Hi,
I have just started to look at freesurfer and decided to run each step to try to understand what recon-all does.
Well, after a bit of teething to put the data in the right orientation, we managed to start, but we have a few questions :-)
First of all, our SPGR data is 1.2x1.2x1.2mm^3 and it is acquired coronally. I used mri_convert to get the data resampled to 1x1x1mm^3.
1) When I run the mri_nu_correct command to generate the nu file I get a lot of "Not yet installed" errors. Do I have to generate this file at all? It seems redundant.
2) When I get to the generation of the T1 file and then the brainmask, this last file is not compatible with the original data or the nu data because of a different voxel size. This causes me the first problem with the mri_em_register command, which fails if I use the --mask option with my brainmask image and the nu data, giving me a segmentation fault. If I use the T1 data, then the command runs fine! Is there a reason why we can't use the T1 file instead of the nu or orig file?
3) We also have a problem with the commands that use the $FREESURFER_HOME/average/RB40_talairach_2005-12-30.gca file because it is not in the directory. Can we use the RB_all_2006-02-15.gca file instead? What is the difference between these two files?
4) Has anybody got a feeling on how freesurfer works on brains with MS lesions?
5) Is there any way to find descriptions and info on commands that do not have an official page?
Sorry for the basic questions and I hope to hear from you soon.
Claudia