A Python SDK tool for auditing gear run data

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License: MIT License

Author: Tinashe M. Tapera

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Project description

fw-gear-audit

A Python SDK tool for auditing gear run data

Use this tool to fetch data from Flywheel describing which gears have been run within a project and how they were configured. You can also join SeqInfo data to help filter your data by sequences.

usage: FlywheelGearAudit.py [-h] --project PROJECT [PROJECT ...]
                            [--subject SUBJECT [SUBJECT ...]]
                            [--session SESSION [SESSION ...]] [--verbose]
                            [--dry_run] (--path PATH | --fname FNAME)
                            (--by-runs | --by-sequences)

Goal

You can run many analysis gears on Flywheel. Keeping track of these within a subject is easy with the GUI, but to view this data en masse requires the use of the SDK to loop over each subject and collect their gear run data. This becomes troublesome when, for example with fMRIPrep, there can be many runs of the same gear due to version updates, feature testing, incorrect configs, or random errors causing gears to crash.

This leaves users in a situation where they may not be sure if the correct version and configuration of fMRIPrep was run successfully for 100% of the participants in their 200-cohort study.

fw-gear-audit aims to remedy this situation by quickly and efficiently gathering data about gear runs and providing the user with a tabular .csv file for their records.

Features

  • Use the --subject and --session flags to filter your data within project by subject or session labels.
  • By default, gear run data includes the gear name, version, runtime and date, and completion status. Use the --verbose flag to output both gear run data and configuration information for each run
  • Choose between --by-runs to output a table where each row is a gear run, or --by-sequences to output a table where each gear run is accompanied by a seqInfo subtable

By Run:

subject session gearName gearVersion runLabel runDatetime runRuntimeMS runStatus
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed
104059 10762 fmriprep125 0.1.7_1.2.5 fmriprep_SDK_010762_2019-04-22_17:32 2019-04-22 21:33:25.870000+00:00 14055 failed
104059 10762 fmriprep125 0.1.7_1.2.5 fmriprep_SDK_010762_2019-04-24_11:31 2019-04-24 15:36:34.178000+00:00 287719 failed
104059 10762 fmriprep125 0.1.7_1.2.5 fmriprep_SDK_010762_2019-04-24_16:45 2019-04-24 20:45:21.188000+00:00 55392635 complete
104059 10762 xcpengine-fw 1.063 XCP_SDK 2019-05-17 11:35:54.021070 2019-05-17 15:35:54.085000+00:00 5553043 complete
104059 10762 xcpengine-fw 1.0633 XCP_SDK 2019-06-17 16:44:12.682716 2019-06-17 20:44:12.754000+00:00 312121575 failed
