Hi Fleur
FreeSurfer provides tools that take an approximately isotropic T1-weighted input volume with voxel dimensions around .7-1.5mm and reconstructs models of most macroscopically visible structures. There are other algorithms around that take a set of orthogonal anisotropic acquisitions and estimate an isotropic one using some type of optimality criterion (e.g. max likelihood), but we don't do that directly. If you find one and generate something isotropic you can give that to FreeSurfer
Cheers Bruce
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Fleur GAUDFERNAU Sent: Thursday, January 14, 2021 11:48 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] 3D reconstruction of brain MRI
External Email - Use Caution Dear all,
I have just started using Freesurfer. I have an issue when trying to perform volumetric reconstruction from MRI files. Sorry if my question is naive. Data description: for each subject, 3 DICOM folders, each one containing 2D MRI slices along one axis. (I also have them in nifti format.) Goal: volume reconstruction to obtain a single 3D volume of the subject brain. What I did: recon-all -all -i path/to/mri_axial.nii -i path/to/mri_coronal.nii -i path/to/mri_sagittal.nii -s subject Error message: inputs have mismatched dimensions! 512 x 512 x 50 / 512 x 512 x 14 / 512 x 512 x 22
(The mismatched dimensions being totally normal, considering the number of slices along each axis does not have to be the same.) However, if I use recon-all on only 1 of the 3 files, it works perfectly. I think I misunderstood the use of recon-all: it does not really perform volume reconstruction, i.e. transforming 3 series of 2D slices into a single 3D volume? If not, could someone tell me which software can perform this task? (So far the only one I know, NiftyMIC, is dedicated to fetal brain MRIs - but the task remains the same).
Thanks in advance, Fleur Gaudfernau