Dear FreeSurfer experts,

There are some image processing tools from the MINC toolkit I have been testing out on some FreeSurfer files, that all require the image to be in MINC format. I am able to convert the *.mgz files to *.mgz, but I have been unable to perform the conversion in the other direction (MNC -> MGZ), as forewarned in the mri_convert help file.

The error I get when attempting the conversion is "Not a netCDF file." (in full below)

Would anyone have suggestions for a workaround to get the modified MNC file back into MGZ FreeSurfer format and in the correct orientation?

Thank you for your time,

evl2001@jake:~/Desktop$ mri_convert -it minc head.mnc -ot mgz head.mgz

mri_convert -it minc head.mnc -ot mgz head.mgz 

$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $

reading from head.mnc...

ncopen: filename "/dir/head.mnc": Not a netCDF file

miopen: MINC package entry point

Error opening /dir/head.mnc

mincRead(): error reading volume from file /dir/head.mnc