104059 10762 xcpengine-fw 1.06338 XCP_SDK_task_module_2019-06-26 13:08:13.199392 2019-06-26 17:08:13.274000+00:00 28015 complete
104059 10762 xcpengine-fw 1.06338 XCP_SDK_taskregress_module_2019-06-26 19:10:02 2019-06-26 19:10:02.888000+00:00 27375 complete
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_11196 2019-04-15 20:45:35.356000+00:00 44505363 failed
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_11196 2019-04-16 16:27:13.458000+00:00 44010936 failed
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/17/2019 11:33:10 2019-04-17 15:33:57.530000+00:00 30092 failed
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/17/2019 12:36:44 2019-04-17 16:37:15.579000+00:00 73098331 complete
86486 11196 fmriprep125 0.1.7_1.2.5 fmriprep_SDK_11196_2019-04-22_17:32 2019-04-22 21:33:36.983000+00:00 16347 failed
86486 11196 fmriprep125 0.1.7_1.2.5 fmriprep125 04/23/2019 16:07:28 2019-04-23 20:07:49.717000+00:00 17150 failed
86486 11196 fmriprep125 0.1.7_1.2.5 fmriprep125 04/23/2019 16:17:26 2019-04-23 20:17:45.532000+00:00 65726568 complete
86486 11196 fmriprep125 0.1.7_1.2.5 fmriprep_SDK_11196_2019-04-24_11:31 2019-04-24 15:36:42.723000+00:00 52406897 complete
86486 11196 xcpengine-fw 1.063 xcpengine-fw 04/27/2019 19:33:41 2019-04-27 23:34:13.359000+00:00 4775298 complete
86486 11196 fw-heudiconv 0.1.11_0.1.0 fw-heudiconv 05/10/2019 15:14:42 2019-05-10 19:14:57.904000+00:00 14759 complete
86486 11196 xcpengine-fw 1.063 xcpengine-fw 05/15/2019 10:37:09 2019-05-15 14:37:37.681000+00:00 320600623 complete
86486 11196 xcpengine-fw 1.063 xcpengine-fw 05/15/2019 10:37:44 2019-05-15 14:43:11.425000+00:00 318911954 complete
86486 11196 xcpengine-fw 1.063 xcpenginestruct 05/25/2019 19:14:49 2019-05-25 23:15:35.105000+00:00 322438769 complete
86486 11196 xcpengine-fw 1.0631 xcpengine-fw 06/13/2019 12:59:24 2019-06-13 17:00:03.867000+00:00 1457 failed
86486 11196 xcpengine-fw 1.0633 XCP_SDK 2019-06-17 16:45:31.934948 2019-06-17 20:45:32.002000+00:00 316570122 failed
86486 11196 xcpengine-fw 1.06336 xcpengine-fw 06/25/2019 14:50:03 2019-06-25 18:50:46.914000+00:00 31014 complete
86486 11196 xcpengine-fw 1.06337 xcpengine-fw 06/25/2019 15:41:09 2019-06-25 19:42:04.137000+00:00 1030893 complete
86486 11196 xcpengine-fw 1.06337 xcpengine-fw 06/25/2019 15:56:22 2019-06-25 19:57:17.108000+00:00 1534523 complete
86486 11196 xcpengine-fw 1.06338 XCP_SDK_task_module_2019-06-26 13:08:18.700338 2019-06-26 17:08:18.774000+00:00 1562030 complete
86486 11196 xcpengine-fw 1.06338 XCP_SDK_taskregress_module_2019-06-26 19:10:09 2019-06-26 19:10:09.688000+00:00 1031698 complete
86486 11196 xcpengine-fw 1.06339 xcpengine-fw 07/02/2019 12:38:10 2019-07-02 16:39:02.284000+00:00 1292985 complete

