(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut> echo "on master branch"
on master branch


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut> dcm2bids_scaffold -o bids_project
(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut> cd .\bids_project\


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids_helper -d sourcedata/dcm_qa_nih/In/
Error: Output folder invalid: C:UsersDUALGPUdcm2bids-tutbids_projecttmp_dcm2bidshelper
Traceback (most recent call last):
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\Scripts\dcm2bids_helper-script.py", line 33, in <module>
    sys.exit(load_entry_point('dcm2bids', 'console_scripts', 'dcm2bids_helper')())
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\helper.py", line 43, in main
    rsl = app.run()
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2niix.py", line 90, in run
    self.execute()
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2niix.py", line 100, in execute
    output = run_shell_command(cmd)
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\utils.py", line 120, in run_shell_command
    return check_output(shlex.split(commandLine))
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\subprocess.py", line 424, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['dcm2niix', '-b', 'y', '-ba', 'y', '-z', 'y', '-f', '%3s_%f_%p_%t', '-o', 'C:UsersDUALGPUdcm2bids-tutbids_projecttmp_dcm2bidshelper', 'sourcedata/dcm_qa_nih/In/']' returned non-zero exit status 6.


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> echo "trying with autocomplete path with tab"
trying with autocomplete path with tab


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids_helper -d .\sourcedata\dcm_qa_nih\In\
Traceback (most recent call last):
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\Scripts\dcm2bids_helper-script.py", line 33, in <module>
    sys.exit(load_entry_point('dcm2bids', 'console_scripts', 'dcm2bids_helper')())
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\helper.py", line 43, in main
    rsl = app.run()
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2niix.py", line 90, in run
    self.execute()
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2niix.py", line 100, in execute
    output = run_shell_command(cmd)
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\utils.py", line 120, in run_shell_command
    return check_output(shlex.split(commandLine))
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\shlex.py", line 315, in split
    return list(lex)
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\shlex.py", line 300, in __next__
    token = self.get_token()
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\shlex.py", line 109, in get_token
    raw = self.read_token()
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\shlex.py", line 210, in read_token
    raise ValueError("No escaped character")
ValueError: No escaped character


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> echo "trying to escape escape char"
trying to escape escape char

(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids_helper -d .\\sourcedata\\dcm_qa_nih\\In
Error: Output folder invalid: C:UsersDUALGPUdcm2bids-tutbids_projecttmp_dcm2bidshelper
Traceback (most recent call last):
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\Scripts\dcm2bids_helper-script.py", line 33, in <module>
    sys.exit(load_entry_point('dcm2bids', 'console_scripts', 'dcm2bids_helper')())
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\helper.py", line 43, in main
    rsl = app.run()
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2niix.py", line 90, in run
    self.execute()
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2niix.py", line 100, in execute
    output = run_shell_command(cmd)
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\utils.py", line 120, in run_shell_command
    return check_output(shlex.split(commandLine))
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\subprocess.py", line 424, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['dcm2niix', '-b', 'y', '-ba', 'y', '-z', 'y', '-f', '%3s_%f_%p_%t', '-o', 'C:UsersDUALGPUdcm2bids-tutbids_projecttmp_dcm2bidshelper', '.\\sourcedata\\dcm_qa_nih\\In']' returned non-zero exit status 6.


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids_helper -d .\sourcedata\dcm_qa_nih\In
Error: Input folder invalid: .sourcedatadcm_qa_nihIn
Traceback (most recent call last):
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\Scripts\dcm2bids_helper-script.py", line 33, in <module>
    sys.exit(load_entry_point('dcm2bids', 'console_scripts', 'dcm2bids_helper')())
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\helper.py", line 43, in main
    rsl = app.run()
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2niix.py", line 90, in run
    self.execute()
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2niix.py", line 100, in execute
    output = run_shell_command(cmd)
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\utils.py", line 120, in run_shell_command
    return check_output(shlex.split(commandLine))
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\subprocess.py", line 424, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['dcm2niix', '-b', 'y', '-ba', 'y', '-z', 'y', '-f', '%3s_%f_%p_%t', '-o', 'C:UsersDUALGPUdcm2bids-tutbids_projecttmp_dcm2bidshelper', '.sourcedatadcm_qa_nihIn']' returned non-zero exit status 5.


