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PennLINC / fw-heudiconv

Heuristic-based Data Curation on Flywheel
BSD 3-Clause "New" or "Revised" License
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fw_HeudiConv not registering files in "IntendedFor" field for B0map correction #55

Closed MichaelPeerUpenn closed 4 years ago

MichaelPeerUpenn commented 4 years ago

Dear Tinashe,

I am attempting to run fw_heudiconv on my data, which works fine (I can run the whole fMRIPrep pipeline on it), but does not take into account the B0map files. I realized that the problem is that the "IntendedFor" field in the phasediff file is not written. I am attaching the heuristics script and logfile. It seems that the problem is at the end of the logfile, where it writes "missing paths" - it cannot find the files. I also saw that in the filename it is looking for, the session name does not have "ses-" before it. I tried all of the variations of adding or removing "ses-" and "sub-" before the {session} and {subject} respectively, in the last part of the script (the IntendedFor), but none of these options worked. (I'll mention that my subjects' names are "sub-seg01", "sub-seg02", and so on - so the "sub-" is already included in the filename). The project I'm working on is "segmentation" at the Epstein Lab.

The log file is as follows: 5db9a766e74aa3006007e4c9_logs.txt

And the script: segmentation_heudiconv10b.py.zip

If you have any idea, or could point me to someone who can, I would really appreciate it.

Thank you!

Michael Peer Postdoc, Epstein Lab

TinasheMTapera commented 4 years ago

Hey Michael,

Thanks for your patience. Could you give v0.2.4_0.1.2 a try either on flywheel or at the command line pip install --upgrade fw-heudiconv

MichaelPeerUpenn commented 4 years ago

Dear Tinashe, I tried but cannot see this version on Flywheel... (the latest version is 0.2.4_0.1.1) I am not familiar with running gears through the command line, but would be happy try if you tell me how or point me to where I can find out how. Thank you for all of your help!

Michael

On Wed, Oct 30, 2019 at 7:40 PM Tinashe Michael Tapera < notifications@github.com> wrote:

Hey Michael,

Thanks for your patience. Could you give v0.2.4_0.1.2 a try either on flywheel or at the command line pip install --upgrade fw-heudiconv

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TinasheMTapera commented 4 years ago

Hey Michael,

I can see 0.1.2 on flywheel currently, but if you still don't see it you can use the gear from the command line. Installation instructions are here, and usage instructions are here

MichaelPeerUpenn commented 4 years ago

Dear Tinashe, ok, now I can see the 0.1.2 version in Flywheel. I tried running it and now it seems like the filenames at the end of the logfile make sense, but they are still registered as "missing paths" and not entered into the IntendedFor field. I suspect the trouble might be that my subjects' names begin with 'sub-', e.g. 'sub-seg01'. When I press the "bids view" button in the Acquisitions tab, I see that the filenames are something like sub-sub-seg01. However when I ran fMRIPrep on these files in the past, the extra 'sub' was removed from the output file names. Thank you again

Michael

On Fri, Nov 1, 2019 at 10:20 AM Tinashe Michael Tapera < notifications@github.com> wrote:

Hey Michael,

I can see 0.1.2 on flywheel currently, but if you still don't see it you can use the gear from the command line. Installation instructions are here https://github.com/PennBBL/fw-heudiconv/wiki/Installation-Instructions, and usage instructions are here https://github.com/PennBBL/fw-heudiconv/wiki/Step-by-Step-Curation-Tutorial

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Gear Name: fw-heudiconv, Gear Version: 0.2.4_0.1.2 Gear starting... /flywheel/v0/fw_heudiconv/query.py:4: UserWarning: The DICOM readers are highly experimental, unstable, and only work for Siemens time-series at the moment Please use with caution. We would be grateful for your help in improving them from nibabel.nicom.dicomwrappers import wrapper_from_data 191101-18:22:54,560 nipype.utils INFO: Running nipype version 1.2.3 (latest: 1.2.3) INFO: Running nipype version 1.2.3 (latest: 1.2.3) INFO: ==============: fw-heudiconv gear manager starting up :===============