This allows you to filter, for e.g., which subjects successfully ran XCPEngine with version 1.06338

# Tidy R syntax:
df %>% 
  filter(str_detect(gearName, 'xcpengine')) %>% 
  filter(str_detect(runStatus, 'complete')) %>%
  filter(str_detect(gearVersion, '6338'))

By Sequences

This option creates a data frame where each run above is also joined by a sequence info table for that participant:

subject session gearName gearVersion runLabel runDatetime runRuntimeMS runStatus seriesID dcmDirName dim1 dim2 dim3 dim4 TR TE protocolName isMotionCorrected isDerived seriesDescription sequenceName imageType seriesUid
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c75633aba2580002d3902e6 Localizer_1_i00003.nii.gz 512 512 3 -1 0.0086 0.004 Localizer False False Localizer _fl2d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814140178131880096.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c75633aba2580002d3902e6 Localizer_1_i00002.nii.gz 512 512 3 -1 0.0086 0.004 Localizer False False Localizer _fl2d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814140178131880096.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c75633aba2580002d3902e6 Localizer_1_i00001.nii.gz 512 512 3 -1 0.0086 0.004 Localizer False False Localizer _fl2d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814140178131880096.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c756339ba25800038398297 restingBOLD_mb6_1200_10.nii.gz 448 448 1200 -1 0.5 0.025 restingBOLD_mb6_1200 False False restingBOLD_mb6_1200 epfid2d1_64 ('ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC') 1.3.12.2.1107.5.2.43.66044.201804181426368296184317.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c756339ba25800038398298 bbl1_restbold1_124mb_11.nii.gz 448 448 124 -1 3 0.032 bbl1_restbold1_124mb False False bbl1_restbold1_124mb epfid2d1_64 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM', 'MOSAIC') 1.3.12.2.1107.5.2.43.66044.2018041814370267454559619.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c756339ba2580003939a503 ASL_3DSPIRAL_V20_GE_12_Eq_1.nii.gz 64 64 64 -1 0.022 0.01003 False False ()
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c756339ba2580003939a503 ASL_3DSPIRAL_V20_GE_12.nii.gz 64 64 64 -1 4.6255 0.01003 ASL_3DSPIRAL_V20_GE False False ASL_3DSPIRAL_V20_GE_M0 Sp3d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND') 1.3.12.2.1107.5.2.43.66044.2018041814445154289476985.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c756339ba25800038398296 ASL_3DSPIRAL_V20_GE_13.nii.gz 64 64 2560 -1 4.6255 0.01003 ASL_3DSPIRAL_V20_GE False False ASL_3DSPIRAL_V20_GE_ASL Sp3d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND') 1.3.12.2.1107.5.2.43.66044.2018041814445430648677051.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c756339ba2580002e38dd54 ASL_3DSPIRAL_V20_GE_14.nii.gz 64 64 32 -1 4.6255 0.01003 ASL_3DSPIRAL_V20_GE False False ASL_3DSPIRAL_V20_GE_MeanPerf Sp3d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND') 1.3.12.2.1107.5.2.43.66044.2018041814445154291576986.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c756339ba2580002c38d5df DTI_MultiShell_117dir_15.nii.gz 1400 1400 118 -1 3.027 0.0828 DTI_MultiShell_117dir False False DTI_MultiShell_117dir ep_b5#1 ('ORIGINAL', 'PRIMARY', 'DIFFUSION', 'NONE', 'MB', 'ND', 'NORM', 'MOSAIC') 1.3.12.2.1107.5.2.43.66044.2018041814510448864779646.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c756339ba2580002c38d5df DTI_MultiShell_117dir_15.bvec 1400 1400 118 -1 3.027 0.0828 DTI_MultiShell_117dir False False DTI_MultiShell_117dir ep_b5#1 ('ORIGINAL', 'PRIMARY', 'DIFFUSION', 'NONE', 'MB', 'ND', 'NORM', 'MOSAIC') 1.3.12.2.1107.5.2.43.66044.2018041814510448864779646.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c756339ba2580002c38d5df DTI_MultiShell_117dir_15.bval 1400 1400 118 -1 3.027 0.0828 DTI_MultiShell_117dir False False DTI_MultiShell_117dir ep_b5#1 ('ORIGINAL', 'PRIMARY', 'DIFFUSION', 'NONE', 'MB', 'ND', 'NORM', 'MOSAIC') 1.3.12.2.1107.5.2.43.66044.2018041814510448864779646.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c756339ba25800038398294 DTI_MultiShell_topup_ref_17.nii.gz 140 140 92 -1 3.027 0.0828 DTI_MultiShell_topup_ref False False DTI_MultiShell_topup_ref ep_b5#1 ('ORIGINAL', 'PRIMARY', 'DIFFUSION', 'NONE', 'MB', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814573463580034910.