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_borderThe 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.