INFO: Calling fw-heudiconv with the following settings: INFO: Project: Segmentation INFO: Subject(s): ['sub-seg01'] INFO: Session(s): ['day1'] INFO: Heuristic: /flywheel/v0/input/heuristic/segmentation_heudiconv10b.py INFO: Action: Curate INFO: Dry run: False /usr/local/lib/python3.5/site-packages/fw_heudiconv/query.py:4: UserWarning: The DICOM readers are highly experimental, unstable, and only work for Siemens time-series at the moment Please use with caution. We would be grateful for your help in improving them from nibabel.nicom.dicomwrappers import wrapper_from_data 191101-18:22:55,931 nipype.utils INFO: Running nipype version 1.2.3 (latest: 1.2.3) INFO: Running nipype version 1.2.3 (latest: 1.2.3) INFO: =================: fw-heudiconv curator starting up :=================

INFO: Querying Flywheel server... DEBUG: Found project: Segmentation (5d03cc5fa550c6003c6fb70a) DEBUG: Found sessions: day1 (5d081765a550c600467047cf) DEBUG: Found SeqInfos: BOLD_ObjectViewing_1_d1: [TR=2 TE=0.025 shape=(864, 864, 316, -1) image_type=('ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC')] (5d0817a7a550c60048709f16)

BOLD_ObjectViewing_2_d1: 
    [TR=2 TE=0.025 shape=(864, 864, 316, -1) image_type=('ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC')] (5d0817e2a550c600467047e4)

BOLD_Localizer_1: 
    [TR=2 TE=0.025 shape=(864, 864, 168, -1) image_type=('ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC')] (5d081805a550c600467047ee)

BOLD_Localizer_2: 
    [TR=2 TE=0.025 shape=(864, 864, 168, -1) image_type=('ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC')] (5d081827a550c600396fbb1f)

MPRAGE_P2_1mm: 
    [TR=2.2 TE=0.00467 shape=(256, 192, 160, -1) image_type=('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM')] (5d081839a550c600467047f3)

BOLD_Resting: 
    [TR=2 TE=0.025 shape=(864, 864, 180, -1) image_type=('ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC')] (5d08185ea550c600467047f9)

B0map: 
    [TR=0.58 TE=0.00658 shape=(80, 80, 120, -1) image_type=('ORIGINAL', 'PRIMARY', 'M', 'ND')] (5d08186ca550c60048709f52)

B0map: 
    [TR=0.58 TE=0.00412 shape=(80, 80, 120, -1) image_type=('ORIGINAL', 'PRIMARY', 'M', 'ND')] (5d08186ca550c60048709f52)

B0map: 
    [TR=0.58 TE=0.00658 shape=(80, 80, 60, -1) image_type=('ORIGINAL', 'PRIMARY', 'P', 'ND')] (5d081877a550c60048709f56)