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c756339ba25800038398299 MPRAGE_TI1100_ipat2_2.nii.gz 256 192 160 -1 1.81 0.00345 MPRAGE_TI1100_ipat2 False False MPRAGE_TI1100_ipat2 _tfl3d1_16 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814150078639280942.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c756339ba2580003939a505 T2_sagittal_SPACE_3.nii.gz 256 256 176 -1 3.2 0.408 T2_sagittal_SPACE False False T2_sagittal_SPACE _spc_282ns ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814225838675681811.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c75633aba2580002e38dd55 TOF_3D_multi-slab_R2_4.nii.gz 384 288 74 -1 0.022 0.00366 TOF_3D_multi-slab_R2 False False TOF_3D_multi-slab_R2 _fl3d1r_t70 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814230724412383000.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c756339ba2580003839829a TOF_3D_multi-slab_R2_5.nii.gz 142 384 1 -1 0.022 0.00366 TOF_3D_multi-slab_R2 False False TOF_3D_multi-slab_R2_MIP_SAG _fl3d1r_t70 ('ORIGINAL', 'PRIMARY', 'MIP', 'SAG', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814244435763483338.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c75633aba2580003839829b TOF_3D_multi-slab_R2_6.nii.gz 142 288 1 -1 0.022 0.00366 TOF_3D_multi-slab_R2 False False TOF_3D_multi-slab_R2_MIP_COR _fl3d1r_t70 ('ORIGINAL', 'PRIMARY', 'MIP', 'COR', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814244435762983336.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c75633aba2580002a38c710 TOF_3D_multi-slab_R2_7.nii.gz 384 288 1 -1 0.022 0.00366 TOF_3D_multi-slab_R2 False False TOF_3D_multi-slab_R2_MIP_TRA _fl3d1r_t70 ('ORIGINAL', 'PRIMARY', 'MIP', 'TRA', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814244435762083334.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c756339ba2580003939a504 B0map_8_e2.nii.gz 80 80 120 -1 0.58 0.00658 B0map False False B0map _fm2d2r ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814245128954183710.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c756339ba2580003939a504 B0map_8_e1.nii.gz 80 80 120 -1 0.58 0.00412 B0map False False B0map _fm2d2r ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814245128954183710.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-15 20:45:24.774000+00:00 63361 failed 5c756339ba2580002c38d5e0 B0map_9_ph.nii.gz 80 80 60 -1 0.58 0.00658 B0map False False B0map _fm2d2r ('ORIGINAL', 'PRIMARY', 'P', 'ND') 1.3.12.2.1107.5.2.43.66044.2018041814245128955483711.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c75633aba2580002d3902e6 Localizer_1_i00003.nii.gz 512 512 3 -1 0.0086 0.004 Localizer False False Localizer _fl2d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814140178131880096.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c75633aba2580002d3902e6 Localizer_1_i00002.nii.gz 512 512 3 -1 0.0086 0.004 Localizer False False Localizer _fl2d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814140178131880096.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c75633aba2580002d3902e6 Localizer_1_i00001.nii.gz 512 512 3 -1 0.0086 0.004 Localizer False False Localizer _fl2d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814140178131880096.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c756339ba25800038398297 restingBOLD_mb6_1200_10.nii.gz 448 448 1200 -1 0.5 0.025 restingBOLD_mb6_1200 False False restingBOLD_mb6_1200 epfid2d1_64 ('ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC') 1.3.12.2.1107.5.2.43.66044.201804181426368296184317.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c756339ba25800038398298 bbl1_restbold1_124mb_11.nii.gz 448 448 124 -1 3 0.032 bbl1_restbold1_124mb False False bbl1_restbold1_124mb epfid2d1_64 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM', 'MOSAIC') 1.3.12.2.1107.5.2.43.66044.2018041814370267454559619.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c756339ba2580003939a503 ASL_3DSPIRAL_V20_GE_12_Eq_1.nii.gz 64 64 64 -1 0.022 0.01003 False False ()
