Dear FreeSurfers,
I have been processing a group of subjects, firstly using Freesurfer V5.1.0 or V5.3.0, then V5.3.0 after making some editing on WM and pial surface, using the <recon-all> command, without the <-no-isrunning> option.
I have below message at the beginning of the recon-all after editing:
INFO: FreeSurfer build stamps do not match
Subject Stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0
Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
INFO: SUBJECTS_DIR is /home/zixuan/Work/FS/RE_EDIT
Actual
FREESURFER_HOME /usr/share/freesurfer
-rw-r--r--. 1
zixuan users 957929 Dec 20 16:52 /home/zixuan/Work/FS/RE_EDIT/D3358/scripts/recon-all.log
Linux NIL.Melbourne 2.6.32-358.23.2.el6.x86_64 #1 SMP Wed Oct 16 18:37:12 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
INFO: current FREESURFER_HOME does not match that of previous processing.
Current: /usr/share/freesurfer
Previous: /share/apps/freesurfer/5.3.0
#--------------------------------------------
#@#
Mask BFS Wed Apr 2 17:11:43 EST 2014
/home/zixuan/Work/FS/RE_EDIT/D3358/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
However all subjects have been finished without error, which is not the case as what you have discussed in the mail archive.
recon-all -s <subjID> finished without error at Mon Mar 24 03:38:36 EST 2014
The problem is, I found the cortical thickness in regions that I didn’t edit not consistent before and after re-processing, with about 2-10% differences. For some subjects, I have only edited minor pial surface (e.g. entorhinal cortex only),
yet it seems that all values have been affected.
My question is
1), shall I consider my results valid, despite of the “dismatch” thing? Is there any other factors other than editing will affect the final value?
2), I have about 30 subjects processed with V5.1.0, (atrophic brain +++ with heavy editing – extreme time consuming), yet I still found some pial to edit this time, and processed them with V5.3.0. Shall I consider the values valid provided
the message “without error”, despite the different FreeSurfer versions?
Apologies for cross posting, I didn’t found any cases similar to mine in the mail archive.
Many thanks and kind regards,
Zixuan
--
Zixuan YANG
Ph.D candidate
Centre for Healthy Brain Ageing (CHeBA)
School of Psychiatry, UNSW Medicine
NPI, Euroa Centre, Barker Street, Randwick
NSW 2031 AUSTRALIA
T: +61 (2)
9385 0427
______________
Mailing address:
University of New South Wales
Randwick Campus, Building R1f
22-32 King Street, Randwick NSW 2031
Australia