INFO: Loading heuristic file... INFO: Applying heuristic to query results... INFO: Processing IntendedFor fields based on heuristic file DEBUG: Intention map: [('{subject}/{session}/fmap/{subject}_{session}phasediff', ['{session}/func/sub-{subject}{session}_task-func_localizer_run-01bold.nii.gz', '{session}/func/sub-{subject}{session}_task-func_localizer_run-02bold.nii.gz', '{session}/func/sub-{subject}{session}_task-object_viewing_run-01_day-01bold.nii.gz', '{session}/func/sub-{subject}{session}_task-object_viewing_run-02_day-01bold.nii.gz', '{session}/func/sub-{subject}{session}_task-object_viewing_run-01_day-02bold.nii.gz', '{session}/func/sub-{subject}{session}_task-object_viewing_run-02_day-02bold.nii.gz', '{session}/func/sub-{subject}{session}_task-jrd_run-01bold.nii.gz', '{session}/func/sub-{subject}{session}_task-jrd_run-02bold.nii.gz', '{session}/func/sub-{subject}{session}_task-jrd_run-03bold.nii.gz', '{session}/func/sub-{subject}{session}_task-resting_statebold.nii.gz', '{session}/func/sub-{subject}{session}_task-navigationbold.nii.gz'])] INFO: Processing Medatata fields based on heuristic file DEBUG: Metadata extras: defaultdict(<class 'list'>, {('{subject}/{session}/fmap/{subject}{session}_phasediff', ('nii.gz',), None): {'EchoTime2': 0.006, 'EchoTime1': 0.004}}) INFO: Applying changes to files... DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200013247_e1.nii.gz sub-seg01_ses-day1_magnitude1.nii.gz -> sub-seg01/ses-day1/fmap/sub-seg01_ses-day1_magnitude1.nii.gz DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200013247_e2.nii.gz sub-seg01_ses-day1_magnitude2.nii.gz -> sub-seg01/ses-day1/fmap/sub-seg01_ses-day1_magnitude2.nii.gz DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200012446.nii.gz sub-seg01_ses-day1_task-object_viewing_run-02_day-01_bold.nii.gz -> sub-seg01/ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-02_day-01_bold.nii.gz DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200012784.nii.gz sub-seg01_ses-day1_task-func_localizer_run-02_bold.nii.gz -> sub-seg01/ses-day1/func/sub-seg01_ses-day1_task-func_localizer_run-02_bold.nii.gz DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200012615.nii.gz sub-seg01_ses-day1_task-func_localizer_run-01_bold.nii.gz -> sub-seg01/ses-day1/func/sub-seg01_ses-day1_task-func_localizer_run-01_bold.nii.gz DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200013126.nii.gz sub-seg01_ses-day1_task-resting_state_bold.nii.gz -> sub-seg01/ses-day1/func/sub-seg01_ses-day1_task-resting_state_bold.nii.gz DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200012129.nii.gz sub-seg01_ses-day1_task-object_viewing_run-01_day-01_bold.nii.gz -> sub-seg01/ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-01_day-01_bold.nii.gz DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200013308_e2_ph.nii.gz sub-seg01_ses-day1_phasediff.nii.gz -> sub-seg01/ses-day1/fmap/sub-seg01_ses-day1_phasediff.nii.gz DEBUG: 'sub-seg01_ses-day1_phasediff.nii.gz' IntendedFor: ['ses-day1/func/sub-seg01_ses-day1_task-func_localizer_run-01_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-func_localizer_run-02_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-01_day-01_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-02_day-01_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-01_day-02_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-02_day-02_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-jrd_run-01_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-jrd_run-02_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-jrd_run-03_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-resting_state_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-navigation_bold.nii.gz'] DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200013308_e2_ph.nii.gz metadata: {'EchoTime2': 0.006, 'EchoTime1': 0.004} DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200012945.nii.gz sub-seg01_ses-day1_T1w.nii.gz -> sub-seg01/ses-day1/anat/sub-seg01_ses-day1_T1w.nii.gz DEBUG: Ensuring all intentions apply for acquisition B0map: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200013308_e2_ph.nii.gz DEBUG: Missing paths: ['ses-day1/func/sub-seg01_ses-day1_task-func_localizer_run-01_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-func_localizer_run-02_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-01_day-01_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-02_day-01_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-01_day-02_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-02_day-02_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-jrd_run-01_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-jrd_run-02_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-jrd_run-03_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-resting_state_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-navigation_bold.nii.gz'] INFO: Done! INFO: ===================: Exiting fw-heudiconv curator :=================== INFO: Done! INFO: ================: Exiting fw-heudiconv gear manager :=================

Gear completed successfully after running for 20.41s. Uploading results... Job complete.

TinasheMTapera commented 4 years ago

Hey Michael,

Could you try adding the following to the end of your heuristic file:

def ReplaceSubject(str_input):
    import re
    out = re.sub("sub-", "", str_input)
    return(out)
MichaelPeerUpenn commented 4 years ago

Hi, thank you. After adding the lines you have suggested, the file names in the BIDS view look ok, but it still cannot find them when attempting to add the "IntendedFor" designation. (attached are the logfile and the new heuristic). I don't know if it is important, but I'll mention that I am running this on one of two sessions of a subject (both days have B0maps), because I don't want to run on the whole project yet. I thought that might be the problem (it cannot find the second session files) but it seems that the missing paths contain all of the file names, including the first session's ones. Thank you again for all of your help!

Michael

On Fri, Nov 1, 2019 at 2:54 PM Tinashe Michael Tapera < notifications@github.com> wrote:

Hey Michael,

Could you try adding the following to the end of your heuristic file:

def ReplaceSubject(str_input): import re out = re.sub("sub-", "", str_input) return(out)

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/PennBBL/fw-heudiconv/issues/55?email_source=notifications&email_token=ANUMFJR6HL7EXTTMWQTTKWDQRR3OXA5CNFSM4JHACWC2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEC33DHQ#issuecomment-548909470, or unsubscribe https://github.com/notifications/unsubscribe-auth/ANUMFJRWNCBVABCSYWJHKXTQRR3OXANCNFSM4JHACWCQ .