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c756339ba2580003939a503 ASL_3DSPIRAL_V20_GE_12.nii.gz 64 64 64 -1 4.6255 0.01003 ASL_3DSPIRAL_V20_GE False False ASL_3DSPIRAL_V20_GE_M0 Sp3d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND') 1.3.12.2.1107.5.2.43.66044.2018041814445154289476985.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c756339ba25800038398296 ASL_3DSPIRAL_V20_GE_13.nii.gz 64 64 2560 -1 4.6255 0.01003 ASL_3DSPIRAL_V20_GE False False ASL_3DSPIRAL_V20_GE_ASL Sp3d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND') 1.3.12.2.1107.5.2.43.66044.2018041814445430648677051.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c756339ba2580002e38dd54 ASL_3DSPIRAL_V20_GE_14.nii.gz 64 64 32 -1 4.6255 0.01003 ASL_3DSPIRAL_V20_GE False False ASL_3DSPIRAL_V20_GE_MeanPerf Sp3d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND') 1.3.12.2.1107.5.2.43.66044.2018041814445154291576986.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c756339ba2580002c38d5df DTI_MultiShell_117dir_15.nii.gz 1400 1400 118 -1 3.027 0.0828 DTI_MultiShell_117dir False False DTI_MultiShell_117dir ep_b5#1 ('ORIGINAL', 'PRIMARY', 'DIFFUSION', 'NONE', 'MB', 'ND', 'NORM', 'MOSAIC') 1.3.12.2.1107.5.2.43.66044.2018041814510448864779646.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c756339ba2580002c38d5df DTI_MultiShell_117dir_15.bvec 1400 1400 118 -1 3.027 0.0828 DTI_MultiShell_117dir False False DTI_MultiShell_117dir ep_b5#1 ('ORIGINAL', 'PRIMARY', 'DIFFUSION', 'NONE', 'MB', 'ND', 'NORM', 'MOSAIC') 1.3.12.2.1107.5.2.43.66044.2018041814510448864779646.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c756339ba2580002c38d5df DTI_MultiShell_117dir_15.bval 1400 1400 118 -1 3.027 0.0828 DTI_MultiShell_117dir False False DTI_MultiShell_117dir ep_b5#1 ('ORIGINAL', 'PRIMARY', 'DIFFUSION', 'NONE', 'MB', 'ND', 'NORM', 'MOSAIC') 1.3.12.2.1107.5.2.43.66044.2018041814510448864779646.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c756339ba25800038398294 DTI_MultiShell_topup_ref_17.nii.gz 140 140 92 -1 3.027 0.0828 DTI_MultiShell_topup_ref False False DTI_MultiShell_topup_ref ep_b5#1 ('ORIGINAL', 'PRIMARY', 'DIFFUSION', 'NONE', 'MB', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814573463580034910.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c756339ba25800038398299 MPRAGE_TI1100_ipat2_2.nii.gz 256 192 160 -1 1.81 0.00345 MPRAGE_TI1100_ipat2 False False MPRAGE_TI1100_ipat2 _tfl3d1_16 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814150078639280942.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c756339ba2580003939a505 T2_sagittal_SPACE_3.nii.gz 256 256 176 -1 3.2 0.408 T2_sagittal_SPACE False False T2_sagittal_SPACE _spc_282ns ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814225838675681811.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c75633aba2580002e38dd55 TOF_3D_multi-slab_R2_4.nii.gz 384 288 74 -1 0.022 0.00366 TOF_3D_multi-slab_R2 False False TOF_3D_multi-slab_R2 _fl3d1r_t70 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814230724412383000.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c756339ba2580003839829a TOF_3D_multi-slab_R2_5.nii.gz 142 384 1 -1 0.022 0.00366 TOF_3D_multi-slab_R2 False False TOF_3D_multi-slab_R2_MIP_SAG _fl3d1r_t70 ('ORIGINAL', 'PRIMARY', 'MIP', 'SAG', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814244435763483338.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c75633aba2580003839829b TOF_3D_multi-slab_R2_6.nii.gz 142 288 1 -1 0.022 0.00366 TOF_3D_multi-slab_R2 False False TOF_3D_multi-slab_R2_MIP_COR _fl3d1r_t70 ('ORIGINAL', 'PRIMARY', 'MIP', 'COR', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814244435762983336.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c75633aba2580002a38c710 TOF_3D_multi-slab_R2_7.nii.gz 384 288 1 -1 0.022 0.00366 TOF_3D_multi-slab_R2 False False TOF_3D_multi-slab_R2_MIP_TRA _fl3d1r_t70 ('ORIGINAL', 'PRIMARY', 'MIP', 'TRA', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814244435762083334.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c756339ba2580003939a504 B0map_8_e2.nii.gz 80 80 120 -1 0.58 0.00658 B0map False False B0map _fm2d2r ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814245128954183710.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c756339ba2580003939a504 B0map_8_e1.nii.gz 80 80 120 -1 0.58 0.00412 B0map False False B0map _fm2d2r ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.2018041814245128954183710.0.0.0
