[Anand Joshi]

Hi, The labeled volume should be automatically stored in the same directory as the MRI scan. They have filenames <subjectid>.svreg.label.nii.gz
Are you able to find that file?
Here is the list of output files
http://brainsuite.org/processing/svreg/output/

Please let me know if you find these files generated in your mri directory.

[amysore3]

Thank you for the response but I am not able to see these files in the same directory as my MRI scan. It feels like they aren’t getting saved. But I am not getting any error either which I believe means that the SVreg is running successfully but isn’t saving the labelled volumes. Please let me know what I could.

[Anand Joshi]

What are the files do you see in the mri directory? Do you have the .dfs files there?

[amysore3]

Yes, I do see all the .dfs files in the MRI directory

[amysore3]

I see only “.hemi.label.nii.gz”, “.pvc.label.nii.gz” and “.skull.label.nii.gz” labelled volumes and I see all the .dfs files.

[Anand Joshi]

Are there any files with svreg extension (e.g. *.svreg.dfs)

[amysore3]

Yes., there are about 8-10 files with .svreg.dfs.

[Anand Joshi]

That means svreg has finished, however perhaps only the surface registration has run.
Please make sure that the ‘surface registration only’ box us unchecked.
http://brainsuite.org/quickstart/svreg/

[amysore3]

Thank you. I will try running it again.

[amysore3]

That worked. Thank you!

[Anand Joshi]

Awesome!

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