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Dear freesurfer developers Execuse me, I have a problem on subcortical segmentation, about how to output a segmentation which has the same shape with the input MRI image.
The input shape of my MRI image is 197*233*189 and I run <recon-all -i mysubject.nii.gz -s bert -all>. Then Freesurfer output files in different foders such as 'label', 'mri', 'scripts' and so on. In the folder called 'mri', there are files about segmentation. and I convert the 'aseg.mgz' file into .nii.gz file by using <mri_convert> After that I load the .nii.gz file into MATLAB, so that I could compare the result with a mannual segmentation with shape of 197*233*189. However the shape of .nii.gz file converted from aseg.mgz is 256*256*256. But what I expect is the shape with 197*233*189 (the same shape with the imput MRI image). Then what should I do?
Because I run Freesurfer on a server without GUI, the Graphical User Interface, so the freeview will not work. So could you please give me some help on how to solve the problem using command line?
Looking forward to your reply Thank you Mingyuan Liu