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Hello FreeSurfer Developers,
I converted a label map (<in volume>), given as Nifti image of type float32 and located in Freesurfer conform space, back to native space using the native T1 in Nifti format and with type int16 as reference <reference volume> . During conversion, the datatype was automatically converted to that of the reference T1. Unfortunately, the labels changed during this conversion, probably because of applying a scaling (slope), which is not saved correctly to the Nifti header. I come to this conclusion, because the maximum label in the output has the maximum value, possible with int16 datatype, i.e. 32767
Here the exact command I used: mri_convert -rt nearest -rl <reference volume> <in volume> <out volume>
The problem of changed labels in the output can be avoided by using the —no change option, which keeps the datatype of the input: mri_convert --nochange -rt nearest -rl <reference volume> <in volume> <out volume>
I used Fresurfer 7.2.0
Best Regards, Benno Gesierich