Hi Kaley,

if you scroll down the log file you should find something like new invocation of recon-all with the correct time stamp and v6 text. The old log is kept and the new one is appended.

I am also not sure it is OK to re-run the base with 6.0. It could be that this looks OK in single cases and fails in others. The reason is that in 6.0 the position of the base image could be (slightly?) different than 5.3. So your edits, e.g. control points, would not be at the right anatomical spot. This is not a problem when re-running cross runs.

You should check if the norm.mgz is at the same location in 5.3 base and the 6.0 base. Also I would re-run the long from scratch. (probably there are no edits in long anyway)? Optimally re-run bases also from scratch, could be you don’t need any edits because 6.0 is awesome (maybe).

Best, Martin

On 25. Jun 2018, at 18:41, KALEY E ELLIS keedwards2@wisc.edu wrote:

Hello FreeSurfer experts,

I previously emailed regarding processing longitudinal data in v6.0 using bases with manual edits that had been completed in v5.3. I went ahead and ran recon-all -all on the base of a subject (originally generated in v5.3) in v6.0, but it looks like the header of the recon-all.log still indicates v5.3. Looking at the /stats output, all files indicate v6.0. Below is the head of the log from running recon-all -all on this subject. Is this what you would expect if you ran recon-all -all on a subject_base in v6.0 that was generated in v5.3? If so, is this okay?

Recon-all log: setenv SUBJECTS_DIR /study1/nccam3/data/mri/freesurfer_v6/subjects FREESURFER_HOME /apps/x86_64_sci7/freesurfer-latest Actual FREESURFER_HOME /apps/freesurfer-5.3.0/x86_64_sci6 build-stamp.txt: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Linux c139.keck.waisman.wisc.edu http://c139.keck.waisman.wisc.edu/ 3.10.0-514.6.1.el7.x86_64 #1 SMP Tue Jan 17 11:12:41 CST 2017 x86_64 x86_64 x86_64 GNU/Linux

Thank you! Kaley Ellis

Associate Research Specialist Center for Healthy Minds Waisman Center for Brain Imaging and Behavior University of Wisconsin-Madison _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer