fMRI PREP: FileNotFoundError: [Errno 2] No such file or directory: 'dcm2niix'

Hi, I’m trying to get started running fMRI Prep and I downloaded dcm2bids using pip install.
While trying to get started turning the dicom files into nifti, I’ve run into the following error:
dcm2bids_helper -d /mnt/storage/Jessica_Lab/analyses/Rachel_Pract ice/dcm2bids-tutorial/sourcedata/wsu-con-0004-02
Traceback (most recent call last):
File “/home/RScott/.local/bin/dcm2bids_helper”, line 8, in
File “/home/RScott/.local/lib/python3.8/site-packages/dcm2bids/”, lin e 42, in main
rsl =
File “/home/RScott/.local/lib/python3.8/site-packages/dcm2bids/”, l ine 90, in run
File “/home/RScott/.local/lib/python3.8/site-packages/dcm2bids/”, l ine 100, in execute
output = run_shell_command(cmd)
File “/home/RScott/.local/lib/python3.8/site-packages/dcm2bids/”, line 113, in run_shell_command
return check_output(shlex.split(commandLine))
File “/usr/lib/python3.8/”, line 415, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
File “/usr/lib/python3.8/”, line 493, in run
with Popen(*popenargs, **kwargs) as process:
File “/usr/lib/python3.8/”, line 858, in init
self._execute_child(args, executable, preexec_fn, close_fds,
File “/usr/lib/python3.8/”, line 1704, in _execute_child
raise child_exception_type(errno_num, err_msg, err_filename)
FileNotFoundError: [Errno 2] No such file or directory: ‘dcm2niix’

Any help would be greatly appreciated!


I would change the title of this post, since this problem is not related to fMRIPrep. Did you download dcm2niix? conda install -c conda-forge dcm2niix


Hi @Rachel_Scott ,

First you need to install dcm2niix. Here is a link.

@Steven is right. The issue does not come from fMRIPrep but more a dcm2bids dependance issue, please change the title and if it works please tag it as solved.
Best Arnaud