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> echo "trying with quotes"
trying with quotes


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids_helper -d ".\sourcedata\dcm_qa_nih\In"
Error: Input folder invalid: .sourcedatadcm_qa_nihIn
Traceback (most recent call last):
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\Scripts\dcm2bids_helper-script.py", line 33, in <module>
    sys.exit(load_entry_point('dcm2bids', 'console_scripts', 'dcm2bids_helper')())
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\helper.py", line 43, in main
    rsl = app.run()
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2niix.py", line 90, in run
    self.execute()
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2niix.py", line 100, in execute
    output = run_shell_command(cmd)
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\utils.py", line 120, in run_shell_command
    return check_output(shlex.split(commandLine))
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\subprocess.py", line 424, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['dcm2niix', '-b', 'y', '-ba', 'y', '-z', 'y', '-f', '%3s_%f_%p_%t', '-o', 'C:UsersDUALGPUdcm2bids-tutbids_projecttmp_dcm2bidshelper', '.sourcedatadcm_qa_nihIn']' returned non-zero exit status 5.


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids -d sourcedata/dcm_qa_nih/In/ -p ID01 -c code/dcm2bids_config.json
Traceback (most recent call last):
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\Scripts\dcm2bids-script.py", line 33, in <module>
    sys.exit(load_entry_point('dcm2bids', 'console_scripts', 'dcm2bids')())
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 301, in main
    app = Dcm2bids(**vars(args))
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 51, in __init__
    self.config = load_json(config)
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\utils.py", line 61, in load_json
    with open(filename, "r") as f:
FileNotFoundError: [Errno 2] No such file or directory: 'code/dcm2bids_config.json'


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids -d sourcedata/dcm_qa_nih/In/ -p ID01 -c code/dcm2bids_config.json
INFO:dcm2bids.dcm2bids:--- dcm2bids start ---
INFO:dcm2bids.dcm2bids:OS:version: Windows-10-10.0.19044-SP0
INFO:dcm2bids.dcm2bids:python:version: 3.9.12 (main, Apr  4 2022, 05:22:27) [MSC v.1916 64 bit (AMD64)]
INFO:dcm2bids.dcm2bids:dcm2bids:version: 2.1.6
INFO:dcm2bids.dcm2bids:dcm2niix:version: v1.0.20211006
INFO:dcm2bids.dcm2bids:participant: sub-ID01
INFO:dcm2bids.dcm2bids:session:
INFO:dcm2bids.dcm2bids:config: C:\Users\DUALGPU\dcm2bids-tut\bids_project\code\dcm2bids_config.json
INFO:dcm2bids.dcm2bids:BIDS directory: C:\Users\DUALGPU\dcm2bids-tut\bids_project
INFO:dcm2bids.utils:Running dcm2niix -b y -ba y -z y -f '%3s_%f_%p_%t' -o C:\Users\DUALGPU\dcm2bids-tut\bids_project\tmp_dcm2bids\sub-ID01 sourcedata/dcm_qa_nih/In/
Error: Output folder invalid: C:UsersDUALGPUdcm2bids-tutbids_projecttmp_dcm2bidssub-ID01
Traceback (most recent call last):
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\Scripts\dcm2bids-script.py", line 33, in <module>
    sys.exit(load_entry_point('dcm2bids', 'console_scripts', 'dcm2bids')())
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 302, in main
    return app.run()
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 120, in run
    dcm2niix.run(self.forceDcm2niix)
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2niix.py", line 90, in run
    self.execute()
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2niix.py", line 100, in execute
    output = run_shell_command(cmd)
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\utils.py", line 120, in run_shell_command
    return check_output(shlex.split(commandLine))
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\subprocess.py", line 424, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['dcm2niix', '-b', 'y', '-ba', 'y', '-z', 'y', '-f', '%3s_%f_%p_%t', '-o', 'C:UsersDUALGPUdcm2bids-tutbids_projecttmp_dcm2bidssub-ID01', 'sourcedata/dcm_qa_nih/In/']' returned non-zero exit status 6.


