-{subject}_{session}_acq-{acq}_rec-{rec}_run-01_UNIT1') inverse1 = create_key('sub-{subject}/{session}/anat/sub-{subject}_{session}_acq-{acq}_rec-{rec}_run-01_inv-1_MP2RAGE') inverse2 = create_key('sub-{subject}/{session}/anat/sub-{subject}_{session}_acq-{acq}_rec-{rec}_run-01_inv-2_MP2RAGE') dwi = create_key('sub-{subject}/{session}/dwi/sub-{subject}_{session}_acq-{acq}_run-01_dwi') dwi_PA = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_acq-{acq}_dir-PA_run-01_epi') task1 = create_key('sub-{subject}/{session}/func/sub-{subject}_{session}_task-{task}_run-01_part-{part}_bold') task1_PA = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_acq-{acq}_dir-PA_run-01_part-{part}_epi') # note: In case of complex (magnitude and phase) images. Heudiconv automatically adds part- pairs to sbref image names task1_sbref = create_key('sub-{subject}/{session}/func/sub-{subject}_{session}_task-{task}_run-01_sbref') task1_PA_sbref = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_acq-{acq}_dir-PA_run-01_sbref') # there is only the mag part: therefore the part-label pair needs to be added explicitly task2_PA_sbref = create_key('sub-{subject}/{session}/fmap/sub-{subject}_{session}_acq-{acq}_dir-PA_run-01_part-{part}_sbref') info = {t23d: [], unit: [], inverse1: [], inverse2: [], dwi: [], dwi_PA: [], task1: [], task1_PA: [], task1_sbref: [], task1_PA_sbref: [], task2_PA_sbref: []} # Loop through each file sequence identified by heudiconv for idx, s in enumerate(seqinfo): ## T2w ########################################################################################################################## if ('t2_space_sag_iso_p2_ellscan_lowbw' in s.series_description) and (s.is_motion_corrected == False) and (s.dim3 == 224): acq = 't23d' info[t23d].append({'item': s.series_id, 'acq': acq}) # potential new T2 for VIA19 if ('anat_T2w_acq_T2space' in s.series_description) and (s.is_motion_corrected == False) and (s.dim3 == 224): acq = 't23d' info[t23d].append({'item': s.series_id, 'acq': acq}) ## MP2RAGE: GDC ################################################################################################################## if ('PRJ0320_MP2RAGE_fatnavs_p3_ES7.1_UNI_Images' in s.series_description) and (s.is_motion_corrected == False) and ('DIS3D' in s.image_type) and (s.dim3 == 192): acq = 'mp2rage' rec = 'GDC' info[unit].append({'item': s.series_id, 'acq': acq, 'rec': rec}) if ('PRJ0320_MP2RAGE_fatnavs_p3_ES7.1_INV1' in s.series_description) and (s.is_motion_corrected == False) and ('DIS3D' in s.image_type) and (s.dim3 == 192): acq = 'mp2rage' rec = 'GDC' info[inverse1].append({'item': s.series_id, 'acq': acq, 'rec': rec}) if ('PRJ0320_MP2RAGE_fatnavs_p3_ES7.1_INV2' in s.series_description) and (s.is_motion_corrected == False) and ('DIS3D' in s.image_type) and (s.dim3 == 192): acq = 'mp2rage' rec = 'GDC' info[inverse2].append({'item': s.series_id, 'acq': acq, 'rec': rec}) ## MP2RAGE: noGDC ################################################################################################################## if ('PRJ0320_MP2RAGE_fatnavs_p3_ES7.1_UNI_Images' in s.series_description) and (s.is_motion_corrected == False) and ('ND' in s.image_type) and (s.dim3 == 192): acq = 'mp2rage' rec = 'noGDC' info[unit].append({'item': s.series_id, 'acq': acq, 'rec': rec}) if ('PRJ0320_MP2RAGE_fatnavs_p3_ES7.1_INV1' in s.series_description) and (s.is_motion_corrected == False) and ('ND' in s.image_type) and (s.dim3 == 192): acq = 'mp2rage' rec = 'noGDC' info[inverse1].append({'item': s.series_id, 'acq': acq, 'rec': rec}) if ('PRJ0320_MP2RAGE_fatnavs_p3_ES7.1_INV2' in s.series_description) and (s.is_motion_corrected == False) and ('ND' in s.image_type) and (s.dim3 == 192): acq = 'mp2rage' rec = 'noGDC' info[inverse2].append({'item': s.series_id, 'acq': acq, 'rec': rec}) ## DWI HARDI ################################################################################################################## if ('cmrr_mbep2d_diff_multidir_AP' in s.series_description) and (s.is_motion_corrected == False) and (s.dim4 == 94): acq = 'hardi' info[dwi].append({'item': s.series_id, 'acq': acq}) if ('cmrr_mbep2d_diff_b0_PA' in s.series_description) and (s.is_motion_corrected == False) and (s.dim4 == 6): acq = 'hardi' info[dwi_PA].append({'item': s.series_id, 'acq': acq}) ## DWI DKI ################################################################################################################## if ('cmrr_mbep2d_diff_199_AP_SCnone' in s.series_description) and (s.is_motion_corrected == False) and (s.dim4 == 43): acq = 'dki' info[dwi].append({'item': s.series_id, 'acq': acq}) if ('cmrr_mbep2d_diff_199_PA_SCnone' in s.series_description) and (s.is_motion_corrected == False) and (s.dim4 == 24): acq = 'dki' info[dwi_PA].append({'item': s.series_id, 'acq': acq}) ## flanker ################################################################################################################## if ('fMRI_CMRR_p2_2.5_2466_flanker' in s.series_description) and (s.is_motion_corrected == False) and ('M' in s.image_type) and (s.dim4 == 520): task = 'flanker' part = 'mag' info[task1].append({'item': s.series_id, 'task': task, 'part': part}) if ('fMRI_CMRR_p2_2.5_2466_flanker' in s.series_description) and (s.is_motion_corrected == False) and ('P' in s.image_type) and (s.dim4 == 520): task = 'flanker' part = 'phase' info[task1].append({'item': s.series_id, 'task': task, 'part': part}) if ('fMRI_CMRR_p2_2.5_2466_PA1' in s.series_description) and (s.is_motion_corrected == False) and ('M' in s.image_type) and (s.dim4 == 5): acq = 'flanker' part = 'mag' info[task1_PA].append({'item': s.series_id, 'acq': acq, 'part': part}) if ('fMRI_CMRR_p2_2.5_2466_PA1' in s.series_description) and (s.is_motion_corrected == False) and ('P' in s.image_type) and (s.dim4 == 5): acq = 'flanker' part = 'phase' info[task1_PA].append({'item': s.series_id, 'acq': acq, 'part': part}) # as there is a phase and mag part for the task. the SBREF image is automatically saved with a mag and phase part if ('fMRI_CMRR_p2_2.5_2466_flanker_SBRef' in s.series_description) and (s.is_motion_corrected == False) and (s.dim4 == 2): task = 'flanker' info[task1_sbref].append({'item': s.series_id, 'task': task}) # there is only the mag part: therefor the part-label pair needs to be added explicit if ('fMRI_CMRR_p2_2.5_2466_PA1_SBRef' in s.series_description) and (s.is_motion_corrected == False) and ('M' in s.image_type) and (s.dim4 == 1): acq = 'flanker' part = 'mag' info[task2_PA_sbref].append({'item': s.series_id, 'acq': acq, 'part': part}) ## at ################################################################################################################## if ('fMRI_CMRR_p2_2.5_2466_AT' in s.series_description) and (s.is_motion_corrected == False) and ('M' in s.image_type) and (s.dim4 == 520): task = 'at' part = 'mag' info[task1].append({'item': s.series_id, 'task': task, 'part': part}) if ('fMRI_CMRR_p2_2.5_2466_AT' in s.series_description) and (s.is_motion_corrected == False) and ('P' in s.image_type) and (s.dim4 == 520): task = 'at' part = 'phase' info[task1].append({'item': s.series_id, 'task': task, 'part': part}) if ('fMRI_CMRR_p2_2.5_2466_PA2' in s.series_description) and (s.is_motion_corrected == False) and ('M' in s.image_type) and (s.dim4 == 5): acq = 'at' part = 'mag' info[task1_PA].append({'item': s.series_id, 'acq': acq, 'part': part}) if ('fMRI_CMRR_p2_2.5_2466_PA2' in s.series_description) and (s.is_motion_corrected == False) and ('P' in s.image_type) and (s.dim4 == 5): acq = 'at' part = 'phase' info[task1_PA].append({'item': s.series_id, 'acq': acq, 'part': part}) # as there is a phase and mag part for the task. the SBREF image is automatically saved with a mag and phase part if ('fMRI_CMRR_p2_2.5_2466_AT_SBRef' in s.series_description) and (s.is_motion_corrected == False) and (s.dim4 == 2): task = 'at' info[task1_sbref].append({'item': s.series_id, 'task': task}) # there is only the mag part: therefor the part-label pair needs to be added explicit if ('fMRI_CMRR_p2_2.5_2466_PA2_SBRef' in s.series_description) and (s.is_motion_corrected == False) and ('M' in s.image_type) and (s.dim4 == 1): acq = 'at' part = 'mag' info[task2_PA_sbref].append({'item': s.series_id, 'acq': acq, 'part': part}) ## reward ################################################################################################################## if ('fMRI_76_slices_MB4_p2_1.8iso_reward' in s.series_description) and (s.is_motion_corrected == False) and ('M' in s.image_type) and (s.dim4 == 563): task = 'reward' part = 'mag' info[task1].append({'item': s.series_id, 'task': task, 'part': part}) if ('fMRI_76_slices_MB4_p2_1.8iso_reward' in s.series_description) and (s.is_motion_corrected == False) and ('P' in s.image_type) and (s.dim4 == 563): task = 'reward' part = 'phase' info[task1].append({'item': s.series_id, 'task': task, 'part': part}) if ('fMRI_76_slices_MB4_p2_1.8iso_PA3' in s.series_description) and (s.is_motion_corrected == False) and ('M' in s.image_type) and (s.dim4 == 5): acq = 'reward' part = 'mag' info[task1_PA].append({'item': s.series_id, 'acq': acq, 'part': part}) if ('fMRI_76_slices_MB4_p2_1.8iso_PA3' in s.series_description) and (s.is_motion_corrected == False) and ('P' in s.image_type) and (s.dim4 == 5): acq = 'reward' part = 'phase' info[task1_PA].append({'item': s.series_id, 'acq': acq, 'part': part}) # as there is a phase and mag part for the task, the SBREF image is automatically saved with a mag and phase part if ('fMRI_76_slices_MB4_p2_1.8iso_reward_SBRef' in s.series_description) and (s.is_motion_corrected == False) and (s.dim4 == 2): task = 'reward' info[task1_sbref].append({'item': s.series_id, 'task': task}) if ('fMRI_76_slices_MB4_p2_1.8iso_PA3_SBRef' in s.series_description) and (s.is_motion_corrected == False) and (s.dim4 == 2): acq = 'reward' info[task1_PA_sbref].append({'item': s.series_id, 'acq': acq}) return info ```