104059 10762 fmriprep125 0.1.2_1.2.5 fmriprep_SDK_010762 2019-04-16 16:27:02.664000+00:00 15829 failed 5c756339ba2580002c38d5e0 B0map_9_ph.nii.gz 80 80 60 -1 0.58 0.00658 B0map False False B0map _fm2d2r ('ORIGINAL', 'PRIMARY', 'P', 'ND') 1.3.12.2.1107.5.2.43.66044.2018041814245128955483711.0.0.0
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93c0a6f546b6002abdfe43 1.3.12.2.1107.5.2.43.66044.30000019032116274975300004569.nii.gz 64 64 2560 -1 4 0.01003 ASL_3DSPIRAL_V20_GE False False ASL_3DSPIRAL_V20_GE_ASL Sp3d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300004569
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93be6df546b6002cbe1b65 1.3.12.2.1107.5.2.43.66044.30000019032116274975300002008_Eq_1.nii.gz 64 64 64 -1 False False ()
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93be6df546b6002cbe1b65 1.3.12.2.1107.5.2.43.66044.30000019032116274975300002008.nii.gz 64 64 64 -1 4 0.01003 ASL_3DSPIRAL_V20_GE False False ASL_3DSPIRAL_V20_GE_M0 Sp3d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300002008
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93c0b0f546b6002fbf3a7e 1.3.12.2.1107.5.2.43.66044.30000019032116274975300004602.nii.gz 64 64 32 -1 4 0.01003 ASL_3DSPIRAL_V20_GE False False ASL_3DSPIRAL_V20_GE_MeanPerf Sp3d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300004602
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93bcebf546b6002cbe1b61 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000556_e2.nii.gz 80 80 120 -1 0.58 0.00658 B0map False False B0map _fm2d2r ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000556
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93bcebf546b6002cbe1b61 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000556_e1.nii.gz 80 80 120 -1 0.58 0.00412 B0map False False B0map _fm2d2r ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000556
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93bcfbf546b6002cbe1b63 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000617_e2_ph.nii.gz 80 80 60 -1 0.58 0.00658 B0map False False B0map _fm2d2r ('ORIGINAL', 'PRIMARY', 'P', 'ND') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000617
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93c0f3f546b6002abdfe45 1.3.12.2.1107.5.2.43.66044.30000019032116274975300004721.nii.gz 1400 1400 118 -1 3.027 0.0828 DTI_MultiShell_117dir False False DTI_MultiShell_117dir ep_b5#1 ('ORIGINAL', 'PRIMARY', 'DIFFUSION', 'NONE', 'MB', 'ND', 'NORM', 'MOSAIC') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300004721
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93c0f3f546b6002abdfe45 1.3.12.2.1107.5.2.43.66044.30000019032116274975300004721.bvec 1400 1400 118 -1 3.027 0.0828 DTI_MultiShell_117dir False False DTI_MultiShell_117dir ep_b5#1 ('ORIGINAL', 'PRIMARY', 'DIFFUSION', 'NONE', 'MB', 'ND', 'NORM', 'MOSAIC') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300004721
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93c0f3f546b6002abdfe45 1.3.12.2.1107.5.2.43.66044.30000019032116274975300004721.bval 1400 1400 118 -1 3.027 0.0828 DTI_MultiShell_117dir False False DTI_MultiShell_117dir ep_b5#1 ('ORIGINAL', 'PRIMARY', 'DIFFUSION', 'NONE', 'MB', 'ND', 'NORM', 'MOSAIC') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300004721
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93c221f546b6002dbe38b3 1.3.12.2.1107.5.2.43.66044.30000019032116274975300005919.nii.gz 140 140 92 -1 3.027 0.0828 DTI_MultiShell_topup_ref False False DTI_MultiShell_topup_ref ep_b5#1 ('ORIGINAL', 'PRIMARY', 'DIFFUSION', 'NONE', 'MB', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300005919
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93bc57f546b6002ebe99b0 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000016_i00003.nii.gz 512 512 3 -1 0.0086 0.004 Localizer False False Localizer _fl2d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000016
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93bc57f546b6002ebe99b0 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000016_i00002.nii.gz 512 512 3 -1 0.0086 0.004 Localizer False False Localizer _fl2d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000016