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids -d sourcedata\dcm_qa_nih\In -p ID01 -c code\dcm2bids_config.json
INFO:dcm2bids.dcm2bids:--- dcm2bids start ---
INFO:dcm2bids.dcm2bids:OS:version: Windows-10-10.0.19044-SP0
INFO:dcm2bids.dcm2bids:python:version: 3.9.12 (main, Apr  4 2022, 05:22:27) [MSC v.1916 64 bit (AMD64)]
INFO:dcm2bids.dcm2bids:dcm2bids:version: 2.1.6
INFO:dcm2bids.dcm2bids:dcm2niix:version: v1.0.20211006
INFO:dcm2bids.dcm2bids:participant: sub-ID01
INFO:dcm2bids.dcm2bids:session:
INFO:dcm2bids.dcm2bids:config: C:\Users\DUALGPU\dcm2bids-tut\bids_project\code\dcm2bids_config.json
INFO:dcm2bids.dcm2bids:BIDS directory: C:\Users\DUALGPU\dcm2bids-tut\bids_project
INFO:dcm2bids.utils:Running dcm2niix -b y -ba y -z y -f '%3s_%f_%p_%t' -o C:\Users\DUALGPU\dcm2bids-tut\bids_project\tmp_dcm2bids\sub-ID01 sourcedata\dcm_qa_nih\In
Error: Input folder invalid: sourcedatadcm_qa_nihIn
Traceback (most recent call last):
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\Scripts\dcm2bids-script.py", line 33, in <module>
    sys.exit(load_entry_point('dcm2bids', 'console_scripts', 'dcm2bids')())
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 302, in main
    return app.run()
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 120, in run
    dcm2niix.run(self.forceDcm2niix)
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2niix.py", line 90, in run
    self.execute()
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2niix.py", line 100, in execute
    output = run_shell_command(cmd)
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\utils.py", line 120, in run_shell_command
    return check_output(shlex.split(commandLine))
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\subprocess.py", line 424, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['dcm2niix', '-b', 'y', '-ba', 'y', '-z', 'y', '-f', '%3s_%f_%p_%t', '-o', 'C:UsersDUALGPUdcm2bids-tutbids_projecttmp_dcm2bidssub-ID01', 'sourcedatadcm_qa_nihIn']' returned non-zero exit status 5.

###############################################################################
###                         fix_windows_paths                               ###
###############################################################################


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut> echo "on fix_windows_paths branch"
on fix_windows_paths branch

(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut> dcm2bids_scaffold -o bids_project
(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut> cd .\bids_project\


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids_helper -d sourcedata/dcm_qa_nih/In
Example in:
C:\Users\DUALGPU\dcm2bids-tut\bids_project\tmp_dcm2bids\helper


