Issue with the coordinate

[Tiansang-Psy]

Hello,

I'm trying to use pypreclin singularity to do preprocessing of data, and here is my test data

1. Macaque_F99_LR_brian_1p5.nii (template, RAS)
2. Kk_T1_brain_highRes_reorigin.nii (subject T1, IAL)
3. Task.nii.gz (subject task)
   Singularity code used are as follows:

singularity run '/home/sangtian/ST_floder/tmp/pypreclin_test/pypreclin-ubuntu.simg' -V 2 -o 'test_out' -s test -f 'task.nii.gz' -a 'kk_T1_brain_highRes_reorigin.nii.gz' -r 2 -t 'Macaque_F99_LR_brain_1p5.nii' -NA RAS -NF RAS -C /etc/fsl/5.0/fsl.sh -j /i2bm/local/jip-Linux-x86_64/bin

When the program executes to Normalise, an error occurs as:
“Source file 'kk_T1_brain_highRes_reorigin.nii.gz' (LAS) and taget file 'Macaque_F99_LR_brain_1p5.nii' (RAS) must have the same orientation for JIP to work properly.”

I checked the output of code, it had already done Slice timing, reorient, Realign, but empty in the folder Normalization

So then I check the coordinate of subject T1 and template in FSLeyes, the coordinate of subject T1 is original as IAL, and the template is RAS. Then I try to change the coordinate of subject T1 from IAL to RAS, I used the function reorient_image and check_orientation from \pypreclin-master\pypreclin\utils\reorient.py

But even after the preprocessing, the orientation of subject T1 is still IAL, I am confused about it and I am using the following code:

`

from reorient import reorient_image, check_orientation

data_path = '../pypreclin_data/'
T1_data = data_path + 'kk_T1_brain_highRes_reorigin.nii'
RAS_T1_data = data_path + 'RAS_kk_T1_brain_highRes_reorigin.nii.gz'

reorient_image(T1_data, 'RAS', 'RAS_', data_path)
print(check_orientation([T1_data, RAS_T1_data]))

`

the output of the code is: (True, ['IAL', 'IAL'])

From the output, the reorient_image function does not change the coordinate of subject T1, and I don't know what the problem is.

I have also used other packages to orientate the coordinates, e.g. fslreorient2std, fslorient, fslswapdim, and I can convert the coordinates to "LAS" but never to RAS!

At this point, I thought, orient such a process seems to be easily integrated in the singularity step, it seems unnecessary to let us operate separately, so I checked the output folder, and I did find that there was an orient folder in the second step, so I assumed that the container had already completed the reorientation step

But I checked the coordinate of the output file named ‘dRAS_kk_T1_brain_highRes_reorigin.nii.gz’ generated by singularity is still ‘LAS’, so I am really confused about the result, I can't use Pypreclin and FSL's toolkit to solve this coordinate, and also the problem seems to be unsuccessfully handled by the official container, So I really don't know what to do with what's happening right now.

What exactly should I do to keep singularity's program running?

[monami-nishio]

Hi @Tiansang-Psy , have you found a solution for this?
I’m facing the exact same problem and am unsure how to resolve it.

[Tiansang-Psy]

Hi @monami-nishio, I couldn't fix the issue, and I tried to contact the author via email for help (February 17, 2023 ~ March 14, 2023), but in the end couldn't get a solution either.