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

 

http://www.jeiglesias.com 

 

 

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