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids -d sourcedata/dcm_qa_nih/In/ -p ID01 -c code/dcm2bids_config.json
INFO:dcm2bids.dcm2bids:--- dcm2bids start ---
INFO:dcm2bids.dcm2bids:OS:version: Windows-10-10.0.19044-SP0
INFO:dcm2bids.dcm2bids:python:version: 3.9.12 (main, Apr  4 2022, 05:22:27) [MSC v.1916 64 bit (AMD64)]
INFO:dcm2bids.dcm2bids:dcm2bids:version: 2.1.6
INFO:dcm2bids.dcm2bids:dcm2niix:version: v1.0.20211006
INFO:dcm2bids.dcm2bids:participant: sub-ID01
INFO:dcm2bids.dcm2bids:session:
INFO:dcm2bids.dcm2bids:config: C:\Users\DUALGPU\dcm2bids-tut\bids_project\code\dcm2bids_config.json
INFO:dcm2bids.dcm2bids:BIDS directory: C:\Users\DUALGPU\dcm2bids-tut\bids_project
INFO:dcm2bids.utils:Running ['dcm2niix', '-b', 'y', '-ba', 'y', '-z', 'y', '-f', '%3s_%f_%p_%t', '-o', 'C:\\Users\\DUALGPU\\dcm2bids-tut\\bids_project\\tmp_dcm2bids\\sub-ID01', 'sourcedata\\dcm_qa_nih\\In']
INFO:dcm2bids.dcm2niix:Check log file for dcm2niix output
INFO:dcm2bids.sidecar:Sidecars pairing:
INFO:dcm2bids.sidecar:_dir-AP_epi  <-  003_In_EPI_PE=AP_20180918121230
INFO:dcm2bids.sidecar:_task-rest_bold  <-  004_In_DCM2NIIX_regression_test_20180918114023
INFO:dcm2bids.sidecar:_dir-PA_epi  <-  004_In_EPI_PE=PA_20180918121230
INFO:dcm2bids.sidecar:No Pairing  <-  005_In_DCM2NIIX_regression_test_20180918114023
INFO:dcm2bids.sidecar:No Pairing  <-  005_In_EPI_PE=RL_20180918121230
INFO:dcm2bids.sidecar:No Pairing  <-  006_In_DCM2NIIX_regression_test_20180918114023
INFO:dcm2bids.sidecar:No Pairing  <-  006_In_EPI_PE=LR_20180918121230
INFO:dcm2bids.sidecar:No Pairing  <-  007_In_DCM2NIIX_regression_test_20180918114023
INFO:dcm2bids.dcm2bids:moving acquisitions into BIDS folder


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> echo "testing with all kinds of path sep"
testing with all kinds of path sep


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids -d sourcedata\dcm_qa_nih/In -p ID02 -c code\dcm2bids_config.json
INFO:dcm2bids.dcm2bids:--- dcm2bids start ---
INFO:dcm2bids.dcm2bids:OS:version: Windows-10-10.0.19044-SP0
INFO:dcm2bids.dcm2bids:python:version: 3.9.12 (main, Apr  4 2022, 05:22:27) [MSC v.1916 64 bit (AMD64)]
INFO:dcm2bids.dcm2bids:dcm2bids:version: 2.1.6
INFO:dcm2bids.dcm2bids:dcm2niix:version: v1.0.20211006
INFO:dcm2bids.dcm2bids:participant: sub-ID02
INFO:dcm2bids.dcm2bids:session:
INFO:dcm2bids.dcm2bids:config: C:\Users\DUALGPU\dcm2bids-tut\bids_project\code\dcm2bids_config.json
INFO:dcm2bids.dcm2bids:BIDS directory: C:\Users\DUALGPU\dcm2bids-tut\bids_project
INFO:dcm2bids.utils:Running ['dcm2niix', '-b', 'y', '-ba', 'y', '-z', 'y', '-f', '%3s_%f_%p_%t', '-o', 'C:\\Users\\DUALGPU\\dcm2bids-tut\\bids_project\\tmp_dcm2bids\\sub-ID02', 'sourcedata\\dcm_qa_nih\\In']
INFO:dcm2bids.dcm2niix:Check log file for dcm2niix output
INFO:dcm2bids.sidecar:Sidecars pairing:
INFO:dcm2bids.sidecar:_dir-AP_epi  <-  003_In_EPI_PE=AP_20180918121230
INFO:dcm2bids.sidecar:_task-rest_bold  <-  004_In_DCM2NIIX_regression_test_20180918114023
INFO:dcm2bids.sidecar:_dir-PA_epi  <-  004_In_EPI_PE=PA_20180918121230
INFO:dcm2bids.sidecar:No Pairing  <-  005_In_DCM2NIIX_regression_test_20180918114023
INFO:dcm2bids.sidecar:No Pairing  <-  005_In_EPI_PE=RL_20180918121230
INFO:dcm2bids.sidecar:No Pairing  <-  006_In_DCM2NIIX_regression_test_20180918114023
INFO:dcm2bids.sidecar:No Pairing  <-  006_In_EPI_PE=LR_20180918121230
INFO:dcm2bids.sidecar:No Pairing  <-  007_In_DCM2NIIX_regression_test_20180918114023
INFO:dcm2bids.dcm2bids:moving acquisitions into BIDS folder


