External Email - Use Caution
Dear Manoj,
First question: The one without the suffix is defined at higher resolution, on a voxel grid that does not correspond to the standard FS space (where norm.mgz, aseg.mgz, etc. live). The one with the suffix lives on the voxel grid of norm.mgz, aseg.mgz, etc Both of them live in the physical RAS coordinates or the other volumes, that’s why they look similar when you open them of FreeView. But if you zoom in enough, you’ll notice that the one without the suffix has higher resolution.
Second question: Yes, you first need to register, manually or (preferably) automatically, e.g., with BBregister, mri_robust_register, etc. Then, you can run: mri_convert moving.nii.gz deformed.nii.gz -rl nu.mgz -at [YOURTRANSFORMFILE.LTA] -rt nearest
I hope this helps.
/Eugenio
-- Juan Eugenio Iglesias
ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London
Research staff Martinos Center for Biomedical Imaging Massachusetts General Hospital
Research Affiliate Computer Science and Artificial Intelligence Laboratory (CSAIL) Massachusetts Institute of Technology
Lecturer on Radiology Harvard Medical School
From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Manoj Saranathan manojsar@radiology.arizona.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 29 January 2019 at 19:15 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Thalamic segmentation questions
External Email - Use Caution 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