Using sensitivity maps per contrast leads to changes qform and sform

[nkuegler]

Description of the problem

The problem is very similar this other issue #125 . However, this time it is not the denoising module that causes the change from "Scanner Anat" to "Aligned Anat" but the use of sensitivity maps per contrast in the map_creation module.

Cause of the issue

@lukeje suggested relevant two code snippets that cause the issue:

• That uses spm_imcalc which seems to only save one transform in the header: https://github.com/spm/spm12/blob/main/spm_imcalc.m#L144-L153

• spm_imcalc calls spm_create_vol which sets Aligned Anat explicitly: https://github.com/spm/spm12/blob/main/spm_create_vol.m#L104-L112
  However, I did not find this call of spm_create_vol but it may be nested in a different function.

Output header test

The sform and qform are identical compared to the first PDw echo. However sform_name, sform_code, qform_name, and qform_code change when using the sensitivity maps.

original PDw echo-01:

> fslhd sub-002_ses-01_acq-PDw_rec-loraksRsos_echo-01_flip-2_mt-off_part-mag_MPM.nii | grep form_
qform_name	Scanner Anat
qform_code	1
qform_xorient	Posterior-to-Anterior
qform_yorient	Superior-to-Inferior
qform_zorient	Left-to-Right
sform_name	Scanner Anat
sform_code	1
sform_xorient	Posterior-to-Anterior
sform_yorient	Superior-to-Inferior
sform_zorient	Left-to-Right

> fslhd sub-002_ses-01_acq-PDw_rec-loraksRsos_echo-01_flip-2_mt-off_part-mag_MPM.nii | grep sto
sto_xyz:1	0.000000 0.000000 0.600000 -86.099998 
sto_xyz:2	0.520448 0.300481 0.000000 -149.624771 
sto_xyz:3	0.300481 -0.520448 0.000000 40.442566 
sto_xyz:4	0.000000 0.000000 0.000000 1.000000 

qMRI maps without denoising and without smaps:

> fslhd sub-002_ses-01_acq-PDw_rec-loraksRsos_echo-01_flip-2_mt-off_part-mag_MPM_R2s_OLS.nii | grep form_
qform_name	Scanner Anat
qform_code	1
qform_xorient	Posterior-to-Anterior
qform_yorient	Superior-to-Inferior
qform_zorient	Left-to-Right
sform_name	Scanner Anat
sform_code	1
sform_xorient	Posterior-to-Anterior
sform_yorient	Superior-to-Inferior
sform_zorient	Left-to-Right

> fslhd sub-002_ses-01_acq-PDw_rec-loraksRsos_echo-01_flip-2_mt-off_part-mag_MPM_R2s_OLS.nii | grep sto
sto_xyz:1	0.000000 0.000000 0.600000 -86.099998 
sto_xyz:2	0.520448 0.300481 0.000000 -149.624771 
sto_xyz:3	0.300481 -0.520448 0.000000 40.442566 
sto_xyz:4	0.000000 0.000000 0.000000 1.000000 

qMRI maps without denoising but using smaps:

> fslhd sub-002_ses-01_acq-PDw_rec-loraksRsos_echo-01_flip-2_mt-off_part-mag_MPM_RFSC_R2s_OLS.nii | grep form_
qform_name	Aligned Anat
qform_code	2
qform_xorient	Posterior-to-Anterior
qform_yorient	Superior-to-Inferior
qform_zorient	Left-to-Right
sform_name	Aligned Anat
sform_code	2
sform_xorient	Posterior-to-Anterior
sform_yorient	Superior-to-Inferior
sform_zorient	Left-to-Right

> fslhd sub-002_ses-01_acq-PDw_rec-loraksRsos_echo-01_flip-2_mt-off_part-mag_MPM_RFSC_R2s_OLS.nii | grep sto
sto_xyz:1	0.000000 0.000000 0.600000 -86.099998 
sto_xyz:2	0.520448 0.300481 0.000000 -149.624771 
sto_xyz:3	0.300481 -0.520448 0.000000 40.442566 
sto_xyz:4	0.000000 0.000000 0.000000 1.000000 

[Barisevrenugur]

yes, this is obvious, spm_create_vols sets it to aligned here:

https://github.com/neurodebian/spm12/blob/b86f0712da80daa4fae7939eeebebe0b2629cbc0/spm_create_vol.m#L82

then submit this issue to SPM

https://github.com/spm/spm

if they believe that your issue is valid and deserves a change, we will discuss incorporating their change into the spm code here as well.

as this issue concerns an external repo, closed.

for the case of denoising module, I already coded this

#126

you can try it

[lukeje]

Hi Baris, this is not an SPM issue. From their perspective they have no idea what space the space of the final image represents, and so they set it to the generic 'Aligned', as the output will be aligned with the space of the first(?) input image. However, we as hMRI toolbox developers have more information: we know that we do not change the space of the images, and so we can be more specific. Therefore, this is something that we can fix.

[Barisevrenugur]

feel free to make the PR then, I already coded the denoising module case here:

#126

Hi Baris, this is not an SPM issue. From their perspective they have no idea what space the space of the final image represents, and so they set it to the generic 'Aligned', as the output will be aligned with the space of the first(?) input image. However, we as hMRI toolbox developers have more information: we know that we do not change the space of the images, and so we can be more specific. Therefore, this is something that we can fix.