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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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