Heudiconv version: 1.2.0

WilliamFCB commented 1 week ago

Output: heudiconv 1.2.0.:

``` INFO: Running heudiconv version 1.2.0 latest 1.2.0 INFO: Analyzing 1737 dicoms INFO: Generated sequence info with 1 entries WARNING: Heuristic is missing an infotoids method, assigning empty method and using provided subject id viakaninen003. Provide session and locator fields for best results. INFO: Study session for StudySessionInfo(locator=None, session='03DRCMRprisma', subject='viakaninen003') INFO: Need to process 1 study sessions INFO: PROCESSING STARTS: {'subject': 'viakaninen003', 'outdir': '/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/', 'session': '03DRCMRprisma'} INFO: Processing 25 pre-sorted seqinfo entries INFO: Doing conversion using dcm2niix INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-t23d_run-01_T2w (224 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_UNIT1 (192 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_UNIT1 (192 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_inv-1_MP2RAGE (192 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_inv-1_MP2RAGE (192 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_inv-2_MP2RAGE (192 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_inv-2_MP2RAGE (192 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi/sub-viakaninen003_ses-03DRCMRprisma_acq-dki_run-01_dwi (43 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi/sub-viakaninen003_ses-03DRCMRprisma_acq-hardi_run-01_dwi (94 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-dki_dir-PA_run-01_epi (24 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-hardi_dir-PA_run-01_epi (6 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-flanker_dir-PA_run-01_part-mag_epi (5 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-at_dir-PA_run-01_part-mag_epi (5 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-mag_epi (5 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-phase_epi (5 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-flanker_run-01_sbref (2 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-at_run-01_sbref (2 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-reward_run-01_sbref (2 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_sbref (2 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-flanker_dir-PA_run-01_part-mag_sbref (1 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: nii.gz INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-at_dir-PA_run-01_part-mag_sbref (1 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: nii.gz INFO: Populating template files under /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/ Traceback (most recent call last): File "/opt/miniconda-py39_4.12.0/bin/heudiconv", line 8, in sys.exit(main()) File "/src/heudiconv/heudiconv/cli/run.py", line 30, in main workflow(**kwargs) File "/src/heudiconv/heudiconv/main.py", line 479, in workflow prep_conversion( File "/src/heudiconv/heudiconv/convert.py", line 295, in prep_conversion populate_bids_templates( File "/src/heudiconv/heudiconv/bids.py", line 207, in populate_bids_templates populate_aggregated_jsons(path) File "/src/heudiconv/heudiconv/bids.py", line 279, in populate_aggregated_jsons with open(events_file, "w") as fp: PermissionError: [Errno 13] Permission denied: '/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-via006/ses-02DRCMRprisma/func/sub-via006_ses-02DRCMRprisma_task-at_run-01_part-mag_events.tsv' chmod 750 ${RAWBIDS_DIR}/.bidsignore ```

Output: heudiconv 0.10.0:

