unable to run NIfTI-> NIfTI

[artemmikheev]

With the latest version I am trying to use the nifti input and generate the nifti output

So I use this command (under Windows PowerShell)

docker run --rm --user 0 --gpus all -v d:\Temp:/work deepmi/fastsurfer:latest --sid one --sd /work/fsout --t1 /work/fs_src.nii --asegdkt_segfile /work/result.nii --seg_only --allow_root

FS complains:

ERROR: Specified segmentation output and conformed image output do not have same
file type. You passed --asegdkt_segfile /work/result.nii and
--conformed_name /work/fsout/one/mri/orig.mgz.
Make sure these have the same file-format and adjust the names passed to the
flags accordingly!

Thank you

[m-reuter]

Thanks. Currently intermediate or output files cannot be nifti, only the input. The reason is, that for internal processing we still rely on some FreeSurfer functions and they behave differently for nifti, so we stay with mgz internally.
Just convert the output to nifti afterwards e.g. with mri_convert :

docker run --rm --user 0 -v d:\Temp:/work --entrypoint /opt/freesurfer/bin/mri_convert deepmi/fastsurfer:latest -h

replacing -h with the paths inside the docker image to input mgz and output nii files.

[m-reuter]

PS in an earlier version this was possible as only the surface stream converted everything to mgz and the segmentation stream could run completely with nifti. But then lots of files would be duplicated with different file types. And final surface-based outputs would still be mgz format (if someone ran the surface module). We can check if FreeSurfer fully supports nifti also for its intermediate files and if so, we can then switch to nifti completely as the default (which is a wish of mine for a long time, even dating back to when I was creating the longitudinal stream in FreeSurfer).

[dkuegler]

Technically you can also modify the intermediate file orig.mgz (if you are running --seg_only -- i.e. no surfaces) by adding the flag --conformed_name /work/fsout/one/mri/orig.nii.gz.

  --conformed_name <conf.mgz>
                          Name of the file in which the conformed input
                            image will be saved. Requires an ABSOLUTE Path!
                            Default location:
                            $SUBJECTS_DIR/$sid/mri/orig.mgz.

[artemmikheev]

Thank you. If I understood it correctly, here is my modified command:

docker run --rm --user 0 --gpus all -v d:\Temp:/work deepmi/fastsurfer:latest --sid one --sd /work/fsout --t1 /work/fs_src.nii --seg_only --conformed_name /work/fsout/one/mri/orig.nii.gz --allow_root

But it still complains: "ERROR: Specified segmentation output and conformed image output do not have same
file type. You passed --asegdkt_segfile /work/fsout/one/mri/aparc.DKTatlas+aseg.deep.mgz and
--conformed_name /work/fsout/one/mri/orig.nii.gz.
Make sure these have the same file-format and adjust the names passed to the
flags accordingly!"

[dkuegler]

Try this please

docker run --rm --user 0 --gpus all -v d:\Temp:/work deepmi/fastsurfer:latest --sid one --sd /work/fsout --t1 /work/fs_src.nii --seg_only --conformed_name /work/fsout/one/mri/orig.nii.gz --allow_root --asegdkt_segfile /work/result.nii.gz

The issue is that the detection is based on the file extension, which needs to be consistent, e.g. consistently ".nii.gz" or ".nii" or ".mgz"

docker run --rm --user 0 --gpus all -v d:\Temp:/work deepmi/fastsurfer:latest --sid one --sd /work/fsout --t1 /work/fs_src.nii --seg_only --conformed_name /work/fsout/one/mri/orig.mgz --allow_root --asegdkt_segfile /work/result.mgz


docker run --rm --user 0 --gpus all -v d:\Temp:/work deepmi/fastsurfer:latest --sid one --sd /work/fsout --t1 /work/fs_src.nii --seg_only --conformed_name /work/fsout/one/mri/orig.nii --allow_root --asegdkt_segfile /work/result.nii

I am not really sure, why we check this, but that is what would be happening under the hood.