Hi Erik

yes, those numbers are always estimated from the data unless you specify otherwise. And please remember to cc the list so that others can answer/see the answers in case they are interested in the same type of issue.

cheers Bruce

On Wed, 12 Feb 2014, Erik Lindberg wrote:

OK Thanks

• I suspected that. What made me a bit confused what that I went in and had

a look at the recon-all log file. And numbers from this file was different for different subjects at the same batch.

two subjects setting MIN_GRAY_AT_WHITE_BORDER to 67.9 (was 70) setting MAX_BORDER_WHITE to 107.3 (was 105) setting MIN_BORDER_WHITE to 79.0 (was 85) setting MAX_CSF to 56.7 (was 40) setting MAX_GRAY to 94.7 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 73.4 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 45.6 (was 40)

setting MIN_GRAY_AT_WHITE_BORDER to 71.5 (was 70) setting MAX_BORDER_WHITE to 108.1 (was 105) setting MIN_BORDER_WHITE to 82.0 (was 85) setting MAX_CSF to 61.0 (was 40) setting MAX_GRAY to 95.9 (was 95) setting MAX_GRAY_AT_CSF_BORDER to 76.7 (was 75) setting MIN_GRAY_AT_CSF_BORDER to 50.5 (was 40)

On Wed, Feb 12, 2014 at 2:31 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Erik

  is there a reason not to do it for the whole group? I guess if
  the one subject you uploaded had significant motion (which
  caused the blurryness) then it might be the case that it needs
  separate parameters. In general though it's good to hold this
  kind of thing constant as it will definitely bias you to having
  greater thickness. Try it on some of the other subjects and see
  if the surfaces are at least as accurate as without, and if so
  do it uniformly

  cheers
  Bruce

  On Wed, 12 Feb 2014, Erik Lindberg wrote:

        Dear Freesufers,
        I am trying to understand what happens if I go in
        and edit the numbers for
        -min_border_white  -min_gray_at_white_border  in a
        single subjects in a
        large group.

        Generally we aim to set everything identical when
        running a group of
        subjects in FS.  I went in and had a look at the
        recon-all log file and I
        can see that the numbers for -min_border_white
         -min_gray_at_white_border  different for different
        subjects.

        Thus - what will happened if I go and edit the
        -min_border_white
         -min_gray_at_white_border numbers for  a single
        subjects in a large bach
        .... will I still be able compare cortical thickness
        with subjects that I
        did not edit?

        Or is it necessary to keep the number identical for
        all subjects when
        editing the min_border_white
         -min_gray_at_white_border 

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