Gear Name: fw-heudiconv, Gear Version: 0.2.4_0.1.2 Gear starting... /flywheel/v0/fw_heudiconv/query.py:4: UserWarning: The DICOM readers are highly experimental, unstable, and only work for Siemens time-series at the moment Please use with caution. We would be grateful for your help in improving them from nibabel.nicom.dicomwrappers import wrapper_from_data INFO: Running nipype version 1.2.3 (latest: 1.2.3) 191101-19:26:09,921 nipype.utils INFO: Running nipype version 1.2.3 (latest: 1.2.3) INFO: ==============: fw-heudiconv gear manager starting up :===============

INFO: Calling fw-heudiconv with the following settings: INFO: Project: Segmentation INFO: Subject(s): ['sub-seg01'] INFO: Session(s): ['day1'] INFO: Heuristic: /flywheel/v0/input/heuristic/segmentation_heudiconv10d.py INFO: Action: Curate INFO: Dry run: False /usr/local/lib/python3.5/site-packages/fw_heudiconv/query.py:4: UserWarning: The DICOM readers are highly experimental, unstable, and only work for Siemens time-series at the moment Please use with caution. We would be grateful for your help in improving them from nibabel.nicom.dicomwrappers import wrapper_from_data 191101-19:26:11,388 nipype.utils INFO: Running nipype version 1.2.3 (latest: 1.2.3) INFO: Running nipype version 1.2.3 (latest: 1.2.3) INFO: =================: fw-heudiconv curator starting up :=================

INFO: Querying Flywheel server... DEBUG: Found project: Segmentation (5d03cc5fa550c6003c6fb70a) DEBUG: Found sessions: day1 (5d081765a550c600467047cf) DEBUG: Found SeqInfos: BOLD_ObjectViewing_1_d1: [TR=2 TE=0.025 shape=(864, 864, 316, -1) image_type=('ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC')] (5d0817a7a550c60048709f16)

BOLD_ObjectViewing_2_d1: 
    [TR=2 TE=0.025 shape=(864, 864, 316, -1) image_type=('ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC')] (5d0817e2a550c600467047e4)

BOLD_Localizer_1: 
    [TR=2 TE=0.025 shape=(864, 864, 168, -1) image_type=('ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC')] (5d081805a550c600467047ee)

BOLD_Localizer_2: 
    [TR=2 TE=0.025 shape=(864, 864, 168, -1) image_type=('ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC')] (5d081827a550c600396fbb1f)

MPRAGE_P2_1mm: 
    [TR=2.2 TE=0.00467 shape=(256, 192, 160, -1) image_type=('ORIGINAL', 'PRIMARY', 'M', 'ND', 'NORM')] (5d081839a550c600467047f3)

BOLD_Resting: 
    [TR=2 TE=0.025 shape=(864, 864, 180, -1) image_type=('ORIGINAL', 'PRIMARY', 'M', 'MB', 'ND', 'NORM', 'MOSAIC')] (5d08185ea550c600467047f9)

B0map: 
    [TR=0.58 TE=0.00658 shape=(80, 80, 120, -1) image_type=('ORIGINAL', 'PRIMARY', 'M', 'ND')] (5d08186ca550c60048709f52)

B0map: 
    [TR=0.58 TE=0.00412 shape=(80, 80, 120, -1) image_type=('ORIGINAL', 'PRIMARY', 'M', 'ND')] (5d08186ca550c60048709f52)

B0map: 
    [TR=0.58 TE=0.00658 shape=(80, 80, 60, -1) image_type=('ORIGINAL', 'PRIMARY', 'P', 'ND')] (5d081877a550c60048709f56)

