Orientation information is different between images

Software Support
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After preprocessing with fMRIprep, there are minor differences in the orientation information of functional images, which, although small, lead to errors when using SPM for further analysis.
屏幕截图 2023-08-01 223204
(This is part of the orientation information)
I’m puzzled , as the portion with differences accounts for only 16% of the total images, but I used the same command to process all the images.

Summary of what happened: Orientation information is different between subjects’ images

Command used (and if a helper script was used, a link to the helper script or the command generated): fmriprep-docker /…/Bids dir. /…/output dir. participant --participant_label xxx --fs-no-reconall -w /…/working dir. --use-syn-sdc --fs-license-file /…/license.txt

Version: 23.1.3

Environment (Docker, Singularity, custom installation): Docker

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

Relevant log outputs (up to 20 lines):

Screenshots / relevant information:

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3

Maybe someone else can comment on why these minor differences in the last decimal place happened exactly, but it’s likely some difference in rounding or reading and writing from a text file somewhere along the processing. In any case, these are possible workarounds that change the header of the datasets to match each other. Mucking around with the header is risky, so work with copies of the data.

  1. nifti_tool. Use the “-mod_hdr -mod_field” options to change fields, copying the values from one of the datasets to the others. Check the fields with “nifti_tool -disp_hdr -infiles …”. This extract shows the ones that deal with orientation and voxel dimensions:
  pixdim                76      8    1.0 0.25 0.25 0.25 0.0 0.0 0.0 0.0
  qform_code           252      1    5
  sform_code           254      1    5
  quatern_b            256      1    0.0
  quatern_c            260      1    -0.0
  quatern_d            264      1    0.0
  qoffset_x            268      1    -39.75
  qoffset_y            272      1    -58.0
  qoffset_z            276      1    -32.25
  srow_x               280      4    0.25 -0.0 -0.0 -39.75
  srow_y               296      4    -0.0 0.25 -0.0 -58.0
  srow_z               312      4    0.0 0.0 0.25 -32.25
  1. 3drefit. AFNI’s 3drefit can copy over attributes from one dataset to another. This should work with multiple NIFTI files as input:
3drefit -atrcopy IJK_TO_DICOM_REAL original_dset modified_dsets
  1. SPM matlab. Since you are working with SPM, you might consider the Matlab way proposed here to copy headers.
    matlab - Copy one Nifti header to another - Stack Overflow
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hi@dglen，
Thanks so much,I truly believe the various methods you provided can fully address my Issue！