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93bc57f546b6002ebe99b0 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000016_i00001.nii.gz 512 512 3 -1 0.0086 0.004 Localizer False False Localizer _fl2d1 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000016
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93bc82f546b6002abdfe33 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000177.nii.gz 256 192 160 -1 1.81 0.00345 MPRAGE_TI1100_ipat2 False False MPRAGE_TI1100_ipat2 _tfl3d1_16 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000177
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93bcaef546b6002fbf3a3c 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000354.nii.gz 256 256 176 -1 3.2 0.408 T2_sagittal_SPACE False False T2_sagittal_SPACE _spc_282ns ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000354
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93bcc3f546b6002fbf3a40 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000429.nii.gz 384 288 74 -1 0.022 0.00366 TOF_3D_multi-slab_R2 False False TOF_3D_multi-slab_R2 _fl3d1r_t70 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000429
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93bcc9f546b6002fbf3a45 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000433.nii.gz 142 288 1 -1 0.022 0.00366 TOF_3D_multi-slab_R2 False False TOF_3D_multi-slab_R2_MIP_COR _fl3d1r_t70 ('ORIGINAL', 'PRIMARY', 'MIP', 'COR', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000433
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93bcc6f546b6002abdfe35 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000431.nii.gz 142 384 1 -1 0.022 0.00366 TOF_3D_multi-slab_R2 False False TOF_3D_multi-slab_R2_MIP_SAG _fl3d1r_t70 ('ORIGINAL', 'PRIMARY', 'MIP', 'SAG', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000431
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93bcccf546b6002fbf3a49 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000435.nii.gz 384 288 1 -1 0.022 0.00366 TOF_3D_multi-slab_R2 False False TOF_3D_multi-slab_R2_MIP_TRA _fl3d1r_t70 ('ORIGINAL', 'PRIMARY', 'MIP', 'TRA', 'ND', 'NORM') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300000435
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93c261f546b6002abdfe49 1.3.12.2.1107.5.2.43.66044.30000019032116274975300006151.nii.gz 448 448 231 -1 3 0.032 bbl1_fracback1_231mb False False bbl1_fracback1_231mb epfid2d1_64 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM', 'MOSAIC') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300006151
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93be5cf546b6002fbf3a50 1.3.12.2.1107.5.2.43.66044.30000019032116274975300001943.nii.gz 448 448 124 -1 3 0.032 bbl1_restbold1_124mb False False bbl1_restbold1_124mb epfid2d1_64 ('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM', 'MOSAIC') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300001943
86486 11196 fmriprep125 0.1.2_1.2.5 fmriprep125 04/05/2019 14:59:38 2019-04-05 19:00:04.294000+00:00 73752452 complete 5c93be3af546b6002ebe99ba 1.3.12.2.1107.5.2.43.66044.30000019032116274975300001818.nii.gz 448 448 1200 -1 0.5 0.025 restingBOLD_mb6_1200 False False restingBOLD_mb6_1200 epfid2d1_64 ('ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC') 1.3.12.2.1107.5.2.43.66044.30000019032116274975300001818

i.e. for every run, there is a full set of sequences, gathered/pivoted vertically. This long table now gives you the added option of filtering by sequence specific preconditions, e.g. any subject with a T1w image should have an fMRIPrep run:

# Tidy R syntax:
df %>% 
  filter(str_detect(tolower(gearName), 'fmriprep')) %>% 
  filter(str_detect(runStatus, 'complete')) %>%
  filter(str_detect(tolower(protocolName), 't1w'))

Conclusion

fw-gear-audit allows users to get a tabular, indexable, searchable overview of the progress of gears run on Flywheel.

Please submit any bug reports, feature requests, or questions to the issues page.

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License: MIT License

Author: Tinashe M. Tapera

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