Path does not exist

[alienx-zero]

Hi, I am new to start fmriprep and also first time using docker. Anyone could tell me what is the problem. I think the path is right... C:\Users\99488>docker run poldracklab/fmriprep E:\OPT\research\fMRI\2475376 E:\OPT\research\fMRI\output {participant} --participant-label 2475376 --fs-license-file E:\OPT\research\fMRI\license.txt You are using fMRIPrep-20.1.1, and a newer version of fMRIPrep is available: 20.1.2. Please check out our documentation about how and when to upgrade: https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading usage: fmriprep [-h] [--version] [--skip_bids_validation] [--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-t TASK_ID] [--echo-idx ECHO_IDX] [--bids-filter-file FILE] [--anat-derivatives PATH] [--nprocs NPROCS] [--omp-nthreads OMP_NTHREADS] [--mem MEMORY_GB] [--low-mem] [--use-plugin FILE] [--anat-only] [--boilerplate_only] [--md-only-boilerplate] [--error-on-aroma-warnings] [-v] [--ignore {fieldmaps,slicetiming,sbref} [{fieldmaps,slicetiming,sbref} ...]] [--longitudinal] [--output-spaces [OUTPUT_SPACES [OUTPUT_SPACES ...]]] [--bold2t1w-init {register,header}] [--bold2t1w-dof {6,9,12}] [--force-bbr] [--force-no-bbr] [--medial-surface-nan] [--dummy-scans DUMMY_SCANS] [--random-seed RANDOM_SEED] [--use-aroma] [--aroma-melodic-dimensionality AROMA_MELODIC_DIM] [--return-all-components] [--fd-spike-threshold REGRESSORS_FD_TH] [--dvars-spike-threshold REGRESSORS_DVARS_TH] [--skull-strip-template SKULL_STRIP_TEMPLATE] [--skull-strip-fixed-seed] [--skull-strip-t1w {auto,skip,force}] [--fmap-bspline] [--fmap-no-demean] [--use-syn-sdc] [--force-syn] [--fs-license-file FILE] [--fs-subjects-dir PATH] [--no-submm-recon] [--cifti-output [{91k,170k}] | --fs-no-reconall] [-w WORK_DIR] [--clean-workdir] [--resource-monitor] [--reports-only] [--run-uuid RUN_UUID] [--write-graph] [--stop-on-first-crash] [--notrack] [--sloppy] bids_dir output_dir {participant} fmriprep: error: Path does not exist: <E:\OPT\research\fMRI\2475376>.

[alienx-zero]

[mgxd]

Local paths won't be visible within the docker container unless you specifically include them, such as using the -v flag.

To make the docker process easier, we package a docker wrapper, more information can be found at https://fmriprep.org/en/stable/docker.html#running-fmriprep-with-the-fmriprep-docker-wrapper

[effigies]

To be clear, it looks like what you want is:

fmriprep-docker E:\OPT\research\fMRI\2475376 E:\OPT\research\fMRI\output participant --participnat-label 2475376 --fs-license-file E:\OPT\research\fMRI\license.txt

You will almost certainly want to add a -w argument to use a work directory outside the container.

[alienx-zero]

Sorry, I try either -v or -w, the license.txt path could not be recognized

[effigies]

Is the fmriprep-docker command not working for you? It was written to help avoid spending a lot of time debugging docker invocations. I see there was something that got at least to the validation stage above...

[alienx-zero]

validation stage error is that after I remove the line --fs-license-file E:\OPT\research\fMRI\license.txt, it would report such error~ If I direclty run fmriprep-docker(F-D) in cmd, theywill say that F-D is not recognized as command as following:

C:\Users\99488>fmriprep-docker -w E:\OPT\research\fMRI\2475376 -w E:\OPT\research\fMRI\output participant --participnat-label 2475376 --fs-license-file E:\OPT\research\fMRI\license.txt 'fmriprep-docker' is not recognized as an internal or external command, operable program or batch file.