``` INFO: Running heudiconv version 0.10.0 latest 1.2.0 INFO: Analyzing 1737 dicoms INFO: Generated sequence info with 1 entries WARNING: Heuristic is missing an `infotoids` method, assigning empty method and using provided subject id viakaninen003. Provide `session` and `locator` fields for best results. INFO: Study session for StudySessionInfo(locator=None, session='03DRCMRprisma', subject='viakaninen003') INFO: Need to process 1 study sessions INFO: PROCESSING STARTS: {'subject': 'viakaninen003', 'outdir': '/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/', 'session': '03DRCMRprisma'} INFO: Processing 25 pre-sorted seqinfo entries INFO: Reloading existing filegroup.json because /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/.heudiconv/viakaninen003/ses-03DRCMRprisma/info/viakaninen003_ses-03DRCMRprisma.edit.txt exists INFO: Doing conversion using dcm2niix INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_UNIT1 (192 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:25,996 nipype.utils WARNING: A newer version (1.8.4) of nipy/nipype is available. You are using 1.7.1 WARNING: A newer version (1.8.4) of nipy/nipype is available. You are using 1.7.1 240917-07:18:26,2 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixj17qg781/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixj17qg781/convert". 240917-07:18:26,66 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:26,418 nipype.interface INFO: stdout 2024-09-17T07:18:26.417890:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:26.417890:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:26,418 nipype.interface INFO: stdout 2024-09-17T07:18:26.417890:Found 192 DICOM file(s) INFO: stdout 2024-09-17T07:18:26.417890:Found 192 DICOM file(s) 240917-07:18:26,418 nipype.interface INFO: stdout 2024-09-17T07:18:26.417890:Convert 192 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_UNIT1_heudiconv148 (288x288x192x1) INFO: stdout 2024-09-17T07:18:26.417890:Convert 192 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_UNIT1_heudiconv148 (288x288x192x1) 240917-07:18:27,136 nipype.interface INFO: stdout 2024-09-17T07:18:27.136539:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_UNIT1_heudiconv148.nii" INFO: stdout 2024-09-17T07:18:27.136539:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_UNIT1_heudiconv148.nii" 240917-07:18:27,136 nipype.interface INFO: stdout 2024-09-17T07:18:27.136539:Conversion required 0.985742 seconds (0.213408 for core code). INFO: stdout 2024-09-17T07:18:27.136539:Conversion required 0.985742 seconds (0.213408 for core code). 240917-07:18:27,158 nipype.workflow INFO: [Node] Finished "convert", elapsed time 1.030912s. INFO: [Node] Finished "convert", elapsed time 1.030912s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_UNIT1.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_UNIT1.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_UNIT1 (192 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:27,189 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixjb9qwv46/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixjb9qwv46/convert". 240917-07:18:27,260 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:27,548 nipype.interface INFO: stdout 2024-09-17T07:18:27.548280:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:27.548280:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:27,548 nipype.interface INFO: stdout 2024-09-17T07:18:27.548280:Found 192 DICOM file(s) INFO: stdout 2024-09-17T07:18:27.548280:Found 192 DICOM file(s) 240917-07:18:27,548 nipype.interface INFO: stdout 2024-09-17T07:18:27.548280:Convert 192 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_UNIT1_heudiconv672 (288x288x192x1) INFO: stdout 2024-09-17T07:18:27.548280:Convert 192 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_UNIT1_heudiconv672 (288x288x192x1) 240917-07:18:28,129 nipype.interface INFO: stdout 2024-09-17T07:18:28.129752:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_UNIT1_heudiconv672.nii" INFO: stdout 2024-09-17T07:18:28.129752:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_UNIT1_heudiconv672.nii" 240917-07:18:28,129 nipype.interface INFO: stdout 2024-09-17T07:18:28.129752:Conversion required 0.843811 seconds (0.206493 for core code). INFO: stdout 2024-09-17T07:18:28.129752:Conversion required 0.843811 seconds (0.206493 for core code). 240917-07:18:28,148 nipype.workflow INFO: [Node] Finished "convert", elapsed time 0.886471s. INFO: [Node] Finished "convert", elapsed time 0.886471s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_UNIT1.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_UNIT1.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_inv-1_MP2RAGE (192 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:28,171 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix8tso4vf3/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix8tso4vf3/convert". 240917-07:18:28,234 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:28,527 nipype.interface INFO: stdout 2024-09-17T07:18:28.527026:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:28.527026:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:28,527 nipype.interface INFO: stdout 2024-09-17T07:18:28.527026:Found 192 DICOM file(s) INFO: stdout 2024-09-17T07:18:28.527026:Found 192 DICOM file(s) 240917-07:18:28,527 nipype.interface INFO: stdout 2024-09-17T07:18:28.527026:Convert 192 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_inv-1_MP2RAGE_heudiconv824 (288x288x192x1) INFO: stdout 2024-09-17T07:18:28.527026:Convert 192 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_inv-1_MP2RAGE_heudiconv824 (288x288x192x1) 240917-07:18:29,557 nipype.interface INFO: stdout 2024-09-17T07:18:29.557068:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_inv-1_MP2RAGE_heudiconv824.nii" INFO: stdout 2024-09-17T07:18:29.557068:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_inv-1_MP2RAGE_heudiconv824.nii" 240917-07:18:29,557 nipype.interface INFO: stdout 2024-09-17T07:18:29.557068:Conversion required 1.297597 seconds (0.206502 for core code). INFO: stdout 2024-09-17T07:18:29.557068:Conversion required 1.297597 seconds (0.206502 for core code). 240917-07:18:29,575 nipype.workflow INFO: [Node] Finished "convert", elapsed time 1.340513s. INFO: [Node] Finished "convert", elapsed time 1.340513s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_inv-1_MP2RAGE.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_inv-1_MP2RAGE.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_inv-1_MP2RAGE (192 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:29,599 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixsqra1vje/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixsqra1vje/convert". 240917-07:18:29,662 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:29,954 nipype.interface INFO: stdout 2024-09-17T07:18:29.953885:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:29.953885:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:29,954 nipype.interface INFO: stdout 2024-09-17T07:18:29.953885:Found 192 DICOM file(s) INFO: stdout 2024-09-17T07:18:29.953885:Found 192 DICOM file(s) 240917-07:18:29,954 nipype.interface INFO: stdout 2024-09-17T07:18:29.953885:Convert 192 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_inv-1_MP2RAGE_heudiconv121 (288x288x192x1) INFO: stdout 2024-09-17T07:18:29.953885:Convert 192 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_inv-1_MP2RAGE_heudiconv121 (288x288x192x1) 240917-07:18:30,928 nipype.interface INFO: stdout 2024-09-17T07:18:30.928781:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_inv-1_MP2RAGE_heudiconv121.nii" INFO: stdout 2024-09-17T07:18:30.928781:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_inv-1_MP2RAGE_heudiconv121.nii" 240917-07:18:30,928 nipype.interface INFO: stdout 2024-09-17T07:18:30.928781:Conversion required 1.242319 seconds (0.209450 for core code). INFO: stdout 2024-09-17T07:18:30.928781:Conversion required 1.242319 seconds (0.209450 for core code). 240917-07:18:30,948 nipype.workflow INFO: [Node] Finished "convert", elapsed time 1.285414s. INFO: [Node] Finished "convert", elapsed time 1.285414s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_inv-1_MP2RAGE.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_inv-1_MP2RAGE.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_inv-2_MP2RAGE (192 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:30,972 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixf0ga8ir_/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixf0ga8ir_/convert". 240917-07:18:31,37 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:31,330 nipype.interface INFO: stdout 2024-09-17T07:18:31.330489:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:31.330489:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:31,330 nipype.interface INFO: stdout 2024-09-17T07:18:31.330489:Found 192 DICOM file(s) INFO: stdout 2024-09-17T07:18:31.330489:Found 192 DICOM file(s) 240917-07:18:31,330 nipype.interface INFO: stdout 2024-09-17T07:18:31.330489:Convert 192 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_inv-2_MP2RAGE_heudiconv119 (288x288x192x1) INFO: stdout 2024-09-17T07:18:31.330489:Convert 192 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_inv-2_MP2RAGE_heudiconv119 (288x288x192x1) 240917-07:18:32,226 nipype.interface INFO: stdout 2024-09-17T07:18:32.226488:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_inv-2_MP2RAGE_heudiconv119.nii" INFO: stdout 2024-09-17T07:18:32.226488:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_inv-2_MP2RAGE_heudiconv119.nii" 240917-07:18:32,226 nipype.interface INFO: stdout 2024-09-17T07:18:32.226488:Conversion required 1.164542 seconds (0.212980 for core code). INFO: stdout 2024-09-17T07:18:32.226488:Conversion required 1.164542 seconds (0.212980 for core code). 