Hi,
We're having trouble using mri_convert as wrapped within mne_flash_bem to create the bem surfaces from our FLASH volumes. The script runs but the inner_skull and outer_skull surfaces that it outputs seem to be rotated, for example if we display the surfaces on the T1 coronal, we see what looks like the sagittal inner_skull surface.
I'm guessing this is some kind of registration problem. I noticed that we are getting a warning at one point in the process when the flash is being registered with the MPRAGE, which I've pasted below.
I am wondering if this might have something to do with the switch to version 5.0.0. For this dataset, we ran the reconstruction and all the subsequent processing on v5.0.0. However, I have gotten the exact same error (rotated inner and outer skull surfaces) when I accidentally ran mne_flash_bem in v5.0 with a previous dataset that was reconstructed in v4.5.0. When I re-ran mne_flash_bem in v4.5.0 the surfaces came out correctly for the previous dataset. But I was reluctant to try this with my new dataset since ideally we'd like to be able to switch completely over to v5.0.0.
Thanks, Ellen
--------------- [kerryave:test] (nmr-std-env) which mri_convert /usr/local/freesurfer/stable5/bin/mri_convert
setenv SUBJECTS_DIR /cluster/kuperberg/SemPrMM/MRI/structurals/subjects/
selected output from mne_flash_bem containing the warning:
/autofs/cluster/kuperberg/SemPrMM/MRI/structurals/subjects/ya1/mri/flash/parameter_maps mri_convert ./fsl_rigid_register.7595/outvol.fsl_rigid_register.nii flash5_reg.mgz mri_convert ./fsl_rigid_register.7595/outvol.fsl_rigid_register.nii flash5_reg.mgz $Id: mri_convert.c,v 1.166.2.4 2010/09/20 17:29:33 nicks Exp $ reading from ./fsl_rigid_register.7595/outvol.fsl_rigid_register.nii... TR=1000.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 5.63785e-17) j_ras = (0, 3.67872e-08, -1) k_ras = (0, 1, -1.5134e-08) writing to flash5_reg.mgz... /autofs/cluster/kuperberg/SemPrMM/MRI/structurals/subjects/ya1/mri/flash/parameter_maps mri_copy_params flash5_reg.mgz flash5.mgz flash5_reg.mgz WARNING: volume sizes are different in_vol : 256, 256, 256 temp_vol : 256, 256, 176 Cleaning up