Anatomical reference of the fieldmap and the target EPI alignment issue

[sapmango]

Summary of what happened:

• in the fmriprep report, there is a mismatch of alignment in this part: Alignment between the anatomical reference of the fieldmap and the target EPI:
  

  

• the Preprocessed mapping of phase-difference acquisition looks fine:
  

  

• I checked the alignment of the images, the sub-0772_magnitude1.nii.gz, sub-0772_magnitude2.nii.gz, and sub-0772_phasediff.nii.gz does not align with sub-0772_T1w.nii.gz.
  

  

• fslhd information below:
  do I have to make all fmap files below parameters same as task_bold to solve the problem?

qform_name Scanner Anat

qform_code 1

qto_xyz:1 -3.312500 0.000000 0.000000 106.000000

qto_xyz:2 0.000000 -3.312500 0.000000 123.627121

qto_xyz:3 0.000000 0.000000 4.000000 -59.694916

qto_xyz:4 0.000000 0.000000 0.000000 1.000000

qform_xorient Right-to-Left

qform_yorient Anterior-to-Posterior

qform_zorient Inferior-to-Superior

sform_name Scanner Anat

sform_code 0

sto_xyz:1 3.312500 0.000000 0.000000 -102.687500

sto_xyz:2 0.000000 3.312500 0.000000 -122.060379

sto_xyz:3 0.000000 0.000000 4.000000 -72.694916

sto_xyz:4 0.000000 0.000000 0.000000 1.000000

sform_xorient Left-to-Right

sform_yorient Posterior-to-Anterior

sform_zorient Inferior-to-Superior

Command used (and if a helper script was used, a link to the helper script or the command generated):

# Run fMRIPrep
fmriprep-docker \
  $bids_root_dir \
  $bids_root_dir/derivatives/fmriprep \
  participant \
  --participant-label $subject \
  --fs-license-file $fs_license \
  --nthreads $nthreads \
  --mem_mb 15000 \
  --stop-on-first-crash \
  --output-spaces MNI152NLin2009cAsym:res-2 T1w \
  --return-all-components \
  --work-dir $work_dir \
  --image nipreps/fmriprep:$FMRIPREP_VER

Version:

FMRIPREP_VER=24.0.1

Environment (Docker, Singularity / Apptainer, custom installation):

docker

Data formatted according to a validatable standard? Please provide the output of the validator:

structure is like this:
/Users/sap/Desktop/rsync/sub-0772_source_reoriented/
├── sub-0772/
    ├── anat/
        └── sub-0772_T1w.nii.gz
    ├── func/
        └── sub-0772_task-rest_bold.nii.gz
    ├── fmap/
        ├── sub-0772_magnitude1.nii.gz
        ├── sub-0772_magnitude2.nii.gz
        └── sub-0772_phasediff.nii.gz

all images has their respective .json file

Relevant log outputs (up to 20 lines):

No errors to report!

Screenshots / relevant information:

SDC and coregistration looks fine:

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