Resampled image is not saved

[Ede1994]

I've tried to use your tool and to save the resampled image. My code:

def synthSeg(src_path, dst_path, resample_path):
    command = ["mri_synthseg", '--i', src_path, '--o', dst_path, '--robust', '--resample', resample_path]

    with subprocess.Popen(command, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True) as proc:
        for line in proc.stdout:
            print('%s: %s', command[0], line.strip())

        for line in proc.stderr:
            print('%s (stderr): %s', command[0], line.strip())
    return

synthSeg(src_path=seg_p,
         dst_path='/tmp/restmp/results/99_test.nii.gz',
         resample_path='/tmp/restmp/results/98_resample.nii.gz')

The output was the following:

%s: %s mri_synthseg SynthSeg-robust 2.0
%s: %s mri_synthseg using 1 thread
%s: %s mri_synthseg predicting 1/1
%s: %s mri_synthseg 
%s: %s mri_synthseg 1/1 [==============================] - ETA: 
%s: %s mri_synthseg 1/1 [==============================] - 91s 91s/step
%s: %s mri_synthseg 
%s: %s mri_synthseg segmentation  saved in:    [/tmp/restmp/results/99_test.nii.gz]
%s: %s mri_synthseg resampled image saved in:  [/tmp/restmp/results/98_resample.nii.gz]
%s: %s mri_synthseg 
%s: %s mri_synthseg If you use this tool in a publication, please cite:
%s: %s mri_synthseg SynthSeg: Segmentation of brain MRI scans of any contrast and resolution without retraining
%s: %s mri_synthseg B. Billot, D.N. Greve, O. Puonti, A. Thielscher, K. Van Leemput, B. Fischl, A.V. Dalca, J.E. Iglesias
%s: %s mri_synthseg Medical Image Analysis, accepted for publication.
%s: %s mri_synthseg 
%s: %s mri_synthseg Robust machine learning segmentation for large-scale analysis of heterogeneous clinical brain MRI datasets
%s: %s mri_synthseg B. Billot, C. Magdamo, Y. Cheng, S.E. Arnold, S. Das, J.E. Iglesias
%s: %s mri_synthseg PNAS, accepted for publication.

But the resampled image is not saved, only the regular output (99_test.nii.gz).

[BBillot]

Are you sure that you want to save the results under different numbers: 99 for the segmentation and 98 for the resampled image ? Is it possible that you're not looking for the right file ?

Anyway, it seems like you've coded a wrapper around the FreeSurfer command (as opposed to the GitHub command). Have you tried calling mri_synthseg directly from the terminal ? This should work, and if it does, it means there's something wrong with your wrapper, although it looks correct to me.

[Ede1994]

You're right. It works fine in the terminal. I don't know exactly why the wrapper is causing a problem, because otherwise it works.