Hi all, I have a question about running fmriprep in a two-step fashion. I’ve first run it using the --anat-only flag, to preprocess my structural data. Now I’m trying to preprocess my functional data, session by session, but not all my sessions have T1w images.
I have an input folder which contains a dataset description, and then data from a single session (in proper bids format)
I have an output folder which contains the outputs of my previous run of fmriprep (–anat-only).
Then I run this command:
sudo docker run -v ~/input:/data:ro -v ~/output:/output -v ~/scratch/:/scratch -v ~/freesurfer:/freesurfer nipreps/fmriprep:latest /data /output participant --participant-label 001 -w /scratch --fs-license-file /freesurfer/license.txt --anat-derivatives /output/fmriprep/sub-001/anat/ --skip_bids_validation
And get this output:
231025-22:02:32,124 nipype.workflow IMPORTANT:
Running fMRIPrep version 23.1.4
License NOTICE ##################################################
fMRIPrep 23.1.4
Copyright 2023 The NiPreps Developers.
This product includes software developed by
the NiPreps Community (https://nipreps.org/).
Portions of this software were developed at the Department of
Psychology at Stanford University, Stanford, CA, US.
This software is also distributed as a Docker container image.
The bootstrapping file for the image ("Dockerfile") is licensed
under the MIT License.
This software may be distributed through an add-on package called
"Docker Wrapper" that is under the BSD 3-clause License.
#################################################################
231025-22:02:32,161 nipype.workflow IMPORTANT:
Building fMRIPrep's workflow:
* BIDS dataset path: /data.
* Participant list: ['001'].
* Run identifier: 20231025-220218_29bc133c-fc77-44bf-a2d5-474268cd15cd.
* Output spaces: MNI152NLin2009cAsym:res-native.
* Anatomical derivatives: /output/fmriprep/sub-001/anat.
* Pre-run FreeSurfer's SUBJECTS_DIR: /output/sourcedata/freesurfer.
231025-22:02:32,337 nipype.workflow WARNING:
Attempted to access pre-existing anatomical derivatives at </output/fmriprep/sub-001/anat>, however not all expectations of fMRIPrep were met (for participant <001>, spaces <MNI152NLin2009cAsym>, reconall <True>).
Process Process-2:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/multiprocessing/process.py", line 314, in _bootstrap
self.run()
File "/opt/conda/envs/fmriprep/lib/python3.10/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/cli/workflow.py", line 115, in build_workflow
retval["workflow"] = init_fmriprep_wf()
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/workflows/base.py", line 93, in init_fmriprep_wf
single_subject_wf = init_single_subject_wf(subject_id)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/fmriprep/workflows/base.py", line 202, in init_single_subject_wf
raise Exception(
Exception: No T1w images found for participant 001. All workflows require T1w images.
Any suggestions? Thanks for the help!