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Hi Douglas,

It looks like the previous processing used 'recon-all -all -norm2-b 20 -norm2-n 5 -no-isrunning', this was from 2012 so I referenced the recon-all.log for this info. According to the log the original data was 0.9 mm size and then confirmed to 1 mm size.

My hypotheses are specific to thickness (whole brain and ROIs based on the Yeo 7-network parcellation). So, basically I am trying to determine if I should convert to the -hires pipeline to take advantage of the submillimeter pipeline to get a more accurate representation of the cortical thickness. Or if using the previously processed 5.3 1mm conformed scan is fine. The cost/benefit really just alludes to the amount of time it will take to QC ~600 scans if I re-run in 7.1. If there is a huge advantage of switching to the -hires pipeline for cortical thickness measures then that is something I can move forward with.

Thank you

________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of freesurfer-request@nmr.mgh.harvard.edu freesurfer-request@nmr.mgh.harvard.edu Sent: Wednesday, July 8, 2020 12:00 PM To: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 197, Issue 16

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Today's Topics:

1. Re: Updating submillimeter data from 5.3 to 7.1 with -hires? (Douglas N. Greve) 2. Re: Freesurfer Hippocampal Subfield Misalignment (Jenna Katherine Blujus)

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Message: 1 Date: Wed, 8 Jul 2020 11:15:56 -0400 From: "Douglas N. Greve" dgreve@mgh.harvard.edu Subject: Re: [Freesurfer] Updating submillimeter data from 5.3 to 7.1 with -hires? To: freesurfer@nmr.mgh.harvard.edu Message-ID: 8f7a8545-49e3-4a51-575f-3caa60db80e0@mgh.harvard.edu Content-Type: text/plain; charset="windows-1252"

How did you do the 5.3 analysis? in 1mm/conformed space? And what are you hoping to accomplish by running it in v7.1 with -hires?

On 7/8/2020 10:46 AM, Daniel Westfall wrote:

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Hi Everyone,

I have access to two large datasets (~600 scans) that were previously collected, processed, QC'd, and manually edited where necessary in Freesurfer 5.3 with recon-all. However, the data is 0.9 mm isotropic collected in a 3T scanner. I am attempting to decide if the cost/benefit is worth switching the pipeline to Freesurfer 7.1 with the -hires flag? The processing time is not the issue, mainly redoing QC and manual corrections is the concern.

1. To publish 0.9 isotropic is it necessary to use the -hires pipeline?
2. Is it appropriate to apply corrections calculated in the Freesurfer 5.3 standard pipeline to Freesurfer 7.1 -hires (and double check). Or do the manual QCs need to be completed from the ground up?
3. With the other 2 questions in mind, is it better to just go ahead and convert the data to Freesurfer 7.1 -hires?

Thank you, Daniel

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