Hi Mark,

Even if the freesurfer recon-all stream images are 256^3, they are still in the same physical RAS space as the input. No need to worry about that.

I don’t know how FSLview handles orientation / RAS coordinates; I encourage you to use FreeSurfer’s Freeview instead.

Regarding the diffusion data registration: Anastasia Yendiki is a much better person than me to answer that ;-)

Cheers,

/Eugenio

 

 

 

 

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Eugenio,

 

Sorry I have a few questions.  The original images were NOT 256x256x256, they were cropped, but it seems that all of the output images from Freesurfer are 256x256x256.  The simplest thing for me to do is to register my DTI images to the norm.mgz image, but I’m not sure how to do that.  I’m used to working with FSL, and I’m not confident that this will work.  When I tried a simple mri_convert on the norm.mgz file to NIFITI, the orientation of the image in fslview was different from the original image (sagittal image is rotated by 90’, axial and coronal images are swapped and coronal image is rotated by 180’).

 

If you could guide me on how to best re-register my DTI NIFTI images to the norm.mgz image, that would be great.

 

Thanks,

 

Mark

 

 

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Dear Mark,

Just to make sure we’re on the same page: I’ll say that two images are in the same voxel space when they have the same size (in voxels, e.g., 256x256x256) and the same vox2ras matrix - the one that maps voxel coordinates to RAS (physical) coordinates.

The subfield segmentation is indeed in the same RAS coordinates as your native T1, but not in the same voxel space.

One option that you have is to convert your subfield mask to the voxel space of the T1, with the option –rl (“reslice like”) of mri_convert:

For probabilistic masks:

mri_convert  subfield_prob.mgz  subfield_prob_T1voxelSpace.mgz -rl norm.mgz -odt float

For discrete masks or segmentations, you can use a similar command, but with nearest neighbor interpolation:

mri_convert subfield_mask.mgz subfield_mask_T1voxelSpace.mgz -rl norm.mgz -odt float -rt nearest

I hope this helps!

Cheers,

/Eugenio

 

 

 

 

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Hi.  I am just getting my feet wet with running my subjects through the Freesurfer processing stream, so the following question night be a bit trivial (I hope):

 

I have run qvlSegmentHippocampal subfields on one of my subjects, and it completed just fine with what seem to be the appropriate outputs in the subject’s mri folder.  I have another 100 subjects to run, but want to make sure I can accomplish what I would like to on this subject first.  The images which I see are sub-images, i.e. these have fewer voxels compared to the original image, but in the native T1 space resolution (= 1 mm3).  I would now like to register the subfields in the native space (my DTI/NODDI maps are already registered into this space), to obtain mean values within each subfield.  How can I transform these sub-field images back into the native T1 space, or is there a method within Freesurfer to perform the math (e.g. similar to fslmaths)?

 

Thanks,

 

Mark

 

____________________
Mark Wagshul, PhD
Associate Professor
Gruss Magnetic Resonance Research Center
Albert Einstein College of Medicine
Bronx, NY 10461

Ph: 718-430-4011

FAX: 718-430-3399

Email: mark.wagshul@einstein.yu.edu

 

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