Different dimensions T1 and ASHS output

[Marianna Pope]

Hi all, 

I'm trying to run ASHS-T1 on T1 scans- they're isotropic 1mm- and have an issue with the dimensions of the output. The segmentation is running fine, but when I try to view the final output (heur) in ITK-Snap I cannot open the output as a segmentation due to different dimensions. I can open it just fine as an overlay-but this is not a great way to examine the quality and you cannot see the different regions. 

The dimensions of the T1 are 256x256x256 and of the ASHS segmentation are 512x512x256. 

I also tried the c3d resample command (as seen on another conversation here) and although it worked, so I can open the ASHS heur output as a segmentation in ITK-Snap, it led to very odd labeling of the regions- like little pixels all mixed up belonging to different regions.

Our T1s are from the Freesurfer pipeline. The original T1s do not work as they are from 7T and are not 1mm isotropic- I tried them both locally and through the ASHS Cloud Segmentation service.

Any ideas on how to solve this issue would be great.

Thanks, 

Marianna