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> echo "testing with an ending \, expect to break"
testing with an ending \


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids -d sourcedata\dcm_qa_nih/In\ -p ID03 -c code\dcm2bids_config.json
INFO:dcm2bids.dcm2bids:--- dcm2bids start ---
INFO:dcm2bids.dcm2bids:OS:version: Windows-10-10.0.19044-SP0
INFO:dcm2bids.dcm2bids:python:version: 3.9.12 (main, Apr  4 2022, 05:22:27) [MSC v.1916 64 bit (AMD64)]
INFO:dcm2bids.dcm2bids:dcm2bids:version: 2.1.6
INFO:dcm2bids.dcm2bids:dcm2niix:version: v1.0.20211006
INFO:dcm2bids.dcm2bids:participant: sub-ID03
INFO:dcm2bids.dcm2bids:session:
INFO:dcm2bids.dcm2bids:config: C:\Users\DUALGPU\dcm2bids-tut\bids_project\code\dcm2bids_config.json
INFO:dcm2bids.dcm2bids:BIDS directory: C:\Users\DUALGPU\dcm2bids-tut\bids_project
INFO:dcm2bids.utils:Running ['dcm2niix', '-b', 'y', '-ba', 'y', '-z', 'y', '-f', '%3s_%f_%p_%t', '-o', 'C:\\Users\\DUALGPU\\dcm2bids-tut\\bids_project\\tmp_dcm2bids\\sub-ID03', 'sourcedata\\dcm_qa_nih\\In']
INFO:dcm2bids.dcm2niix:Check log file for dcm2niix output
INFO:dcm2bids.sidecar:Sidecars pairing:
INFO:dcm2bids.sidecar:_dir-AP_epi  <-  003_In_EPI_PE=AP_20180918121230
INFO:dcm2bids.sidecar:_task-rest_bold  <-  004_In_DCM2NIIX_regression_test_20180918114023
INFO:dcm2bids.sidecar:_dir-PA_epi  <-  004_In_EPI_PE=PA_20180918121230
INFO:dcm2bids.sidecar:No Pairing  <-  005_In_DCM2NIIX_regression_test_20180918114023
INFO:dcm2bids.sidecar:No Pairing  <-  005_In_EPI_PE=RL_20180918121230
INFO:dcm2bids.sidecar:No Pairing  <-  006_In_DCM2NIIX_regression_test_20180918114023
INFO:dcm2bids.sidecar:No Pairing  <-  006_In_EPI_PE=LR_20180918121230
INFO:dcm2bids.sidecar:No Pairing  <-  007_In_DCM2NIIX_regression_test_20180918114023
INFO:dcm2bids.dcm2bids:moving acquisitions into BIDS folder
(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project>


###############################################################################
###                         testing spaces in dirs                          ###
###############################################################################


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> cp .\sourcedata\ "source data"
(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> ls


    Directory: C:\Users\DUALGPU\dcm2bids-tut\bids_project


Mode                 LastWriteTime         Length Name
----                 -------------         ------ ----
d-----         4/20/2022   4:30 PM                code
d-----         4/20/2022   4:14 PM                derivatives
d-----         4/20/2022   4:47 PM                source data
d-----         4/20/2022   4:24 PM                sourcedata
d-----         4/20/2022   4:43 PM                sub-ID01
d-----         4/20/2022   4:44 PM                sub-ID02
d-----         4/20/2022   4:45 PM                sub-ID03
d-----         4/20/2022   4:45 PM                tmp_dcm2bids
-a----         4/20/2022   4:39 PM            522 CHANGES
-a----         4/20/2022   4:39 PM            276 dataset_description.json
-a----         4/20/2022   4:39 PM            544 participants.json
-a----         4/20/2022   4:39 PM            114 participants.tsv
-a----         4/20/2022   4:39 PM            903 README


