no, it shouldn't, but make a backup of your data before running it for sure On Mon, 3 Oct 2011, Michelle Umali wrote:

Hi Bruce, Will this undo my wm and pial edits?

Thanks. Michelle

On Sat, Oct 1, 2011 at 3:37 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: try running

  recon-all  -s subject -make all

and leave the -dontrun off. It should bring everything up to date

Bruce

On Sat, 1 Oct 2011, Michelle Umali wrote:

  Dear Freesurfers,
  I'm still getting a MRISripZeros() and MRIScopyMRI
  Surf/src mismatch error
  when running fieldsign-sess.  You suggested that this
  problem was due to the
  surfaces being out of synch.  When I ran  recon-all -s
  subject -make all
  -dontrun, I saw that several steps had not run.  The data
  looked alright and
  the number of vertices matched when I ran -vno-check.

  The mismatch error is still occurring, and I don't know
  how to proceed.

  Please suggest steps that I should take.

  Thanks.
  Michelle

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

Hi Doug, I've attached the output from running fieldsign-sess.

Thanks for all your help. Michelle

On Mon, Oct 3, 2011 at 12:59 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:

Michelle, before you do that, can you run the offending program with -debug and send me the (copious) terminal output? Your anat should not have to be re-run.

doug

Michelle Umali wrote:

...

Hi Bruce, Will this undo my wm and pial edits?

Thanks. Michelle

On Sat, Oct 1, 2011 at 3:37 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu<mailto: fischl@nmr.mgh.**harvard.edu fischl@nmr.mgh.harvard.edu>> wrote:

try running

recon-all -s subject -make all

and leave the -dontrun off. It should bring everything up to date

Bruce

On Sat, 1 Oct 2011, Michelle Umali wrote:

   Dear Freesurfers,
   I'm still getting a MRISripZeros() and MRIScopyMRI Surf/src
   mismatch error
   when running fieldsign-sess.  You suggested that this problem
   was due to the
   surfaces being out of synch.  When I ran  recon-all -s subject
   -make all
   -dontrun, I saw that several steps had not run.  The data
   looked alright and
   the number of vertices matched when I ran -vno-check.

   The mismatch error is still occurring, and I don't know how to
   proceed.

   Please suggest steps that I should take.

   Thanks.
   Michelle

The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.

------------------------------**------------------------------**

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

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