240917-07:18:32,245 nipype.workflow INFO: [Node] Finished "convert", elapsed time 1.206551s. INFO: [Node] Finished "convert", elapsed time 1.206551s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_inv-2_MP2RAGE.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-noGDC_run-01_inv-2_MP2RAGE.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_inv-2_MP2RAGE (192 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:32,278 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixi9aur7aa/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixi9aur7aa/convert". 240917-07:18:32,341 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:32,636 nipype.interface INFO: stdout 2024-09-17T07:18:32.636565:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:32.636565:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:32,636 nipype.interface INFO: stdout 2024-09-17T07:18:32.636565:Found 192 DICOM file(s) INFO: stdout 2024-09-17T07:18:32.636565:Found 192 DICOM file(s) 240917-07:18:32,636 nipype.interface INFO: stdout 2024-09-17T07:18:32.636565:Convert 192 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_inv-2_MP2RAGE_heudiconv079 (288x288x192x1) INFO: stdout 2024-09-17T07:18:32.636565:Convert 192 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_inv-2_MP2RAGE_heudiconv079 (288x288x192x1) 240917-07:18:33,463 nipype.interface INFO: stdout 2024-09-17T07:18:33.463805:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_inv-2_MP2RAGE_heudiconv079.nii" INFO: stdout 2024-09-17T07:18:33.463805:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_inv-2_MP2RAGE_heudiconv079.nii" 240917-07:18:33,464 nipype.interface INFO: stdout 2024-09-17T07:18:33.463805:Conversion required 1.097301 seconds (0.207113 for core code). INFO: stdout 2024-09-17T07:18:33.463805:Conversion required 1.097301 seconds (0.207113 for core code). 240917-07:18:33,483 nipype.workflow INFO: [Node] Finished "convert", elapsed time 1.141573s. INFO: [Node] Finished "convert", elapsed time 1.141573s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_inv-2_MP2RAGE.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-mp2rage_rec-GDC_run-01_inv-2_MP2RAGE.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-t23d_run-01_T2w (224 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:33,508 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixboq9_wa4/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixboq9_wa4/convert". 240917-07:18:33,583 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:33,910 nipype.interface INFO: stdout 2024-09-17T07:18:33.910456:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:33.910456:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:33,910 nipype.interface INFO: stdout 2024-09-17T07:18:33.910456:Found 224 DICOM file(s) INFO: stdout 2024-09-17T07:18:33.910456:Found 224 DICOM file(s) 240917-07:18:33,910 nipype.interface INFO: stdout 2024-09-17T07:18:33.910456:Convert 224 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-t23d_run-01_T2w_heudiconv015 (256x320x224x1) INFO: stdout 2024-09-17T07:18:33.910456:Convert 224 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-t23d_run-01_T2w_heudiconv015 (256x320x224x1) 240917-07:18:34,830 nipype.interface INFO: stdout 2024-09-17T07:18:34.830877:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-t23d_run-01_T2w_heudiconv015.nii" INFO: stdout 2024-09-17T07:18:34.830877:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-t23d_run-01_T2w_heudiconv015.nii" 240917-07:18:34,831 nipype.interface INFO: stdout 2024-09-17T07:18:34.830877:Conversion required 1.222702 seconds (0.252010 for core code). INFO: stdout 2024-09-17T07:18:34.830877:Conversion required 1.222702 seconds (0.252010 for core code). 240917-07:18:34,869 nipype.workflow INFO: [Node] Finished "convert", elapsed time 1.285803s. INFO: [Node] Finished "convert", elapsed time 1.285803s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-t23d_run-01_T2w.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/anat/sub-viakaninen003_ses-03DRCMRprisma_acq-t23d_run-01_T2w.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi/sub-viakaninen003_ses-03DRCMRprisma_acq-dki_run-01_dwi (43 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:34,889 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixev73snj9/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixev73snj9/convert". 240917-07:18:34,904 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:35,136 nipype.interface INFO: stdout 2024-09-17T07:18:35.136878:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:35.136878:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:35,137 nipype.interface INFO: stdout 2024-09-17T07:18:35.136878:Found 43 DICOM file(s) INFO: stdout 2024-09-17T07:18:35.136878:Found 43 DICOM file(s) 240917-07:18:35,137 nipype.interface INFO: stdout 2024-09-17T07:18:35.136878:Convert 43 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi/sub-viakaninen003_ses-03DRCMRprisma_acq-dki_run-01_dwi_heudiconv350 (112x114x75x43) INFO: stdout 2024-09-17T07:18:35.136878:Convert 43 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi/sub-viakaninen003_ses-03DRCMRprisma_acq-dki_run-01_dwi_heudiconv350 (112x114x75x43) 240917-07:18:37,157 nipype.interface INFO: stdout 2024-09-17T07:18:37.157904:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi/sub-viakaninen003_ses-03DRCMRprisma_acq-dki_run-01_dwi_heudiconv350.nii" INFO: stdout 2024-09-17T07:18:37.157904:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi/sub-viakaninen003_ses-03DRCMRprisma_acq-dki_run-01_dwi_heudiconv350.nii" 240917-07:18:37,158 nipype.interface INFO: stdout 2024-09-17T07:18:37.157904:Conversion required 2.229038 seconds (0.198425 for core code). INFO: stdout 2024-09-17T07:18:37.157904:Conversion required 2.229038 seconds (0.198425 for core code). 240917-07:18:37,177 nipype.workflow INFO: [Node] Finished "convert", elapsed time 2.272225s. INFO: [Node] Finished "convert", elapsed time 2.272225s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi/sub-viakaninen003_ses-03DRCMRprisma_acq-dki_run-01_dwi.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi/sub-viakaninen003_ses-03DRCMRprisma_acq-dki_run-01_dwi.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi/sub-viakaninen003_ses-03DRCMRprisma_acq-hardi_run-01_dwi (94 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:37,195 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixpuxenbb6/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixpuxenbb6/convert". 240917-07:18:37,228 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:37,519 nipype.interface INFO: stdout 2024-09-17T07:18:37.518915:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:37.518915:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:37,519 nipype.interface INFO: stdout 2024-09-17T07:18:37.518915:Found 94 DICOM file(s) INFO: stdout 2024-09-17T07:18:37.518915:Found 94 DICOM file(s) 240917-07:18:37,519 nipype.interface INFO: stdout 2024-09-17T07:18:37.518915:Convert 94 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi/sub-viakaninen003_ses-03DRCMRprisma_acq-hardi_run-01_dwi_heudiconv829 (112x114x75x94) INFO: stdout 2024-09-17T07:18:37.518915:Convert 94 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi/sub-viakaninen003_ses-03DRCMRprisma_acq-hardi_run-01_dwi_heudiconv829 (112x114x75x94) 240917-07:18:41,897 nipype.interface INFO: stdout 2024-09-17T07:18:41.897708:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi/sub-viakaninen003_ses-03DRCMRprisma_acq-hardi_run-01_dwi_heudiconv829.nii" INFO: stdout 2024-09-17T07:18:41.897708:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi/sub-viakaninen003_ses-03DRCMRprisma_acq-hardi_run-01_dwi_heudiconv829.nii" 240917-07:18:41,897 nipype.interface INFO: stdout 2024-09-17T07:18:41.897708:Conversion required 4.646193 seconds (0.415143 for core code). INFO: stdout 2024-09-17T07:18:41.897708:Conversion required 4.646193 seconds (0.415143 for core code). 240917-07:18:41,918 nipype.workflow INFO: [Node] Finished "convert", elapsed time 4.689298s. INFO: [Node] Finished "convert", elapsed time 4.689298s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi/sub-viakaninen003_ses-03DRCMRprisma_acq-hardi_run-01_dwi.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/dwi/sub-viakaninen003_ses-03DRCMRprisma_acq-hardi_run-01_dwi.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-dki_dir-PA_run-01_epi (24 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:41,935 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixo6j7xy5v/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixo6j7xy5v/convert". 