External Email - Use Caution Thank you for clarifying.
One big problem was the error in the make file and I think I'm still somewhat suffering from that even though I've replaced the file. The short answer is that if I run recon-all -make all on the same subject twice it will re-run recon-all on that second occasion...I don't know why make isn't detecting that I had just run the command! (There must be an error - it's just strange that it happens on approx 5% of all my scans but in no discernable way!) The main thing I'm trying to do is move from 5.3 to 6.0 processing while keeping the quality control edits that we've spent a lot of time on. We have quantitative R1 maps which means recon-all isn't tuned for the maps and we've done a lot of rounds of manual edits that I don't want to lose! So if anyone knows exactly which files should be copied across to a new folder from our 5.3 backup that will allow 6.0 to run recon-all but still put the surfaces in around about the same place that would be great :) I don't think this will be fixed with 6.0.1! Thank you for clarifying :) Kx On Tue, 11 Dec 2018 at 18:36, Hoopes, Andrew <ahoo...@mgh.harvard.edu> wrote: > Hi Kirstie, sorry for the lack of documentation – there’s practically no > difference between 6.0.0 and 6.0.1. The only update in 6.0.1 is the ability > to point to an external license using the FS_LICENSE environment variable. > What kind of issues are you having with 6.0.0? > > > > Best, > > Andrew > > > > > > *From: *<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Kirstie > Whitaker <kw...@cam.ac.uk> > *Reply-To: *FS Help <freesurfer@nmr.mgh.harvard.edu> > *Date: *Tuesday, December 11, 2018 at 4:28 AM > *To: *FS Help <freesurfer@nmr.mgh.harvard.edu> > *Subject: *[Freesurfer] Version 6.0.0 or 6.0.1? > > > > * External Email - Use Caution * > > Hi Freesurfer team, > > > > On the download website version 6.0.0 is linked: > https://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall > > > > But on this list there has been discussion of version 6.0.1 which can be > downloaded from > https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1 > > > > What's the recommended version to use? > > > > I've been using 6.0.0 but with an updated make file following the > instructions in this email: > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2018-April/056644.html > <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2018-April/056644.html> > > > > Is the makefile updated in 6.0.1? Are there any other differences? I'm > having a lot of difficulty getting recon-all to run reliably with 6.0.0 > (some subjects are fine, others not!) and I'm wondering if that's because > I'm supposed to be using 6.0.1? > > > > Thank you for your help! > > Kirstie > > > > -- > > Kirstie Whitaker, PhD > > > > Research Fellow, Alan Turing Institute > > Research Associate, University of Cambridge > > > *Mailing Address* > Brain Mapping Unit > Department of Psychiatry > Sir William Hardy Building > Downing Street > Cambridge CB2 3EB > > *Phone: *+44 7583 535 307 > > *Website:* https://whitakerlab.github.io > > *Twitter:* @kirstie_j <https://twitter.com/kirstie_j> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Kirstie Whitaker, PhD Research Fellow, Alan Turing Institute Research Associate, University of Cambridge *Mailing Address* Brain Mapping Unit Department of Psychiatry Sir William Hardy Building Downing Street Cambridge CB2 3EB *Phone: *+44 7583 535 307 *Website:* https://whitakerlab.github.io *Twitter:* @kirstie_j <https://twitter.com/kirstie_j>
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