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!

(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