Thanks for your responses!

Sorry for the naive question, but I'm wondering which commands I'd use to re-process all the data from 5.3. Can I run recon-all -all, and it will go through all the steps that it would if I ran it from the start? Or would it skip certain steps if it finds certain files existing already. I'm pretty sure the former is true, but just wanted to confirm.

Thanks again!

Batool

From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.iglesias@ucl.ac.uk]
Sent: Thursday, January 26, 2017 11:01 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] freesurfer 6.0 with some of the analyses

Dear Batool,

Sorry for missing your message.

And dear Adam:

Thanks for covering me! That’s exactly my standard answer to that question ;-)

Juan Eugenio Iglesias

ERC Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/

On 26 Jan 2017, at 15:55, Adam Martersteck <acmarter@gmail.com> wrote:

I believe Dr. Iglesias previous responses on this exact question have been, "yes it's possible, but your results may be harder to reproduce"

e.g. If someone wanted to replicate your study they may have a harder time having to download 2 different versions of freesurfer to achieve comparable results with your study.

I think the general consensus is "how many subjects do you have?" -- if it's less than 50, you may want to just rerun v6 on your subjects as it should preserve the edits -- but it's recommended you still open them up and double check.

-Adam

On Thu, Jan 26, 2017 at 8:37 AM Rizvi, Batool <br2499@cumc.columbia.edu> wrote:

Hi,

Can anyone comment on my question below?

I think the FAQ page mentions that the same version should be used to process all cases within a dataset, but my question is whether I can have the same dataset used for two different versions for separate analyses? This is considering that I've already

processed all my data with 5.3, but am interested in getting hippocampal subfields through 6.0.

Thanks so much!

Batool

From: Rizvi, Batool

Sent: Wednesday, January 25, 2017 12:54 PM

To: freesurfer@nmr.mgh.harvard.edu

Subject: freesurfer 6.0 with some of the analyses

Hi,

I'm wondering if it's okay to run some of the analyses within one study on v.5.3 and the other hippocampal analyses on 6.0?

Or do you recommend us starting over for the analyses we've already done in 5.3 for that study?

Thank you!

Batool

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