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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