Jennifer,
I think what you are seeing is due to randomness in some of the
freesurfer algorithms, as dicom files are converted to mgz during the -i
step (which need only be included once) and should itself not account
for differences. You can include the flag -norandomness to recon-all
which fixes
On the freesurfer wiki, it says that recon-all can be done with DICOM
inputs in addition to mgz inputs.
In doing recon-all using DICOM or mgz (created via unpacksdcmdir), the
volumetric values obtained using mris_volume and mris_wm_volume are
different.
For example in one subject,
with DICOM inpu
