PV6 Supine vs Prone does not change conversion

[gdevenyi]

I have been collecting validation datasets for conversion and run into a conversion bug, which was handled properly in 0.3.4, and is wrong in HEAD.

I have a phantom brain in the scanner, physically in the orientation "Head First Prone". I have collected two scans, with PV6 configured as Quadruped, and one scan "Head First Prone" and another "Head First Supine".

brkraw info properly reports the difference in the data:

$ brkraw info 20200814_164540_CIC_PLANTEST_008_PV6_1_1/
Paravision 6.0.1
----------------
UserAccount:    foujer
Date:           2020-08-14
Researcher:     CIC_PLANTEST_008_PV6
Subject ID:     CIC_PLANTEST_008_PV6
Session ID:     CIC_PLANTEST_008_PV6
Study ID:       1
Date of Birth:  14 Aug 2020
Sex:            unknown
Weight:         0.001 kg
Subject Type:   Quadruped
Position:       Prone           Entry:  HeadFirst

[ScanID]        Sequence::Protocol::[Parameters]
[001]   Bruker:FLASH::1_Localizer_multi_slice::
        [ TR: 15 ms, TE: 3 ms, pixelBW: 212.30 Hz, FlipAngle: 10 degree]
    [01] dim: 2D, matrix_size: 192 x 192 x 15, fov_size: 25 x 25 (unit:mm)
         spatial_resol: 0.130 x 0.130 x 2.000 (unit:mm), temporal_resol: 129600.000 (unit:msec)
[002]   Bruker:FLASH::T1_FLASH_3D::
        [ TR: 10 ms, TE: 4 ms, pixelBW: 300.48 Hz, FlipAngle: 10 degree]
    [01] dim: 3D, matrix_size: 96 x 96 x 96, fov_size: 20 x 20 x 20 (unit:mm)
         spatial_resol: 0.208 x 0.208 x 0.208 (unit:mm), temporal_resol: 92160.000 (unit:msec)

$ brkraw info 20200814_170107_CIC_PLANTEST_008_PV6_1_2/
Paravision 6.0.1
----------------
UserAccount:    foujer
Date:           2020-08-14
Researcher:     CIC_PLANTEST_008_PV6
Subject ID:     CIC_PLANTEST_008_PV6
Session ID:     CIC_PLANTEST_008_PV6_HFS
Study ID:       2
Date of Birth:  14 Aug 2020
Sex:            unknown
Weight:         0.001 kg
Subject Type:   Quadruped
Position:       Supine          Entry:  HeadFirst

[ScanID]        Sequence::Protocol::[Parameters]
[001]   Bruker:FLASH::1_Localizer::
        [ TR: 100 ms, TE: 2.50 ms, pixelBW: 256.99 Hz, FlipAngle: 30 degree]
    [01] dim: 2D, matrix_size: 256 x 256 x 3, fov_size: 30 x 30 (unit:mm)
         spatial_resol: 0.117 x 0.117 x 2.000 (unit:mm), temporal_resol: 12800.000 (unit:msec)
[002]   Bruker:FLASH::T1_FLASH_3D::
        [ TR: 10 ms, TE: 4 ms, pixelBW: 300.48 Hz, FlipAngle: 10 degree]
    [01] dim: 3D, matrix_size: 96 x 96 x 96, fov_size: 20 x 20 x 20 (unit:mm)
         spatial_resol: 0.208 x 0.208 x 0.208 (unit:mm), temporal_resol: 92160.000 (unit:msec)
[003]   Bruker:FLASH::T1_FLASH_3D::
        [ TR: 10 ms, TE: 4 ms, pixelBW: 300.48 Hz, FlipAngle: 10 degree]
    [01] dim: 3D, matrix_size: 96 x 96 x 96, fov_size: 20 x 20 x 20 (unit:mm)
         spatial_resol: 0.208 x 0.208 x 0.208 (unit:mm), temporal_resol: 92160.000 (unit:msec)

However, after conversion, both the datasets are in the same orientation:

Left: correct orientation Middle: incorrect orientation, should be rotated

The last commit to touch this code was: https://github.com/BrkRaw/bruker/commit/eaa6db06fd6114922670840b35c0dff041cf4e61

In 0.3.4, it looks like subj_position is ignored for PV6 and applied to PV5, where as in master, it is applied unconditionally.

[gdevenyi]

It looks like perhaps the existing affine from bruker is actually correct and the additional corrections added were due to confusion regarding the exact orientation of previous phantom test data?

[gdevenyi]

Confirmed with PV5 as well, that just skipping the correction orientation by adding pass here: https://github.com/BrkRaw/bruker/blob/master/brkraw/lib/orient.py#L24

Results in correct orientations for the Supine/Prone positions.

I will hold off on making any changes yet, as I want to collect all orientations and "subject types" in both PV5 and PV6 in a single session with the phantom universally in the "Head First Prone" position. I think perhaps we may be able to do away with most of this code.

[dvm-shlee]

@gdevenyi Sorry for the delay regarding the update of this software. I tried to make the final orientation to be oriented on subject whether the animal positioned supine or prone. So if the resulted orientation is always the same. I think it is correct.

Please let me know if I mis-catch your point. Thanks!

[gdevenyi]

Sorry for the delay, please see email to your github listed email for a orientation dataset to sort this out.