External Email - Use Caution
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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
freesurfer-requ...@nmr.mgh.harvard.edu <freesurfer-requ...@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
Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu
To subscribe or unsubscribe via the World Wide Web, visit
https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cwestfall.d%40northeastern.edu%7C4af6aa0f915646edaa6d08d823580354%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637298208206398559&sdata=XZvDl05lUQfQYOJyk8pIQsGfEEUnkH9FZ4YEZbiU3T8%3D&reserved=0
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu
You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu
When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."
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)
----------------------------------------------------------------------
Message: 1
Date: Wed, 8 Jul 2020 11:15:56 -0400
From: "Douglas N. Greve" <dgr...@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-3caa60db8...@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
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cwestfall.d%40northeastern.edu%7C4af6aa0f915646edaa6d08d823580354%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637298208206398559&sdata=XZvDl05lUQfQYOJyk8pIQsGfEEUnkH9FZ4YEZbiU3T8%3D&reserved=0
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20200708%2F77617f14%2Fattachment-0001.html&data=02%7C01%7Cwestfall.d%40northeastern.edu%7C4af6aa0f915646edaa6d08d823580354%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637298208206398559&sdata=%2FdX0criMwj0ep4%2BxS4lx6oCjTdyRoNaHmlEvqPmpkKY%3D&reserved=0
------------------------------
Message: 2
Date: Wed, 8 Jul 2020 15:36:47 +0000
From: Jenna Katherine Blujus <jkblu...@uwm.edu>
Subject: Re: [Freesurfer] Freesurfer Hippocampal Subfield Misalignment
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<dm5pr16mb22940691f0a4b71aa3a95bbbd9...@dm5pr16mb2294.namprd16.prod.outlook.com>
Content-Type: text/plain; charset="us-ascii"
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." <jiglesiasgonza...@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-01a7e8258...@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)
https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jeiglesias.com%2F&data=02%7C01%7Cwestfall.d%40northeastern.edu%7C4af6aa0f915646edaa6d08d823580354%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637298208206398559&sdata=IHOJZd8wF8BXFAhvqYKhJ9sbTXKTDDJQFrck9V0962g%3D&reserved=0
Reply
Forward
Jenna K. Blujus, M.S.
Graduate Student
Neurobiology of Aging Laboratory
University of Wisconsin-Milwaukee
jkblu...@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&data=02%7C01%7Cwestfall.d%40northeastern.edu%7C4af6aa0f915646edaa6d08d823580354%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637298208206398559&sdata=YxtSYbJ2s2api6DOyUPws33VsMvhjbxNGvZbVas%2FMXo%3D&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&data=02%7C01%7Cwestfall.d%40northeastern.edu%7C4af6aa0f915646edaa6d08d823580354%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637298208206398559&sdata=5sOE6mJ%2B7AVKG1zv4Xn3UWCEStABwu9Big24Ul0%2BlnE%3D&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
-------------- next part --------------
An HTML attachment was scrubbed...
URL:
https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20200708%2F9d32f857%2Fattachment-0001.html&data=02%7C01%7Cwestfall.d%40northeastern.edu%7C4af6aa0f915646edaa6d08d823580354%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637298208206398559&sdata=ncW%2F9rIOC6dX74FYLC%2BAC53q2K6O8kkRTe8yqD2WyNU%3D&reserved=0
------------------------------
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7Cwestfall.d%40northeastern.edu%7C4af6aa0f915646edaa6d08d823580354%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C637298208206398559&sdata=XZvDl05lUQfQYOJyk8pIQsGfEEUnkH9FZ4YEZbiU3T8%3D&reserved=0
End of Freesurfer Digest, Vol 197, Issue 16
*******************************************
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
