Fmriprep error: problem with phasediff and magnitude 1 image

Hi all.
I am new to fMRI Prep. I’ve done lots of reading on forums and troubleshooting but can can’t resolve an issue I am having.

I’m trying to run fMRIPrep with singularity on a HPC cluster. I have a single anatomical (T1w) image, a multi-echo multi-slice resting state sequence and fieldmaps (2 magnitude images and a phase diff image). I get a warning immediately in the terminal :

1: [WARN] Each _phasediff.nii[.gz] file should be associated with a _magnitude1.nii[.gz] file. (code: 92 - MISSING_MAGNITUDE1_FILE)

The directory tree for each sub is attached.

Do I need to manually edit the .json file of the phase diff image to associate it with mag 1? I have already manually edited the .json file for the phasediff image to include the 2 echo times associated with mag1 and mag2 respectively.

Thank you,


I think this warning is linked to the fact that the magnitude1 file and phasediff file don’t have the same name. You could try to name them:
sub-EF20422_acq-gre_magnitude1{.nii.gz,.json} and sub-EF20422_acq-gre_phasediff{.nii.gz,.json} for instance

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Thank you for our quick reply, I appreciate it. Another question: in the phasediff .json file, should there be an “IntendedFor” field with the paths to each of the 4 resting state images (for the 4 echos)?

First point: which fmriprep version are you using?

Recently, It was recommended to the tags B0FieldIdentifier and B0FieldSource in addition to IntendedFor (more details here: Magnetic Resonance Imaging - Brain Imaging Data Structure v1.7.0).

Yes I think you should populate the json files for both _magnitude1 and _phasediff files with the fields: ÌntendedForandB0FieldIdentifier`. See the example in the example for case 1 in the link I pasted.

I am using fmriprep version 1.4.0

I would encourage you to upgrade to one of the newest version: like 21.0.2 for instance. You can see the list of versions here along with the corresponding changes here: Releases · nipreps/fmriprep · GitHub

Me again. Thank you for your help previously with this error. Your advice regarding changing the file names of the magnitude 1 and phase diff images to ensure they were named the same, resolved the error I was getting. I have now encountered another error.

I am using fMRIPrep v 21.0.1 on one subject, and now I am getting this error:

File “/opt/conda/lib/python3.8/site-packages/sdcflows/”, line 385, in attrs_post_init
raise ValueError(
ValueError: Only one phase-encoding direction found across sources.

My fmap dir for that subject is attached as screenshot

When I check the meta data (.json) for mag 1 and phase diff images the phase encode direction is listed as “i-”. This is the same for the functional resting state multi-echo multi-band sequence.
However, for the reverse phase images (labeled in the fmap dir as dir-LRecho1_epi.nii.gz (for 1 through 4), the phase encode is “i”.

Question: foes fMRIPrep use both the fieldmaps and reverse phase images for B0 correction? Do I need to alter the phase encode dir as listed in the meta data?

Finally (sanity check): in the .json file for the phase diff I have added IntendedFor and then the path to to functional resting state scans (1-4 as there are 4 echos). Do I also need to add this into the mag 1 (and mag 2) meta data files? If the relative path can be given & my dir structure is
how do I specify the path to the rs images in the func dir for the fmap .json files?

fMRIprep will use fieldmaps by order of priority. If both Phase Difference Field maps and Pepolar images are present, fmriprep v 21.0.1 (which is using SDCFlow) will give higher priority to the Phase Difference image).

The source of this information is here:

For your IntendedFor field, in your case you will have to write:

  "IntendedFor": [

I don’t think you need to specify the other echoes but you will need confirmation there.

I think the IntendedFor field for the phasediff json file is enough but don’t take my word for granted, I am not specialist with this kind of fieldmaps nor multi-echo fmri.