Dear Christian, Both options are OK, as long as you report on your paper how you obtained your results. Rerunning everything with 6.0 has the advantage that the results are easier to reproduce but, if you’ve already QCed large amounts of data processed with 5.3, not rerunning in understandable and, in my opinion, a perfectly valid option. Cheers, /Eugenio
Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/
On 12 Dec 2016, at 09:39, Christian Krog Tamnes <c.k.tamnes@psykologi.uio.nomailto:c.k.tamnes@psykologi.uio.no> wrote:
Hi again Eugenio,
Sorry for the picky follow-up question regarding the longitudinal hippocampal subfields processing, but do you suggest that when the official version 6 comes out, we rerun everything (including the standard FS long processing) or would it be ok to just rerun the hippocampal part (on scan processed with 5.3)?
For us, the first option might necessitate a new round of QC, which would be very time consuming for a large longitudinal dataset.
regards, Christian
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Christian Krog Tamnes <c.k.tamnes@psykologi.uio.nomailto:c.k.tamnes@psykologi.uio.no> Sent: 30 November 2016 15:57 To: Freesurfer support list Subject: Re: [Freesurfer] longHippoSubfields
We will get the beta for now then. Thanks Eugenio!
regards, Christian
________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> Sent: 30 November 2016 15:46 To: Freesurfer support list Subject: Re: [Freesurfer] longHippoSubfields
Hi Christian, I believe you were unlucky enough to download the dev version during the days that this module was broken. I would strongly suggest that you either download the beta version of 6.0 or wait until the official release of this version, which should be happening soon. Cheers, /Eugenio
Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.comhttp://www.jeiglesias.com/ http://cmictig.cs.ucl.ac.uk/
On 30 Nov 2016, at 14:26, Christian Krog Tamnes <c.k.tamnes@psykologi.uio.nomailto:c.k.tamnes@psykologi.uio.no> wrote:
Dear Juan and FreeSurfer team,
We are trying to test out the longitudinal hippocampus subfield segmentation pipeline, but can’t seem to run/find the script (longHippoSubfieldsT1.sh). We have done the standard processing in v5.3 and have the following dev version: freesurfer-Linux-centos6_x86_64-dev-20160914-bdac8bc. Sorry for the basic question, but do we simply need a later dev build?
Best regards, Christian _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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