Just wanted to keep as much of the older analysis as possible to save time, because there are many subjects. Where can I start to save some time?
On Wed, Oct 8, 2008 at 10:04 AM, Bruce Fischl fischl@nmr.mgh.harvard.eduwrote:
you need to run it from earlier in the analysis. Is there any reason you don't want to just rerun them from the start? I guess you could just run the aseg stages individually
On Wed, 8 Oct 2008, R D wrote:
Thanks, this works and it recognizes it as a legacy analysis. Some
subjects work fine this way. But for some other subjects, it exits with an error saying aseg.mgz not found.
mris_make_surfaces: could not read segmentation volume /usr/home/rhdesai/From_old_apu_home3/freesurfer.subjects/335/mri/aseg.mgz
The command was
recon-all -subjid ${s} -legacy -autorecon2-pial -autorecon3
(I ran it first with only autorecon3, but it appears that there the inflated surface has different number of nodes than wm/smoothwm surfaces for these subjects for some reason, so it exits with errors. To make the final surfaces again, autorecon2-pial was used.)
thanks, Rutvik
On Mon, Oct 6, 2008 at 7:07 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu
wrote:
hmm, Doug or Nick would be better at this, but try:
touch $SUBJECTS_DIR/$subjects/scripts/recon-all.status
then rerun the subject. Hopefully it will then recognize that it is a legacy analysis.
cheers, Bruce
On Mon, 6 Oct 2008, R D wrote:
Hello,
I have some surfaces created by freesufer in 2006. Spherical registration was not done at that time, which needs to be done. I ran recon-all with -legacy, but it crashed due to disk space problems. Now it doesn't run either with or without -legacy option. When -legacy is specified, it says "this is not a legacy analysis. It once was, but it has been fixed." Without -legacy, it asks for some files such as filled.mgz and aseg.mgz that are not present. Is there a way to 'reset' the analysis (e.g., change a flag somewhere) so it can start over with -legacy? thanks, Rutvik