Octavian, recon-all does not use --save_distance by default. You can have it add --save_distance to the mris_volmask command line using the "expert options". Run recon-all with -help to get more info. doug
octavian lie wrote:
Dear all,
to follow up on my prior message below, I must say that I called the recon-all -autorecon-all command remotely through a automatic matlab routine in which freesurfer is one leg, with the command nohup. For some reason, when doing this, the step mris_volmask was run without the option --save_distance hence no ?h.dpial.ribbon.mgz fille was created. To fix this, I manually entered the following command in the linux terminal: mris_volmask--label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance SUB002, which created the output files needed.
Now, do you know why running recon-all -all remotely would exclude the option --save_distance for mris_volmask. Is there any way to fix this in the freesurfer itself, so that I do not have to change the matlab code?
Thank you, also see my message below. Octavian. On Sat, Feb 25, 2012 at 6:46 PM, octavian lie <octavian.lie@gmail.com mailto:octavian.lie@gmail.com> wrote:
Dear Bruce & FreeSurfers, I ran freesurfer (86x64_64 centos version 5.1.0) on my new linux box (Ubuntu 11.10 64 bit, NVIDIA GEforce GTX 580, no CUDA for now) using recon-all -all; it went on for 8 hours, I got the message (Recon complete without errors) in the output.txt file in my subject directory. However, when trying to use mri_convert or tkmedit to see the lh.dpial.ribbon.mgz, there was an error (could not open file). I searched for the file in all the /mri folder and the whole file system on my box, could not find it. I found lh.ribbon.mgz, rh.ribbon.mgz, and ribbon.mgz, but not the dpial.ribbon.mgz file or any other ?.ribbon.mgz variety. I appreciate your suggestions. Octavian.
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