Dcm2bids No escape charecter

1

Hi,
I am trying to get the following command to work on in anaconda for windows.

dcm2bids -d LocationDICOM -p 01 -c CONFIGFILE

LocationDICOM = Z:\scs\groups\rawdata\asd_01\dieghei\

I keep getting "ValueError: No escaped character"

When I go into the log - it appears to be having an issue with the dsm2niix command. When I copy and paste this command from the log - it runs.

What obvious thing am I missing here?

What I have tried

  • changing the direction of the location slashes
  • doing the dcm2niix on it’s own and then trying dcm2bids - it still fails
  • Moving the dicoms more locally
2

Try putting quotes around all of your inputs

3

When I do this, it outputs the error…
error: the following arguments are required: -p/–participant, -c/–config

These values are entered in the command - so assuming it has issues with the quotes. When I take the quotes away, I get the above error again.

4

Can you print the precise command you input please?

5

You don’t want to put quotes around the name of the arguments e.g. -p, just what is fed into those arguments.

6

I should clarify this question further, I think that what I am having trouble with is running a linux command (or linux based docker in windows). In other words…

I am remotely connecting to another Windows 10 computer.

On the remote computer, I am trying to run a linux based docker container on files in a drive that is NOT c. This data is large and I don’t have the space on my computer to move it to the c drive. It looks like the c drive is the only one that is mounted in WSL2.

Is there a simple way to mount another drive in WSL2 so that I can work on it within a linux based docker container?

For example to run…

docker run -it --rm -v /f/location/file some_docker_image (in the example above it is Dcm2bids)

I need an option that is fairly simple as I am not that IT savy. From what I can tell, this is not possible?

7

I should clarify this question further, I think that what I am having trouble with is running a linux command (or linux based docker in windows). In other words…

I am remotely connecting to another Windows 10 computer.

On the remote computer, I am trying to run a linux based docker container on files in a drive that is NOT c. This data is large and I don’t have the space on my computer to move it to the c drive. It looks like the c drive is the only one that is mounted in WSL2.

Is there a simple way to mount another drive in WSL2 so that I can work on it within a linux based docker container?

For example to run…

docker run -it --rm -v /f/location/file some_docker_image (in the example above it is Dcm2bids)

I need an option that is fairly simple as I am not that IT savy. From what I can tell, this is not possible?