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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:
>
> ????????External Email - Use Caution
>
> 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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Message: 2
Date: Wed, 8 Jul 2020 15:36:47 +0000
From: Jenna Katherine Blujus <jkblujus@uwm.edu>
Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <DM5PR16MB22940691F0A4B71AA3A95BBBD9670@DM5PR16MB2294.namprd16.prod.outlook.com>
       
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        External Email - Use Caution       

Hi Eugenio,

Thank you for the tips! This has happened to a number of my subjects but I have finished editing the HC label in their aseg files. How would I copy the HC from aseg.mgz to wmparc.mgz? Can you clarify what you mean by "you still need to fix the surrounding labels"?

Thank you,
Jenna

Message: 3
Date: Tue, 7 Jul 2020 20:53:12 +0000
From: "Iglesias Gonzalez, Juan E." <JIGLESIASGONZALEZ@mgh.harvard.edu>
Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <85489126-5DC1-4464-810B-01A7E825895A@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Dear Jenna,
1.Manually editing aseg.mgz fixes the initialization (super important).
2.Manually editing wmparc.mgz fixes the intensity priors (less important, but still important)
If it?s only 1 subject in a bigger study, I?d probably call it a QC fail and leave it out.
If it?s a single case you?re very interested in, I would edit both aseg.mgz and wmparc.mgz  (you can copy the hippocampus from one into the other, but you still need to fix the surrounding labels).
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
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Reply
Forward




Jenna K. Blujus, M.S.
Graduate Student
Neurobiology of Aging Laboratory
University of Wisconsin-Milwaukee
jkblujus@uwm.edu


________________________________
From: Jenna Katherine Blujus
Sent: Tuesday, July 7, 2020 3:23 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Freesurfer Hippocampal Subfield Misalignment

Hi Experts,

I ran the hippocampal subfield segmentation protocol using a T2 image that does not cover the whole brain in Freesurfer v6.0. I noticed that the alignment of the ?h.hippoSfLabels-T2.v10 output to the anatomical boundaries of the hippocampus in some of my subjects is off. For example, the left hippocampal subfield segmentation in one subject is superior and medial to the hippocampus. I checked the aseg.presurf file (since I am using v6.0) and indeed the whole left hippocampus is off.

I saw in a previous thread (https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg23942.html&amp;data=02%7C01%7Cwestfall.d%40northeastern.edu%7C4af6aa0f915646edaa6d08d823580354%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637298208206398559&amp;sdata=YxtSYbJ2s2api6DOyUPws33VsMvhjbxNGvZbVas%2FMXo%3D&amp;reserved=0) that it was suggested to edit the hippocampal segmentation within the aseg file to potentially improve alignment of the subfield segmentation. However, a more recent post (https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg54543.html&amp;data=02%7C01%7Cwestfall.d%40northeastern.edu%7C4af6aa0f915646edaa6d08d823580354%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637298208206398559&amp;sdata=5sOE6mJ%2B7AVKG1zv4Xn3UWCEStABwu9Big24Ul0%2BlnE%3D&amp;reserved=0) stated that both the wmparc.mgz and aseg.mgz files would need to be edited and that this was not recommended. Do you have any recommendations on how to move forward? I did edit the hippocampal segmentation within the aseg.presurf file in one of my subjects and reran the subfield segmentation command which substantially improved the output (i.e., it overlays on the hippocampus after correction). Would you suggest that I continue with editing the aseg using previously published protocols on segmenting the hippocampus by hand or would you recommend something else?

Thanks in advance!
Jenna

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End of Freesurfer Digest, Vol 197, Issue 16
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