240917-07:18:41,945 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:42,123 nipype.interface INFO: stdout 2024-09-17T07:18:42.123065:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:42.123065:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:42,123 nipype.interface INFO: stdout 2024-09-17T07:18:42.123065:Found 24 DICOM file(s) INFO: stdout 2024-09-17T07:18:42.123065:Found 24 DICOM file(s) 240917-07:18:42,123 nipype.interface INFO: stdout 2024-09-17T07:18:42.123065:Convert 24 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-dki_dir-PA_run-01_epi_heudiconv779 (112x114x75x24) INFO: stdout 2024-09-17T07:18:42.123065:Convert 24 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-dki_dir-PA_run-01_epi_heudiconv779 (112x114x75x24) 240917-07:18:43,168 nipype.interface INFO: stdout 2024-09-17T07:18:43.168438:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-dki_dir-PA_run-01_epi_heudiconv779.nii" INFO: stdout 2024-09-17T07:18:43.168438:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-dki_dir-PA_run-01_epi_heudiconv779.nii" 240917-07:18:43,168 nipype.interface INFO: stdout 2024-09-17T07:18:43.168438:Conversion required 1.198055 seconds (0.116848 for core code). INFO: stdout 2024-09-17T07:18:43.168438:Conversion required 1.198055 seconds (0.116848 for core code). 240917-07:18:43,187 nipype.workflow INFO: [Node] Finished "convert", elapsed time 1.241547s. INFO: [Node] Finished "convert", elapsed time 1.241547s. WARNING: Diffusion-weighted image saved in non dwi folder (/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap) WARNING: .bvec and .bval files will be generated. This is NOT BIDS compliant WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-dki_dir-PA_run-01_epi.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-dki_dir-PA_run-01_epi.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-hardi_dir-PA_run-01_epi (6 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: ('nii.gz',) INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix659htv1s/convert". 240917-07:18:43,201 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix659htv1s/convert". 240917-07:18:43,205 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:43,272 nipype.interface INFO: stdout 2024-09-17T07:18:43.272747:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:43.272747:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:43,273 nipype.interface INFO: stdout 2024-09-17T07:18:43.272747:Found 6 DICOM file(s) INFO: stdout 2024-09-17T07:18:43.272747:Found 6 DICOM file(s) 240917-07:18:43,273 nipype.interface INFO: stdout 2024-09-17T07:18:43.272747:Convert 6 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-hardi_dir-PA_run-01_epi_heudiconv699 (112x114x75x6) INFO: stdout 2024-09-17T07:18:43.272747:Convert 6 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-hardi_dir-PA_run-01_epi_heudiconv699 (112x114x75x6) 240917-07:18:43,485 nipype.interface INFO: stdout 2024-09-17T07:18:43.485268:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-hardi_dir-PA_run-01_epi_heudiconv699.nii" INFO: stdout 2024-09-17T07:18:43.485268:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-hardi_dir-PA_run-01_epi_heudiconv699.nii" 240917-07:18:43,485 nipype.interface INFO: stdout 2024-09-17T07:18:43.485268:Conversion required 0.255716 seconds (0.037567 for core code). INFO: stdout 2024-09-17T07:18:43.485268:Conversion required 0.255716 seconds (0.037567 for core code). 240917-07:18:43,504 nipype.workflow INFO: [Node] Finished "convert", elapsed time 0.298271s. INFO: [Node] Finished "convert", elapsed time 0.298271s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-hardi_dir-PA_run-01_epi.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-hardi_dir-PA_run-01_epi.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-flanker_dir-PA_run-01_part-mag_epi (5 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:43,517 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixsz36bn53/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixsz36bn53/convert". 240917-07:18:43,520 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:43,563 nipype.interface INFO: stdout 2024-09-17T07:18:43.562889:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:43.562889:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:43,563 nipype.interface INFO: stdout 2024-09-17T07:18:43.562889:Found 5 DICOM file(s) INFO: stdout 2024-09-17T07:18:43.562889:Found 5 DICOM file(s) 240917-07:18:43,563 nipype.interface INFO: stdout 2024-09-17T07:18:43.562889:Convert 5 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-flanker_dir-PA_run-01_part-mag_epi_heudiconv655 (78x76x54x5) INFO: stdout 2024-09-17T07:18:43.562889:Convert 5 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-flanker_dir-PA_run-01_part-mag_epi_heudiconv655 (78x76x54x5) 240917-07:18:43,648 nipype.interface INFO: stdout 2024-09-17T07:18:43.648780:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-flanker_dir-PA_run-01_part-mag_epi_heudiconv655.nii" INFO: stdout 2024-09-17T07:18:43.648780:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-flanker_dir-PA_run-01_part-mag_epi_heudiconv655.nii" 240917-07:18:43,648 nipype.interface INFO: stdout 2024-09-17T07:18:43.648780:Conversion required 0.104277 seconds (0.016840 for core code). INFO: stdout 2024-09-17T07:18:43.648780:Conversion required 0.104277 seconds (0.016840 for core code). 240917-07:18:43,667 nipype.workflow INFO: [Node] Finished "convert", elapsed time 0.146791s. INFO: [Node] Finished "convert", elapsed time 0.146791s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-flanker_dir-PA_run-01_part-mag_epi.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-flanker_dir-PA_run-01_part-mag_epi.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-at_dir-PA_run-01_part-mag_epi (5 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:43,684 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixef172pa4/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixef172pa4/convert". 240917-07:18:43,687 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:43,729 nipype.interface INFO: stdout 2024-09-17T07:18:43.729715:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:43.729715:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:43,729 nipype.interface INFO: stdout 2024-09-17T07:18:43.729715:Found 5 DICOM file(s) INFO: stdout 2024-09-17T07:18:43.729715:Found 5 DICOM file(s) 240917-07:18:43,730 nipype.interface INFO: stdout 2024-09-17T07:18:43.729715:Convert 5 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-at_dir-PA_run-01_part-mag_epi_heudiconv543 (78x76x54x5) INFO: stdout 2024-09-17T07:18:43.729715:Convert 5 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-at_dir-PA_run-01_part-mag_epi_heudiconv543 (78x76x54x5) 240917-07:18:43,813 nipype.interface INFO: stdout 2024-09-17T07:18:43.813915:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-at_dir-PA_run-01_part-mag_epi_heudiconv543.nii" INFO: stdout 2024-09-17T07:18:43.813915:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-at_dir-PA_run-01_part-mag_epi_heudiconv543.nii" 240917-07:18:43,814 nipype.interface INFO: stdout 2024-09-17T07:18:43.813915:Conversion required 0.102575 seconds (0.016383 for core code). INFO: stdout 2024-09-17T07:18:43.813915:Conversion required 0.102575 seconds (0.016383 for core code). 240917-07:18:43,832 nipype.workflow INFO: [Node] Finished "convert", elapsed time 0.14424s. INFO: [Node] Finished "convert", elapsed time 0.14424s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-at_dir-PA_run-01_part-mag_epi.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-at_dir-PA_run-01_part-mag_epi.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-mag_epi (5 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:43,849 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixdv1t0udy/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixdv1t0udy/convert". 240917-07:18:43,853 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:43,907 nipype.interface INFO: stdout 2024-09-17T07:18:43.907443:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:43.907443:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:43,907 nipype.interface INFO: stdout 2024-09-17T07:18:43.907443:Found 5 DICOM file(s) INFO: stdout 2024-09-17T07:18:43.907443:Found 5 DICOM file(s) 240917-07:18:43,907 nipype.interface INFO: stdout 2024-09-17T07:18:43.907443:Convert 5 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-mag_epi_heudiconv606 (106x102x76x5) INFO: stdout 2024-09-17T07:18:43.907443:Convert 5 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-mag_epi_heudiconv606 (106x102x76x5) 240917-07:18:44,15 nipype.interface INFO: stdout 2024-09-17T07:18:44.015925:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-mag_epi_heudiconv606.nii" INFO: stdout 2024-09-17T07:18:44.015925:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-mag_epi_heudiconv606.nii" 240917-07:18:44,16 nipype.interface INFO: stdout 2024-09-17T07:18:44.015925:Conversion required 0.139219 seconds (0.034758 for core code). INFO: stdout 2024-09-17T07:18:44.015925:Conversion required 0.139219 seconds (0.034758 for core code). 240917-07:18:44,35 nipype.workflow INFO: [Node] Finished "convert", elapsed time 0.181169s. INFO: [Node] Finished "convert", elapsed time 0.181169s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-mag_epi.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-mag_epi.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-phase_epi (5 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: ('nii.gz',) INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix24rgpx18/convert". 