fmriprep | use pipeline for preprocessing of diverse fMRI data

I am new to docker and containers. I have a container consisting of an MRI analysis software. Within this container are many other software the main software draws its commands from. I would like to run a single command from one of the softwares in this container using research data that is located on an external hard drive which is plugged into my local machine that is running docker.

I know there is a cp command for copying files (such as scripts) into containers and most other questions along these lines seem to recommend copying the files from your local machine into the container and then running the script (or whatever) from the container. In my case I need the container to access data from separate folders in a directory structure and copying over the entire directory is not feasible since it is quite large.

I honestly just want to know how I can run a single command inside the docker using inputs present on my local machine. I have run docker ps to get the CONTAINER_ID which is d8dbcf705ee7. Having looked into executing commands inside containers I tried the following command:

docker exec d8dbcf705ee7 /bin/bash -c "mcflirt -in /Volumes/DISS/FMRIPREP/sub-S06V1A/func/sub-S06V1A_task-compound_run-01_bold.nii -out sub-S06V1A_task-compound_run-01_bold_mcf_COMMAND_TEST.nii.gz -reffile /Volumes/DISS/FMRIPREP_TMP/sub-S06V1A_dof6_ver1.2.5/fmriprep_wf/single_subject_S06V1A_wf/func_preproc_task_compound_run_01_wf/bold_reference_wf/gen_ref/ref_image.nii.gz -mats -plots"

mcflirt is the command I want to run inside the container. I believe the exec command would do what I hope since if I run docker exec d8dbcf705ee7 /bin/bash -c "mcflirt" I will get help output for the mcflirt command which is the expected outcome in that case. The files inside of the /Volume/... paths are the files on my local machine I would like to access. I understand that the location of the files is the problem since I cannot tab complete the paths within this command; when I run this I get the following output:

Image Exception : #22 :: ERROR: Could not open image /Volumes/DISS/FMRIPREP/sub-S06V1A/func/sub-S06V1A_task-compound_run-01_bold terminate called after throwing an instance of 'RBD_COMMON::BaseException'

Can anyone point me in the right direction?

Hello i'm trying to run image docker, which i created from Dockerfile:

I am new to neuroscience and I am learning to work with neuroscience data.

However I am a bit confused. I tried to download the dataset: https://openfmri.org/dataset/ds000116/

but somehow, I cannot understand which files to download, if I click Browse Data For All Revisions on S3 , then I can just find Anatomical and functional Images, but I am looking for both EEG and fMRI data. If I download Raw data on AWS or Curated dataset its really small in size, as compared to Processed data for Subject 1 on AWS for each subject.

So my questions are:

• What is the difference between Browse Data For All Revisions on S3 ,Raw data on AWS,Curated dataset and Processed data for Subject 1 on AWS for each subject on dataset page?
• Which dataset/files should I download?
• Is the dataset Processed data for Subject 1 on AWS for each subject, is pre--processed, if yes then what pre-processing steps have been done?
• can someone point me to resources for pre-processing EEG and fMRI data, can I use fmriprep for fMRI data?