INFO: Loading heuristic file... INFO: Applying heuristic to query results... INFO: Processing IntendedFor fields based on heuristic file DEBUG: Intention map: [('{subject}/{session}/fmap/{subject}_{session}phasediff', ['{session}/func/sub-{subject}{session}_task-func_localizer_run-01bold.nii.gz', '{session}/func/sub-{subject}{session}_task-func_localizer_run-02bold.nii.gz', '{session}/func/sub-{subject}{session}_task-object_viewing_run-01_day-01bold.nii.gz', '{session}/func/sub-{subject}{session}_task-object_viewing_run-02_day-01bold.nii.gz', '{session}/func/sub-{subject}{session}_task-object_viewing_run-01_day-02bold.nii.gz', '{session}/func/sub-{subject}{session}_task-object_viewing_run-02_day-02bold.nii.gz', '{session}/func/sub-{subject}{session}_task-jrd_run-01bold.nii.gz', '{session}/func/sub-{subject}{session}_task-jrd_run-02bold.nii.gz', '{session}/func/sub-{subject}{session}_task-jrd_run-03bold.nii.gz', '{session}/func/sub-{subject}{session}_task-resting_statebold.nii.gz', '{session}/func/sub-{subject}{session}_task-navigationbold.nii.gz'])] INFO: Processing Medatata fields based on heuristic file DEBUG: Metadata extras: defaultdict(<class 'list'>, {('{subject}/{session}/fmap/{subject}{session}_phasediff', ('nii.gz',), None): {'EchoTime2': 0.006, 'EchoTime1': 0.004}}) INFO: Applying changes to files... DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200012446.nii.gz sub-seg01_ses-day1_task-object_viewing_run-02_day-01_bold.nii.gz -> sub-seg01/ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-02_day-01_bold.nii.gz DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200013247_e1.nii.gz sub-seg01_ses-day1_magnitude1.nii.gz -> sub-seg01/ses-day1/fmap/sub-seg01_ses-day1_magnitude1.nii.gz DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200013247_e2.nii.gz sub-seg01_ses-day1_magnitude2.nii.gz -> sub-seg01/ses-day1/fmap/sub-seg01_ses-day1_magnitude2.nii.gz DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200012129.nii.gz sub-seg01_ses-day1_task-object_viewing_run-01_day-01_bold.nii.gz -> sub-seg01/ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-01_day-01_bold.nii.gz DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200012945.nii.gz sub-seg01_ses-day1_T1w.nii.gz -> sub-seg01/ses-day1/anat/sub-seg01_ses-day1_T1w.nii.gz DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200013308_e2_ph.nii.gz sub-seg01_ses-day1_phasediff.nii.gz -> sub-seg01/ses-day1/fmap/sub-seg01_ses-day1_phasediff.nii.gz DEBUG: 'sub-seg01_ses-day1_phasediff.nii.gz' IntendedFor: ['ses-day1/func/sub-seg01_ses-day1_task-func_localizer_run-01_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-func_localizer_run-02_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-01_day-01_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-02_day-01_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-01_day-02_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-02_day-02_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-jrd_run-01_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-jrd_run-02_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-jrd_run-03_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-resting_state_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-navigation_bold.nii.gz'] DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200013308_e2_ph.nii.gz metadata: {'EchoTime2': 0.006, 'EchoTime1': 0.004} DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200012615.nii.gz sub-seg01_ses-day1_task-func_localizer_run-01_bold.nii.gz -> sub-seg01/ses-day1/func/sub-seg01_ses-day1_task-func_localizer_run-01_bold.nii.gz DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200013126.nii.gz sub-seg01_ses-day1_task-resting_state_bold.nii.gz -> sub-seg01/ses-day1/func/sub-seg01_ses-day1_task-resting_state_bold.nii.gz DEBUG: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200012784.nii.gz sub-seg01_ses-day1_task-func_localizer_run-02_bold.nii.gz -> sub-seg01/ses-day1/func/sub-seg01_ses-day1_task-func_localizer_run-02_bold.nii.gz DEBUG: Ensuring all intentions apply for acquisition B0map: 1.3.12.2.1107.5.2.43.167024.30000019061317513597200013308_e2_ph.nii.gz DEBUG: Missing paths: ['ses-day1/func/sub-seg01_ses-day1_task-func_localizer_run-01_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-func_localizer_run-02_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-01_day-01_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-02_day-01_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-01_day-02_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-object_viewing_run-02_day-02_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-jrd_run-01_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-jrd_run-02_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-jrd_run-03_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-resting_state_bold.nii.gz', 'ses-day1/func/sub-seg01_ses-day1_task-navigation_bold.nii.gz'] INFO: Done! INFO: ===================: Exiting fw-heudiconv curator :=================== INFO: Done! INFO: ================: Exiting fw-heudiconv gear manager :=================

Gear completed successfully after running for 23.595s. Uploading results... Job complete.

TinasheMTapera commented 4 years ago

Hi Michael,

I'm having a hard time deciphering what's wrong. If you are available next week maybe we can meet on campus and debug this thing together? Let me know if you have time to meet, I'm in Richards Labs 5th floor Pod A

MichaelPeerUpenn commented 4 years ago

Hi, I would love to meet, thank you so much! I'm pretty free next week, so tell me when you can meet. Thank you!

On Fri, Nov 1, 2019 at 5:08 PM Tinashe Michael Tapera < notifications@github.com> wrote:

Hi Michael,

I'm having a hard time deciphering what's wrong. If you are available next week maybe we can meet on campus and debug this thing together? Let me know if you have time to meet, I'm in Richards Labs 5th floor Pod A

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