240917-07:18:44,59 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix24rgpx18/convert". 240917-07:18:44,62 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:44,119 nipype.interface INFO: stdout 2024-09-17T07:18:44.119096:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:44.119096:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:44,119 nipype.interface INFO: stdout 2024-09-17T07:18:44.119096:Found 5 DICOM file(s) INFO: stdout 2024-09-17T07:18:44.119096:Found 5 DICOM file(s) 240917-07:18:44,119 nipype.interface INFO: stdout 2024-09-17T07:18:44.119096:Convert 5 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-phase_epi_heudiconv112_ph (106x102x76x5) INFO: stdout 2024-09-17T07:18:44.119096:Convert 5 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-phase_epi_heudiconv112_ph (106x102x76x5) 240917-07:18:44,208 nipype.interface INFO: stdout 2024-09-17T07:18:44.207952:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-phase_epi_heudiconv112_ph.nii" INFO: stdout 2024-09-17T07:18:44.207952:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-phase_epi_heudiconv112_ph.nii" 240917-07:18:44,208 nipype.interface INFO: stdout 2024-09-17T07:18:44.207952:Conversion required 0.120526 seconds (0.036352 for core code). INFO: stdout 2024-09-17T07:18:44.207952:Conversion required 0.120526 seconds (0.036352 for core code). 240917-07:18:44,228 nipype.workflow INFO: [Node] Finished "convert", elapsed time 0.165481s. INFO: [Node] Finished "convert", elapsed time 0.165481s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-phase_epi.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-phase_epi.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-flanker_dir-PA_run-01_part-mag_sbref (1 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:44,241 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixsvdueox7/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixsvdueox7/convert". 240917-07:18:44,243 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:44,278 nipype.interface INFO: stdout 2024-09-17T07:18:44.278634:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:44.278634:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:44,278 nipype.interface INFO: stdout 2024-09-17T07:18:44.278634:Found 1 DICOM file(s) INFO: stdout 2024-09-17T07:18:44.278634:Found 1 DICOM file(s) 240917-07:18:44,278 nipype.interface INFO: stdout 2024-09-17T07:18:44.278634:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-flanker_dir-PA_run-01_part-mag_sbref_heudiconv695 (78x76x54x1) INFO: stdout 2024-09-17T07:18:44.278634:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-flanker_dir-PA_run-01_part-mag_sbref_heudiconv695 (78x76x54x1) 240917-07:18:44,295 nipype.interface INFO: stdout 2024-09-17T07:18:44.295724:Compress: "/usr/bin/pigz" -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-flanker_dir-PA_run-01_part-mag_sbref_heudiconv695.nii" INFO: stdout 2024-09-17T07:18:44.295724:Compress: "/usr/bin/pigz" -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-flanker_dir-PA_run-01_part-mag_sbref_heudiconv695.nii" 240917-07:18:44,295 nipype.interface INFO: stdout 2024-09-17T07:18:44.295724:Conversion required 0.027497 seconds (0.008889 for core code). INFO: stdout 2024-09-17T07:18:44.295724:Conversion required 0.027497 seconds (0.008889 for core code). 240917-07:18:44,314 nipype.workflow INFO: [Node] Finished "convert", elapsed time 0.070204s. INFO: [Node] Finished "convert", elapsed time 0.070204s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-flanker_dir-PA_run-01_part-mag_sbref.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-flanker_dir-PA_run-01_part-mag_sbref.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-at_dir-PA_run-01_part-mag_sbref (1 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:44,330 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix4jceoelw/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix4jceoelw/convert". 240917-07:18:44,332 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:44,366 nipype.interface INFO: stdout 2024-09-17T07:18:44.365925:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:44.365925:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:44,366 nipype.interface INFO: stdout 2024-09-17T07:18:44.365925:Found 1 DICOM file(s) INFO: stdout 2024-09-17T07:18:44.365925:Found 1 DICOM file(s) 240917-07:18:44,366 nipype.interface INFO: stdout 2024-09-17T07:18:44.365925:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-at_dir-PA_run-01_part-mag_sbref_heudiconv929 (78x76x54x1) INFO: stdout 2024-09-17T07:18:44.365925:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-at_dir-PA_run-01_part-mag_sbref_heudiconv929 (78x76x54x1) 240917-07:18:44,383 nipype.interface INFO: stdout 2024-09-17T07:18:44.383418:Compress: "/usr/bin/pigz" -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-at_dir-PA_run-01_part-mag_sbref_heudiconv929.nii" INFO: stdout 2024-09-17T07:18:44.383418:Compress: "/usr/bin/pigz" -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-at_dir-PA_run-01_part-mag_sbref_heudiconv929.nii" 240917-07:18:44,383 nipype.interface INFO: stdout 2024-09-17T07:18:44.383418:Conversion required 0.027659 seconds (0.008705 for core code). INFO: stdout 2024-09-17T07:18:44.383418:Conversion required 0.027659 seconds (0.008705 for core code). 240917-07:18:44,405 nipype.workflow INFO: [Node] Finished "convert", elapsed time 0.072736s. INFO: [Node] Finished "convert", elapsed time 0.072736s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-at_dir-PA_run-01_part-mag_sbref.json. INFO: Post-treating /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-at_dir-PA_run-01_part-mag_sbref.json file INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_sbref (2 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:44,422 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix233vegch/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niix233vegch/convert". 240917-07:18:44,425 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:44,463 nipype.interface INFO: stdout 2024-09-17T07:18:44.463447:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:44.463447:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:44,463 nipype.interface INFO: stdout 2024-09-17T07:18:44.463447:Found 2 DICOM file(s) INFO: stdout 2024-09-17T07:18:44.463447:Found 2 DICOM file(s) 240917-07:18:44,463 nipype.interface INFO: stdout 2024-09-17T07:18:44.463447:Slices not stacked: some are phase/real/imaginary/phase maps, others are not. Instances 1 1 INFO: stdout 2024-09-17T07:18:44.463447:Slices not stacked: some are phase/real/imaginary/phase maps, others are not. Instances 1 1 240917-07:18:44,463 nipype.interface INFO: stdout 2024-09-17T07:18:44.463447:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_sbref_heudiconv995 (106x102x76x1) INFO: stdout 2024-09-17T07:18:44.463447:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_sbref_heudiconv995 (106x102x76x1) 240917-07:18:44,528 nipype.interface INFO: stdout 2024-09-17T07:18:44.528120:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_sbref_heudiconv995.nii" INFO: stdout 2024-09-17T07:18:44.528120:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_sbref_heudiconv995.nii" 240917-07:18:44,528 nipype.interface INFO: stdout 2024-09-17T07:18:44.528120:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_sbref_heudiconv995_ph (106x102x76x1) INFO: stdout 2024-09-17T07:18:44.528120:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_sbref_heudiconv995_ph (106x102x76x1) 240917-07:18:44,581 nipype.interface INFO: stdout 2024-09-17T07:18:44.581820:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_sbref_heudiconv995_ph.nii" INFO: stdout 2024-09-17T07:18:44.581820:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_sbref_heudiconv995_ph.nii" 240917-07:18:44,581 nipype.interface INFO: stdout 2024-09-17T07:18:44.581820:Conversion required 0.132165 seconds (0.019677 for core code). INFO: stdout 2024-09-17T07:18:44.581820:Conversion required 0.132165 seconds (0.019677 for core code). 240917-07:18:44,602 nipype.workflow INFO: [Node] Finished "convert", elapsed time 0.176377s. INFO: [Node] Finished "convert", elapsed time 0.176377s. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-mag_sbref.json. WARNING: Failed to find task field in /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/fmap/sub-viakaninen003_ses-03DRCMRprisma_acq-reward_dir-PA_run-01_part-phase_sbref.json. WARNING: For now not embedding BIDS and info generated .nii.gz itself since sequence produced multiple files INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-flanker_run-01_sbref (2 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:44,618 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixcwmarhc8/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixcwmarhc8/convert". 