Hi Dan

it depends what your goal is. I think you could get a decent quality recon with an hour two of work, but I'm not sure I would trust thickness estimates from a scan of that quality cheers Bruce

On Fri, 12 May 2017, Weisholtz, Daniel S.,M.D. wrote:

Dear Bruce, Thank you for your help. I was able to view the defects. It does seem to be an extensive defect—possibly retained dura? I’m not sure of any other way to fix it. Do you think that the poor quality of the source image makes it impossible to generate any kind of surface using free surfer?

Best, Dan

  On May 11, 2017, at 12:00 PM,
  freesurfer-request@nmr.mgh.harvard.edu wrote:

Message: 9 Date: Thu, 11 May 2017 11:38:42 -0400 (EDT) From: Bruce Fischl fischl@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 159, Issue 12 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Message-ID: alpine.LRH.2.20.1705111132360.28473@door.nmr.mgh.harvard.edu Content-Type: text/plain; charset="iso-8859-7"

Hi Dan

that's a pretty low-contrast, severely motion-corrupted scan. We did pretty  well given the input I think. To visualize the defects you can cd into the  subject's mri dir and run:

fv -v brain.mgz  wm.mgz:colormap=heat -f \ ../surf/lh.orig.nofix:overlay=../surf/lh.defect_labels:overlay_threshold=1, 100 \ ../surf/lh.inflated.nofix:overlay=../surf/lh.defect_labels:overlay_threshol d=1,100

then click the "use overlay color" button for the lh.orig.nofix surface.  You can also change the display paramters in "configure overlay" to find a  specific defect by setting the min/max to a narrow range around the one you  are interested in (this will put it in the middle of the range and color it  orange)

cheers Bruce

On Thu, 11 May 2017, Weisholtz, Daniel S.,M.D. wrote:

  Dear Bruce,
  Thank you so much for your suggestions. Unfortunately, I
  was not able to
  open lh.defect_labels in freeview. ?When I try, Freeview
  crashes. ?There are
  no rh surfaces in the surf folder, so I presume this means
  the problem
  occurred in the left hemisphere. I was able to view the
  inflated.nofix and
  orig.nofix but I?m still not exactly sure what the problem
  is, and I would
  be grateful if you could take a look at the subject
  folder. I will upload it
  to the ftp site. It is called s117.

  Thank you!

  Best,
  Dan

       On May 10, 2017, at 10:43 AM,
       freesurfer-request@nmr.mgh.harvard.edu wrote:

  Message: 9
  Date: Tue, 9 May 2017 15:54:12 -0400 (EDT)
  From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
  Subject: Re: [Freesurfer] recon-all freezes while
  CORRECTING DEFECT 60
  To: Freesurfer support list
  <freesurfer@nmr.mgh.harvard.edu>
  Message-ID:
  <alpine.LRH.2.20.1705091553090.16219@door.nmr.mgh.harvard.edu>
  Content-Type: text/plain; charset="iso-8859-15"

  Hi Daniel

  you can load the ?h.defect_labels as an overlay on either
  the?
  inflated.nofix or orig.nofix surface and use it to find
  the location
  of?
  that defect. Usually this means something big is wrong -
  it should be?
  obvious looking at the inflated.nofix I would think. If
  you can't find
  it,?
  upload the subject to our ftp site and I'll take a look
  Bruce



  On Tue, 9 May 2017, Weisholtz, Daniel S.,M.D. wrote:

       Hello Freesurfer Developers,
       I am trying to run recon-all -all and the procedure
  is
       freezing while trying
       to correct what appears to be a large defect
       (vertices=36706). The source T1
       image is not great quality due to rippling artifact,
  but I
       have inspected
       brainmask.mgz, wm.mgz, and aseg.mgz and I cannot
  identify
       a large defect.
       The dura was not completely removed, and I tried
  improving
       this by using
       various watershed thresholds as well as using gcut. I
  also
       tried manually
       removing the remaining dura, but none of this was
  helpful.
       ?I also tried
       using -T2FLAIR, but this did not seem helpful
  either.?

       I am attaching the recon-all.log. This does not
  include
       the edits I made to
       brainmask.mgz. That was done on a separate attempt.
  This
       does include the
       -T2FLAIR, as you can see in the recon-all.log file.

       1) FreeSurfer
       version:?freesurfer-Darwin-lion-stable-pub-v5.3.0
       2) Platform: OS X Yosemite 10.10.5
       3) recon-all.log attached


       I very much appreciate any assistance you can
  provide.
       Happy to send any of
       the data if it would be helpful.

       Sincerely,
       Dan Weisholtz