It will do it's best, how well depends on the size of the resection. FS it assuming that the input is an intact (though perhaps diseased) brain. Away from the resection, it will probably do ok. Near the resection, it will probably fail, but you can probably fix it manually.

doug

octavian lie wrote:

Thank you, Doug,

One unrelated question: can I run freesurfer on postoperative T1 MPRAGE sequences, where the relationship of the gray to white matter (out-in) is disrupted at the site of resection? If so, can you share any good advice on parameters to adjust? Thank you,

Octavian.

On Mon, Feb 27, 2012 at 10:14 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

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>
    <mailto: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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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422
<tel:617-726-7422>

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