240917-07:18:44,620 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:44,654 nipype.interface INFO: stdout 2024-09-17T07:18:44.654618:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:44.654618:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:44,654 nipype.interface INFO: stdout 2024-09-17T07:18:44.654618:Found 2 DICOM file(s) INFO: stdout 2024-09-17T07:18:44.654618:Found 2 DICOM file(s) 240917-07:18:44,654 nipype.interface INFO: stdout 2024-09-17T07:18:44.654618:Slices not stacked: some are phase/real/imaginary/phase maps, others are not. Instances 1 1 INFO: stdout 2024-09-17T07:18:44.654618:Slices not stacked: some are phase/real/imaginary/phase maps, others are not. Instances 1 1 240917-07:18:44,655 nipype.interface INFO: stdout 2024-09-17T07:18:44.654618:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-flanker_run-01_sbref_heudiconv880 (78x76x54x1) INFO: stdout 2024-09-17T07:18:44.654618:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-flanker_run-01_sbref_heudiconv880 (78x76x54x1) 240917-07:18:44,712 nipype.interface INFO: stdout 2024-09-17T07:18:44.712036:Compress: "/usr/bin/pigz" -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-flanker_run-01_sbref_heudiconv880.nii" INFO: stdout 2024-09-17T07:18:44.712036:Compress: "/usr/bin/pigz" -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-flanker_run-01_sbref_heudiconv880.nii" 240917-07:18:44,712 nipype.interface INFO: stdout 2024-09-17T07:18:44.712036:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-flanker_run-01_sbref_heudiconv880_ph (78x76x54x1) INFO: stdout 2024-09-17T07:18:44.712036:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-flanker_run-01_sbref_heudiconv880_ph (78x76x54x1) 240917-07:18:44,727 nipype.interface INFO: stdout 2024-09-17T07:18:44.727361:Compress: "/usr/bin/pigz" -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-flanker_run-01_sbref_heudiconv880_ph.nii" INFO: stdout 2024-09-17T07:18:44.727361:Compress: "/usr/bin/pigz" -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-flanker_run-01_sbref_heudiconv880_ph.nii" 240917-07:18:44,727 nipype.interface INFO: stdout 2024-09-17T07:18:44.727361:Conversion required 0.084087 seconds (0.014108 for core code). INFO: stdout 2024-09-17T07:18:44.727361:Conversion required 0.084087 seconds (0.014108 for core code). 240917-07:18:44,748 nipype.workflow INFO: [Node] Finished "convert", elapsed time 0.126781s. INFO: [Node] Finished "convert", elapsed time 0.126781s. WARNING: For now not embedding BIDS and info generated .nii.gz itself since sequence produced multiple files INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-at_run-01_sbref (2 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:44,779 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixuluom5ok/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixuluom5ok/convert". 240917-07:18:44,781 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:44,818 nipype.interface INFO: stdout 2024-09-17T07:18:44.818041:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:44.818041:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:44,818 nipype.interface INFO: stdout 2024-09-17T07:18:44.818041:Found 2 DICOM file(s) INFO: stdout 2024-09-17T07:18:44.818041:Found 2 DICOM file(s) 240917-07:18:44,818 nipype.interface INFO: stdout 2024-09-17T07:18:44.818041:Slices not stacked: some are phase/real/imaginary/phase maps, others are not. Instances 1 1 INFO: stdout 2024-09-17T07:18:44.818041:Slices not stacked: some are phase/real/imaginary/phase maps, others are not. Instances 1 1 240917-07:18:44,818 nipype.interface INFO: stdout 2024-09-17T07:18:44.818041:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-at_run-01_sbref_heudiconv494_ph (78x76x54x1) INFO: stdout 2024-09-17T07:18:44.818041:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-at_run-01_sbref_heudiconv494_ph (78x76x54x1) 240917-07:18:44,837 nipype.interface INFO: stdout 2024-09-17T07:18:44.837760:Compress: "/usr/bin/pigz" -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-at_run-01_sbref_heudiconv494_ph.nii" INFO: stdout 2024-09-17T07:18:44.837760:Compress: "/usr/bin/pigz" -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-at_run-01_sbref_heudiconv494_ph.nii" 240917-07:18:44,837 nipype.interface INFO: stdout 2024-09-17T07:18:44.837760:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-at_run-01_sbref_heudiconv494 (78x76x54x1) INFO: stdout 2024-09-17T07:18:44.837760:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-at_run-01_sbref_heudiconv494 (78x76x54x1) 240917-07:18:44,853 nipype.interface INFO: stdout 2024-09-17T07:18:44.853908:Compress: "/usr/bin/pigz" -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-at_run-01_sbref_heudiconv494.nii" INFO: stdout 2024-09-17T07:18:44.853908:Compress: "/usr/bin/pigz" -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-at_run-01_sbref_heudiconv494.nii" 240917-07:18:44,853 nipype.interface INFO: stdout 2024-09-17T07:18:44.853908:Conversion required 0.047984 seconds (0.014386 for core code). INFO: stdout 2024-09-17T07:18:44.853908:Conversion required 0.047984 seconds (0.014386 for core code). 240917-07:18:44,873 nipype.workflow INFO: [Node] Finished "convert", elapsed time 0.091268s. INFO: [Node] Finished "convert", elapsed time 0.091268s. WARNING: For now not embedding BIDS and info generated .nii.gz itself since sequence produced multiple files INFO: Converting /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-reward_run-01_sbref (2 DICOMs) -> /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func . Converter: dcm2niix . Output types: ('nii.gz',) 240917-07:18:44,907 nipype.workflow INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixjxu78tj7/convert". INFO: [Node] Setting-up "convert" in "/tmp/dcm2niixjxu78tj7/convert". 240917-07:18:44,909 nipype.workflow INFO: [Node] Executing "convert" INFO: [Node] Executing "convert" 240917-07:18:44,980 nipype.interface INFO: stdout 2024-09-17T07:18:44.979962:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) INFO: stdout 2024-09-17T07:18:44.979962:Chris Rorden's dcm2niiX version v1.0.20211006 GCC10.2.1 x86-64 (64-bit Linux) 240917-07:18:44,980 nipype.interface INFO: stdout 2024-09-17T07:18:44.979962:Found 2 DICOM file(s) INFO: stdout 2024-09-17T07:18:44.979962:Found 2 DICOM file(s) 240917-07:18:44,980 nipype.interface INFO: stdout 2024-09-17T07:18:44.979962:Slices not stacked: some are phase/real/imaginary/phase maps, others are not. Instances 1 1 INFO: stdout 2024-09-17T07:18:44.979962:Slices not stacked: some are phase/real/imaginary/phase maps, others are not. Instances 1 1 240917-07:18:44,980 nipype.interface INFO: stdout 2024-09-17T07:18:44.979962:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-reward_run-01_sbref_heudiconv909 (106x102x76x1) INFO: stdout 2024-09-17T07:18:44.979962:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-reward_run-01_sbref_heudiconv909 (106x102x76x1) 240917-07:18:45,63 nipype.interface INFO: stdout 2024-09-17T07:18:45.063224:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-reward_run-01_sbref_heudiconv909.nii" INFO: stdout 2024-09-17T07:18:45.063224:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-reward_run-01_sbref_heudiconv909.nii" 240917-07:18:45,63 nipype.interface INFO: stdout 2024-09-17T07:18:45.063224:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-reward_run-01_sbref_heudiconv909_ph (106x102x76x1) INFO: stdout 2024-09-17T07:18:45.063224:Convert 1 DICOM as /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-reward_run-01_sbref_heudiconv909_ph (106x102x76x1) 240917-07:18:45,119 nipype.interface INFO: stdout 2024-09-17T07:18:45.119529:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-reward_run-01_sbref_heudiconv909_ph.nii" INFO: stdout 2024-09-17T07:18:45.119529:Compress: "/usr/bin/pigz" -b 960 -n -f -6 "/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-viakaninen003/ses-03DRCMRprisma/func/sub-viakaninen003_ses-03DRCMRprisma_task-reward_run-01_sbref_heudiconv909_ph.nii" 240917-07:18:45,119 nipype.interface INFO: stdout 2024-09-17T07:18:45.119529:Conversion required 0.187578 seconds (0.020177 for core code). INFO: stdout 2024-09-17T07:18:45.119529:Conversion required 0.187578 seconds (0.020177 for core code). 240917-07:18:45,139 nipype.workflow INFO: [Node] Finished "convert", elapsed time 0.230141s. INFO: [Node] Finished "convert", elapsed time 0.230141s. WARNING: For now not embedding BIDS and info generated .nii.gz itself since sequence produced multiple files INFO: Populating template files under /mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/ Traceback (most recent call last): File "/opt/miniconda-latest/bin/heudiconv", line 8, in sys.exit(main()) File "/opt/miniconda-latest/lib/python3.7/site-packages/heudiconv/cli/run.py", line 24, in main workflow(**kwargs) File "/opt/miniconda-latest/lib/python3.7/site-packages/heudiconv/main.py", line 351, in workflow grouping=grouping,) File "/opt/miniconda-latest/lib/python3.7/site-packages/heudiconv/convert.py", line 239, in prep_conversion getattr(heuristic, 'DEFAULT_FIELDS', {})) File "/opt/miniconda-latest/lib/python3.7/site-packages/heudiconv/bids.py", line 127, in populate_bids_templates populate_aggregated_jsons(path) File "/opt/miniconda-latest/lib/python3.7/site-packages/heudiconv/bids.py", line 195, in populate_aggregated_jsons with open(events_file, 'w') as f: PermissionError: [Errno 13] Permission denied: '/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-via006/ses-02DRCMRprisma/func/sub-via006_ses-02DRCMRprisma_task-at_run-01_part-mag_events.tsv' chmod 750 ${RAWBIDS_DIR}/.bidsignore # generate hidden .bidsignore file echo **/*dki_*epi.bval* > ${RAWBIDS_DIR}/.bidsignore echo **/*dki_*epi.bvec* >> ${RAWBIDS_DIR}/.bidsignore echo **/*part*epi.* >> ${RAWBIDS_DIR}/.bidsignore ############################################################ #close output close_logging

Platform details:

Choose one:

[ ] Local environment
[ x Container: singularity build heudiconv-1.2.0.sif docker://nipy/heudiconv:1.2.0

yarikoptic commented 1 week ago

I wrapped dumps into html <details> flag to make this issue manageable.

so what is that PermissionError: [Errno 13] Permission denied: '/mnt/projects/VIA_BIDS/BIDS_MRI_DRCMR/rawdata/sub-via006/ses-02DRCMRprisma/func/sub-via006_ses-02DRCMRprisma_task-at_run-01_part-mag_events.tsv' about? I recommend to fix it up!

this fixup to your heuristic would make it work with released version

--- heuristic.py    2024-09-18 16:06:12.301320883 -0400
+++ heuristic_fixed.py  2024-09-18 16:08:00.845927516 -0400
@@ -1,6 +1,6 @@
 import os

-def create_key(template, outtype=('nii.gz'), annotation_classes=None):
+def create_key(template, outtype=('nii.gz',), annotation_classes=None):
         if template is None or not template:
             raise ValueError('template must be a valid format string')
         return template, outtype, annotation_classes

and #787 should provide workaround at heudiconv level in the future release.

WilliamFCB commented 1 week ago

@yarikoptic, many thanks for condensing the info. I learned something new.

I have no idea what the "that PermissionError: [Errno 13] " is about. That file does not exist. Moreover, why would heudiconv want to access a subjectid that is not ported for conversion? What could cause such behavior?

The added "," did the trick. Many thanks!!

WilliamFCB commented 1 week ago

Think I figured it out. Heudonv goes through all subject id in rawdata// and checks if in func/ task*bold files have an associated events file and, if not, wants to create them. However, I typically make subject directories read only after conversion to prevent accidental deletion. The problem was that I after bids conversion created one event file for each task, and deleted the separate ones for mag and phase parts: eg sub-via519_ses-02DRCMRprisma_task-at_run-01_events.tsv sub-via519_ses-02DRCMRprisma_task-at_run-01_part-mag_bold.json sub-via519_ses-02DRCMRprisma_task-at_run-01_part-mag_bold.nii.gz sub-via519_ses-02DRCMRprisma_task-at_run-01_part-mag_sbref.json sub-via519_ses-02DRCMRprisma_task-at_run-01_part-mag_sbref.nii.gz sub-via519_ses-02DRCMRprisma_task-at_run-01_part-phase_bold.json sub-via519_ses-02DRCMRprisma_task-at_run-01_part-phase_bold.nii.gz sub-via519_ses-02DRCMRprisma_task-at_run-01_part-phase_sbref.json sub-via519_ses-02DRCMRprisma_task-at_run-01_part-phase_sbref.nii.gz sub-via519_ses-02DRCMRprisma_task-flanker_run-01_events.tsv sub-via519_ses-02DRCMRprisma_task-flanker_run-01_part-mag_bold.json sub-via519_ses-02DRCMRprisma_task-flanker_run-01_part-mag_bold.nii.gz sub-via519_ses-02DRCMRprisma_task-flanker_run-01_part-mag_sbref.json sub-via519_ses-02DRCMRprisma_task-flanker_run-01_part-mag_sbref.nii.gz sub-via519_ses-02DRCMRprisma_task-flanker_run-01_part-phase_bold.json sub-via519_ses-02DRCMRprisma_task-flanker_run-01_part-phase_bold.nii.gz sub-via519_ses-02DRCMRprisma_task-flanker_run-01_part-phase_sbref.json sub-via519_ses-02DRCMRprisma_task-flanker_run-01_part-phase_sbref.nii.gz sub-via519_ses-02DRCMRprisma_task-reward_run-01_events.tsv sub-via519_ses-02DRCMRprisma_task-reward_run-01_part-mag_bold.json sub-via519_ses-02DRCMRprisma_task-reward_run-01_part-mag_bold.nii.gz sub-via519_ses-02DRCMRprisma_task-reward_run-01_part-mag_sbref.json sub-via519_ses-02DRCMRprisma_task-reward_run-01_part-mag_sbref.nii.gz sub-via519_ses-02DRCMRprisma_task-reward_run-01_part-phase_bold.json sub-via519_ses-02DRCMRprisma_task-reward_run-01_part-phase_bold.nii.gz sub-via519_ses-02DRCMRprisma_task-reward_run-01_part-phase_sbref.json sub-via519_ses-02DRCMRprisma_task-reward_run-01_part-phase_sbref.nii.gz

I will just revert to the standard behavior of heudiconv and let it create the separate events file again.

yarikoptic commented 1 week ago

However, I typically make subject directories read only after conversion to prevent accidental deletion.

nice strategy! may I recommend DataLad and datalad run command (https://handbook.datalad.org/en/latest/basics/basics-run.html) -- it can help keeping your mind at peace while running anything which could remove/change/etc your data ;-) I tend to keep everything under git/git-annex/datalad for such a reason

WilliamFCB commented 1 week ago

Many thanks for the suggestion. I have no experience with Datalad, but will look into it!

yarikoptic commented 1 week ago

there is even --datalad mode for heudiconv happen you want to try ;-)

nipy / heudiconv

heuristic.py for heudiconv 0.10.0 incompatible with heudiconv 1.20 (or 1.1.6) ? #786

Summary

Platform details: