where run fmriprep??

[smnfouladi]

i have MRI data of 60 Subject. Data for each of these subjects Contains T1 and T2 folder. T1 folder Contains 176 .dcm file.
i install fmriprep using Docker on my lap top.
Where can I run the code to convert dcm file to nifti ?? in python? in command prompt? in linux command??
and where code for this converting???
please help me

[soichih]

@smnfouladi app-fmriprep is a brainlife.io wrapper for fmriprep. If you are just running fmriprep locally, you don't need to run it using this wrapper.

As a brainlife.io developer, I'd of course recommend people to use brainlife.io to run fmriprep. If you'd like to pursuit this route, you can do the following.

1. convert your DICOM files to nifti using any one of dozen dicom to BIDS conversion tools (We are developing a yet another DICOM to BIDS tool called ezBIDS. We believe this allows you to convert DICOM to BIDS easily. If you'd like to test it, you can go here > https://brainlife.io/ezbids Please note that this is an early prototype and it's not quite ready for prime time.. but we welcome your feedback / comments / bug report).

2. Once you have converted your DICOM to BIDS, you can then run bl bids upload brainlife command to upload data to brainlife.io

3. You can then lanuch freesurfer, and fmriprep App on brainlife.io (using pipeline to automate batch submission) and sit and wait.

[francopestilli]

hi @smnfouladi this is the Apps for fmriprep:

• Volume Output https://brainlife.io/app/5c61c69f14027a01b14adcb3
• Surface Output https://brainlife.io/app/5dfceebd32bff0640ce27bbd

These are instructions on how to create a project:
https://brainlife.io/docs/user/project/

A tutorial to use FMRIPrep:
https://brainlife.io/docs/tutorial/fmri-preprocessing-tutorial/