Should I add some file paths into enviroment variables? I do not know whether it work for docker

[alienx-zero]

If I run it by docker run poldracklab/fmriprep instead of run --rm -it, it will report other error... C:\Users\99488>docker run poldracklab/fmriprep -w E:\OPT\research\fMRI\2475376 -w E:\OPT\research\fMRI\output participant --participnat-label 2475376 --fs-license-file E:\OPT\research\fMRI\license.txt You are using fMRIPrep-20.1.1, and a newer version of fMRIPrep is available: 20.1.2. Please check out our documentation about how and when to upgrade: https://fmriprep.readthedocs.io/en/latest/faq.html#upgrading usage: fmriprep [-h] [--version] [--skip_bids_validation] [--participant-label PARTICIPANT_LABEL [PARTICIPANT_LABEL ...]] [-t TASK_ID] [--echo-idx ECHO_IDX] [--bids-filter-file FILE] [--anat-derivatives PATH] [--nprocs NPROCS] [--omp-nthreads OMP_NTHREADS] [--mem MEMORY_GB] [--low-mem] [--use-plugin FILE] [--anat-only] [--boilerplate_only] [--md-only-boilerplate] [--error-on-aroma-warnings] [-v] [--ignore {fieldmaps,slicetiming,sbref} [{fieldmaps,slicetiming,sbref} ...]] [--longitudinal] [--output-spaces [OUTPUT_SPACES [OUTPUT_SPACES ...]]] [--bold2t1w-init {register,header}] [--bold2t1w-dof {6,9,12}] [--force-bbr] [--force-no-bbr] [--medial-surface-nan] [--dummy-scans DUMMY_SCANS] [--random-seed RANDOM_SEED] [--use-aroma] [--aroma-melodic-dimensionality AROMA_MELODIC_DIM] [--return-all-components] [--fd-spike-threshold REGRESSORS_FD_TH] [--dvars-spike-threshold REGRESSORS_DVARS_TH] [--skull-strip-template SKULL_STRIP_TEMPLATE] [--skull-strip-fixed-seed] [--skull-strip-t1w {auto,skip,force}] [--fmap-bspline] [--fmap-no-demean] [--use-syn-sdc] [--force-syn] [--fs-license-file FILE] [--fs-subjects-dir PATH] [--no-submm-recon] [--cifti-output [{91k,170k}] | --fs-no-reconall] [-w WORK_DIR] [--clean-workdir] [--resource-monitor] [--reports-only] [--run-uuid RUN_UUID] [--write-graph] [--stop-on-first-crash] [--notrack] [--sloppy] bids_dir output_dir {participant} fmriprep: error: Path does not exist: .

[alienx-zero]

Sorry, the text miss the next word on last commnet. I show it in this figure .

[effigies]

Do you have Python installed? If so, python -m pip install fmriprep-docker.

The issue is that you need to mount any paths, and all Docker options go before the image.

docker run -v E:\OPT\research\fMRI\2475376:/data -v E:\OPT\research\fMRI\output:/out -v E:\OPT\research\fMRI\license.txt:/opt/freesurfer/license.txt poldracklab/fmriprep:latest /data /out participant --participant-label 2475376

[alienx-zero]

omg, it is fixed~ Thx very much. Like u

[alienx-zero]

Sorry to take your time again... Here is a new problem.. And the data structure is shown as following: These data are dowloaded from http://fcon_1000.projects.nitrc.org/indi/pro/eNKI_RS_TRT/NKI_Rockland_nifti_dl.html shown in the tutorials. Is it completed? Or lack the labels info

[effigies]

That's not a BIDS dataset, so fMRIPrep won't know what to do with it. You will either need to reorganize it into BIDS or find someone who has already done that. I might check on Neurostars.

[alienx-zero]

Get~Thanks for your patient explanation~

[ZhyGao]

Do you have Python installed? If so, python -m pip install fmriprep-docker.

The issue is that you need to mount any paths, and all Docker options go before the image.

docker run -v E:\OPT\research\fMRI\2475376:/data -v E:\OPT\research\fMRI\output:/out -v E:\OPT\research\fMRI\license.txt:/opt/freesurfer/license.txt poldracklab/fmriprep:latest /data /out participant --participant-label 2475376

I have the same question but I don't know why. Can you help me?

docker run -v /home/gzy/tvb-collab-master/input:/data -v /home/gzy/tvb-collab-master/output:/out -v /data/freesurfer/license.txt:/opt/freesurfer/license.txt nipreps/fmriprep:latest /data /out participant --participant-label CON03

there's an error ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked for an existing license file at several paths, in this order: 1) command line argument --fs-license-file; 2) $FS_LICENSE environment variable; and 3) the $FREESURFER_HOME/license.txt path. Get it (for free) by registering at https://surfer.nmr.mgh.harvard.edu/registration.html Thanks for your reply