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 :)

On Tue, 11 Dec 2018 at 18:36, Hoopes, Andrew <AHOOPES@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-bounces@nmr.mgh.harvard.edu> on behalf of Kirstie Whitaker <kw401@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

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

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