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids -d source data\dcm_qa_nih/In\ -p ID03 -c code\dcm2bids_config.json
Traceback (most recent call last):
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\Scripts\dcm2bids-script.py", line 33, in <module>
    sys.exit(load_entry_point('dcm2bids', 'console_scripts', 'dcm2bids')())
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 257, in main
    app = Dcm2bids(**vars(args))
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 54, in __init__
    self.dicomDirs = dicom_dir
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 90, in dicomDirs
    valid_dirs.append(valid_path(_dir, "folder"))
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\utils.py", line 140, in valid_path
    raise NotADirectoryError(in_path)
NotADirectoryError: data\dcm_qa_nih\In


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids -d "source data\dcm_qa_nih/In\" -p ID03 -c code\dcm2bids_config.json
usage: dcm2bids [-h] -d DICOM_DIR [DICOM_DIR ...] -p PARTICIPANT [-s SESSION] -c CONFIG [-o OUTPUT_DIR]
                [--forceDcm2niix] [--clobber] [-l {DEBUG,INFO,WARNING,ERROR,CRITICAL}]
dcm2bids: error: the following arguments are required: -p/--participant, -c/--config


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids -d "source data\dcm_qa_nih/In" -p ID03 -c code\dcm2bids_config.json
Traceback (most recent call last):
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\Scripts\dcm2bids-script.py", line 33, in <module>
    sys.exit(load_entry_point('dcm2bids', 'console_scripts', 'dcm2bids')())
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 257, in main
    app = Dcm2bids(**vars(args))
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 54, in __init__
    self.dicomDirs = dicom_dir
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 90, in dicomDirs
    valid_dirs.append(valid_path(_dir, "folder"))
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\utils.py", line 140, in valid_path
    raise NotADirectoryError(in_path)
NotADirectoryError: source data\dcm_qa_nih\In


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids -d '.\source data\dcm_qa_nih' -p ID03 -c code\dcm2bids_config.json
INFO:dcm2bids.dcm2bids:--- dcm2bids start ---
INFO:dcm2bids.dcm2bids:OS:version: Windows-10-10.0.19044-SP0
INFO:dcm2bids.dcm2bids:python:version: 3.9.12 (main, Apr  4 2022, 05:22:27) [MSC v.1916 64 bit (AMD64)]
INFO:dcm2bids.dcm2bids:dcm2bids:version: 2.1.6
INFO:dcm2bids.dcm2bids:dcm2niix:version: v1.0.20211006
INFO:dcm2bids.dcm2bids:participant: sub-ID03
INFO:dcm2bids.dcm2bids:session:
INFO:dcm2bids.dcm2bids:config: C:\Users\DUALGPU\dcm2bids-tut\bids_project\code\dcm2bids_config.json
INFO:dcm2bids.dcm2bids:BIDS directory: C:\Users\DUALGPU\dcm2bids-tut\bids_project
WARNING:dcm2bids.dcm2niix:Previous dcm2niix directory output found:
WARNING:dcm2bids.dcm2niix:C:\Users\DUALGPU\dcm2bids-tut\bids_project\tmp_dcm2bids\sub-ID03
WARNING:dcm2bids.dcm2niix:Use --forceDcm2niix to rerun dcm2niix
INFO:dcm2bids.sidecar:Sidecars pairing:
INFO:dcm2bids.sidecar:No Pairing  <-  005_In_DCM2NIIX_regression_test_20180918114023
INFO:dcm2bids.sidecar:No Pairing  <-  005_In_EPI_PE=RL_20180918121230
INFO:dcm2bids.sidecar:No Pairing  <-  006_In_DCM2NIIX_regression_test_20180918114023
INFO:dcm2bids.sidecar:No Pairing  <-  006_In_EPI_PE=LR_20180918121230
INFO:dcm2bids.sidecar:No Pairing  <-  007_In_DCM2NIIX_regression_test_20180918114023
INFO:dcm2bids.dcm2bids:moving acquisitions into BIDS folder


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids -d '.\source data\dcm_qa_nih\In' -p ID03 -c code\dcm2bids_config.json
Traceback (most recent call last):
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\Scripts\dcm2bids-script.py", line 33, in <module>
    sys.exit(load_entry_point('dcm2bids', 'console_scripts', 'dcm2bids')())
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 257, in main
    app = Dcm2bids(**vars(args))
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 54, in __init__
    self.dicomDirs = dicom_dir
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 90, in dicomDirs
    valid_dirs.append(valid_path(_dir, "folder"))
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\utils.py", line 140, in valid_path
    raise NotADirectoryError(in_path)
NotADirectoryError: source data\dcm_qa_nih\In


(dcm2bids-windows) PS C:\Users\DUALGPU\dcm2bids-tut\bids_project> dcm2bids -d '.\source data\dcm_qa_nih' -p ID03 -c code\dcm2bids_config.json --forceDcm2niix
INFO:dcm2bids.dcm2bids:--- dcm2bids start ---
INFO:dcm2bids.dcm2bids:OS:version: Windows-10-10.0.19044-SP0
INFO:dcm2bids.dcm2bids:python:version: 3.9.12 (main, Apr  4 2022, 05:22:27) [MSC v.1916 64 bit (AMD64)]
INFO:dcm2bids.dcm2bids:dcm2bids:version: 2.1.6
INFO:dcm2bids.dcm2bids:dcm2niix:version: v1.0.20211006
INFO:dcm2bids.dcm2bids:participant: sub-ID03
INFO:dcm2bids.dcm2bids:session:
INFO:dcm2bids.dcm2bids:config: C:\Users\DUALGPU\dcm2bids-tut\bids_project\code\dcm2bids_config.json
INFO:dcm2bids.dcm2bids:BIDS directory: C:\Users\DUALGPU\dcm2bids-tut\bids_project
WARNING:dcm2bids.dcm2niix:Previous dcm2niix directory output found:
WARNING:dcm2bids.dcm2niix:C:\Users\DUALGPU\dcm2bids-tut\bids_project\tmp_dcm2bids\sub-ID03
WARNING:dcm2bids.dcm2niix:'force' argument is set to True
WARNING:dcm2bids.dcm2niix:Cleaning the previous directory and running dcm2niix
INFO:dcm2bids.utils:Running ['dcm2niix', '-b', 'y', '-ba', 'y', '-z', 'y', '-f', '%3s_%f_%p_%t', '-o', 'C:\\Users\\DUALGPU\\dcm2bids-tut\\bids_project\\tmp_dcm2bids\\sub-ID03', 'source data\\dcm_qa_nih']
Error: Input folder invalid: source data\dcm_qa_nih
Traceback (most recent call last):
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\Scripts\dcm2bids-script.py", line 33, in <module>
    sys.exit(load_entry_point('dcm2bids', 'console_scripts', 'dcm2bids')())
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 258, in main
    return app.run()
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2bids.py", line 120, in run
    dcm2niix.run(self.forceDcm2niix)
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2niix.py", line 78, in run
    self.execute()
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\dcm2niix.py", line 101, in execute
    output = run_shell_command(cmd)
  File "c:\users\dualgpu\dcm2bids\dcm2bids\dcm2bids\utils.py", line 122, in run_shell_command
    return check_output(commandLine)
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\subprocess.py", line 424, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "C:\Users\DUALGPU\anaconda3\envs\dcm2bids-windows\lib\subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['dcm2niix', '-b', 'y', '-ba', 'y', '-z', 'y', '-f', '%3s_%f_%p_%t', '-o', 'C:\\Users\\DUALGPU\\dcm2bids-tut\\bids_project\\tmp_dcm2bids\\sub-ID03', 'source data\\dcm_qa_nih']' returned non-zero exit status 5.