Ran latest version of dcm2bids - tried also running with previous versions of the file. I also tried re-run fMRIprep using previous versions of fmriprep.
I tried to run fMRIPrep (latest version) with fieldmap correction however, I experienced the following error(s):
FileNotFoundError: File path </work/06953/jes6785/ls6/ALMEIDA_LASER/work/derivates/fmriprep-v22.0.1/sub-LSB104/ses-02/fmap/sub-LSB104_ses-02_fmapid-auto00010_desc-coeff_magnitude.nii.gz> does not exist, is a broken link, or it is not a file
ValueError: A fieldmap or phase-difference estimation type was found, but an anatomical reference (magnitude file) is missing.
I also see a similar problem here.
I shouldn’t have a magnitude image for these files as they are epi images in the opposite phase encoding direction. From my understanding, there shouldn’t be any magnitude images associated with them.
Wondering if my naming convention for the fmap folder might have caused the problem?
anat
│ ├── sub-LSB104_ses-01_rec-norm_T1w.json
│ ├── sub-LSB104_ses-01_rec-norm_T1w.nii.gz
│ ├── sub-LSB104_ses-01_rec-orig_T1w.json
│ └── sub-LSB104_ses-01_rec-orig_T1w.nii.gz
├── fmap
│ ├── sub-LSB104_ses-01_acq-cptpnnd_dir-PA_run-01_epi.json
│ ├── sub-LSB104_ses-01_acq-cptpnnd_dir-PA_run-01_epi.nii.gz
│ ├── sub-LSB104_ses-01_acq-cptpnnd_dir-PA_run-02_epi.json
│ ├── sub-LSB104_ses-01_acq-cptpnnd_dir-PA_run-02_epi.nii.gz
│ ├── sub-LSB104_ses-01_acq-midgainloss_dir-PA_epi.json
│ ├── sub-LSB104_ses-01_acq-midgainloss_dir-PA_epi.nii.gz
│ ├── sub-LSB104_ses-01_acq-rest_dir-PA_run-01_epi.json
│ ├── sub-LSB104_ses-01_acq-rest_dir-PA_run-01_epi.nii.gz
│ ├── sub-LSB104_ses-01_acq-rest_dir-PA_run-02_epi.json
│ ├── sub-LSB104_ses-01_acq-rest_dir-PA_run-02_epi.nii.gz
│
├── func
│ ├── sub-LSB104_ses-01_task-cptpnnd_dir-AP_run-01_bold.json
│ ├── sub-LSB104_ses-01_task-cptpnnd_dir-AP_run-01_bold.nii.gz
│ ├── sub-LSB104_ses-01_task-cptpnnd_dir-AP_run-02_bold.json
│ ├── sub-LSB104_ses-01_task-cptpnnd_dir-AP_run-02_bold.nii.gz
│ ├── sub-LSB104_ses-01_task-midgainloss_dir-AP_bold.json
│ ├── sub-LSB104_ses-01_task-midgainloss_dir-AP_bold.nii.gz
│ ├── sub-LSB104_ses-01_task-rest_dir-AP_run-01_bold.json
│ ├── sub-LSB104_ses-01_task-rest_dir-AP_run-01_bold.nii.gz
│ ├── sub-LSB104_ses-01_task-rest_dir-AP_run-02_bold.json
│ └── sub-LSB104_ses-01_task-rest_dir-AP_run-02_bold.nii.gz
└──
What command did you use?
singularity run --cleanenv “$fmriprep” “$localnifty” “$fmriprep_output” participant --participant-label “$id” --fs-license-file “$fsl_license” --skip_bids_validation -w “$workingdir”
What version of fMRIPrep are you running?
22.0.1
How are you running fMRIPrep?
Singularity