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The thalamic nuclei segmentation produces 2 mgz files. One has the FS suffix and other does not. Is the latter without the FS in the native space? If I import and view in freeview, they look same. I want it in native space so I can do some Dice calculations.

My manual segmentations are on a different data set very close to but not necessarily perfectly aligned to the T1 data set used in recon-all. I can use the mri_conver -rl 'reslice like' option but it does not do any registrations does it? It just reslices it in the orientation of the file argument to -rl right. I assume have to manually affine register and propagate the warps if they are not aligned?

Thanks,
manoj



From: Manoj Saranathan
Sent: Tuesday, January 29, 2019 5:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Thalamic segmentation questions
 

The thalamic nuclei segmentation produces 2 mgz files. One has the FS suffix and other does not. Is the latter without the FS in the native space? If I import and view in freeview, they look same. I want it in native space so I can do some Dice calculations.

My manual segmentations are on a different data set very close to but not necessarily perfectly aligned to the T1 data set used in recon-all. I can use the mri_conver -rl 'reslice like' option but it does not do any registrations does it? It just reslices it in the orientation of the file argument to -rl right. I assume have to manually affine register and propagate the warps if they are not aligned?

Thanks,
manoj


From: Manoj Saranathan
Sent: Tuesday, January 29, 2019 5:06 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Thalamic segmentation questions
 

The thalamic registration produces 2 mgz files. One has the FS suffix and other does not. Is the latter without the FS in the native space? If I import and view in freeview, they look same. I want it in native space so I can do some Dice with manual segmentation.

The 'reslice like' option of mri_convert does not do any registrations does it? It just reslices it in the orientation of the file argument to -rl right. I assume have to manually register and propagate the warps if they are not aligned. 

Thanks,
manoj



Manoj Saranathan
Associate Professor, Dept. of Medical Imaging
University of Arizona
Ph: 520-626-6531