Incorrect BOLD func output orientation

[warmxue]

Dear fMRIprep experts,

Thanks for providing such great software.

Our lab has used fMRIprep for a while without any issue, however, some recent data collected with GE’s commercial hyperband sequence after a scanner’s upgrade was not processed as expected, that the output from fMRIprep is showing a wrong orientation. For example, below shows the *_space-MNI152NLin2009cAsym_res-2_desc-preproc_bold.nii.gz in Mricron.

My initial check found out the orientation of the new func data was in a different orientation (RPS) than the single-band reference image (LAS) - the first and second axes were rotated. I am wondering if this is causing the issue if fMRIprep assumes that the two images should have the same orientation so co-registration/normalization matrix derived from the single-band reference image is incorrectly applied to the func data.

Orientation info:
func:

qform_name	Scanner Anat
qform_code	1
qto_xyz:1	0.000000 -2.400000 0.000001 102.568001
qto_xyz:2	-2.335931 0.000000 0.550844 99.948654
qto_xyz:3	-0.550843 -0.000001 -2.335937 112.630508
qto_xyz:4	0.000000 0.000000 0.000000 1.000000
qform_xorient	Anterior-to-Posterior
qform_yorient	Right-to-Left
qform_zorient	Superior-to-Inferior
sform_name	Scanner Anat
sform_code	1
sto_xyz:1	0.000000 -2.400000 0.000000 102.568001
sto_xyz:2	-2.335931 0.000000 0.550842 99.948654
sto_xyz:3	-0.550843 0.000000 -2.335938 112.630508
sto_xyz:4	0.000000 0.000000 0.000000 1.000000
sform_xorient	Anterior-to-Posterior
sform_yorient	Right-to-Left
sform_zorient	Superior-to-Inferior

SB reference:

qform_name	Scanner Anat
qform_code	1
qto_xyz:1	-2.400000 0.000000 -0.000000 102.568001
qto_xyz:2	0.000000 2.335931 -0.550843 -75.449463
qto_xyz:3	0.000000 0.550843 2.335931 -74.214508
qto_xyz:4	0.000000 0.000000 0.000000 1.000000
qform_xorient	Right-to-Left
qform_yorient	Posterior-to-Anterior
qform_zorient	Inferior-to-Superior
sform_name	Scanner Anat
sform_code	1
sto_xyz:1	-2.400000 0.000000 -0.000000 102.568001
sto_xyz:2	-0.000000 2.335931 -0.550844 -75.449463
sto_xyz:3	0.000000 0.550843 2.335933 -74.214508
sto_xyz:4	0.000000 0.000000 0.000000 1.000000
sform_xorient	Right-to-Left
sform_yorient	Posterior-to-Anterior
sform_zorient	Inferior-to-Superior

Sorry I can not post the screenshot of the fMRIprep report, because I can only post one screenshot. There was no error or warning, the co-registration looks okay which I think was showing between the SB reference and T1w, however, the CompCorr ROIs and brain mask are showing the wrong underlay with the same orientation issue.

I want to ask:

1. Is there any way to generate the intermediate output from fMRIprep so I can check step by step and figure out what is causing the issue?

2. Currently I am running some tests and expect to have the output in a day, but it would be great to have suggestions from you, I tried:

1. removing SB reference image and re-run fMRIprep
   This is not optimal because of the poor contrast of multiband data, just to test if my above guess is correct.

2. fslreorient2std func data into the same orientation as the SB reference image.
   It seems I will also need to modify the .json file especially the phase encoding direction if I do so, is there any guide on that? I read #260 but am not exactly sure what to modify.

Thanks in advance for your help!

Best,
Xue

[warmxue]

Sharing the screenshot of the report:

Also for context, I viewed the original func and SB reference data, and they all display in the right orientation to me.

[warmxue]

Updates: removing SBref solved the problem!

Would be great to get those speculations/questions confirmed by experts:

1. Does fMRIprep assume that the orientation and all other aspects of SBref should match the MB data except the TR? Any workaround for not-matched SBref?
2. If the orientation of the SBref and MB is different, does it mean the acquisition is also different in addition to TR difference? If so, should I worry about this?

Any suggestion would be really appreciated.

[jsein]

Hi, thank you for explaining in great details your observations.
The very intringuing thing in your story is the starting point: how is it that the SBref is in different orientation than the func data? Which algorithm did you use for converting the DICOM images to NIFTI (and BIDS)?

Otherwise, to discard quickly the SBref images in your execution (without the need to remove the files), you can just pass the argument -ignore sbref in your fmriprep command (starting from fmriprep v20.2.2).

Also, FYI, if the SBref files are ignored, fmriprep has its own heuristic to build a reference image with better contrast: one strategy is to use the non-steady state volumes that has better contrast than steady-state volumes.
As a side note, I noticed from our data that the realignment step with mcflirt was a little bit erratic when the SBref images were used a a target for realignment, which was not the case when the SBref images were ignored. (more details on this point here: https://github.com/nipreps/fmriprep/issues/2360 ).

[warmxue]

Hi thanks for offering help, just to update you after re-checking the data I figured out, for that both the original functional data and the original sbref data, the .json sidecar and the nifti were not generated using a same package and the default orientation of the two packages for .json and nifti are different. When I just use dcm2niix to generate both .json and nifti file, this issue was solved.