Re: [Freesurfer] WM surface ignoring wm.mgz edits - Freesurfer

7 Jul 2017

      Hi Bruce,
We are using the "voxel-edit" tool and "recon editing" is selected.
Thank you,
Kaley
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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: Friday, July 7, 2017 11:00 AM
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Subject: Freesurfer Digest, Vol 161, Issue 16
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Message: 1
Date: Fri, 7 Jul 2017 10:42:23 -0400 (EDT)
From: Bruce Fischl fischl@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] WM surface ignoring wm.mgz edits
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Message-ID:
        alpine.LRH.2.20.1707071041590.9265@door.nmr.mgh.harvard.edu
Content-Type: text/plain; charset="iso-8859-15"
Hi Kaley
are you using the "recon edit" tool in freeview?
cheers
Bruce
On Fri, 7 Jul 2017, KALEY E
ELLIS wrote:
...
Dear?FreeSurfer?Developers,
We are attempting to make manual white matter edits to our subjects. The
edits are saving; however, after running with recon-all, the WM surface does
not appear to be taking into account our edits made to wm.mgz. Below is
additional information, and I have attached our recon-all.log. We are only
editing the cross because our dataset is comprised of single timepoints.
We are using?FreeSurfer?v5.3 and our operating system is OS X El?Capitan
version 10.11.6.
Command to open and edit WM:?
freeview -v mri/T1.mgz mri/brainmask.mgz mri/wm.mgz:opacity=0.5 -f
surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red
surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=red
Command to submit edits:
recon-all -autorecon2-wm -autorecon3 -subjid?
Recon-all log (see attached)
Thank you,
Kaley?Ellis
Associate Research Specialist
Center for?Healthy Minds
Waisman Center for Brain Imaging and Behavior
University of Wisconsin-Madison
------------------------------
Message: 2
Date: Fri, 7 Jul 2017 14:51:53 +0000
From: "Boyd, Emma" EBOYD2@mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all on newborn
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Message-ID:
        MWHPR04MB0558426F0D765C043BEDCABAD1AA0@MWHPR04MB0558.namprd04.prod.outlook.com
Content-Type: text/plain; charset="us-ascii"
Hi Sarbani,
Please see this paper for more information:
https://www.ncbi.nlm.nih.gov/pubmed/25741260
A FreeSurfer-compliant consistent manual segmentation of ...https://www.ncbi.nlm.nih.gov/pubmed/25741260
www.ncbi.nlm.nih.gov
1. Front Hum Neurosci. 2015 Feb 18;9:21. doi: 10.3389/fnhum.2015.00021. eCollection 2015. A FreeSurfer-compliant consistent manual segmentation of infant ...
Emma
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Das S. Sarbani.Das@soton.ac.uk
Sent: Friday, July 7, 2017 4:58:39 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all on newborn
Is there any paper that you can share that can explain why recon-all is not suitable for neonates brain apart from atlas.
Sarbani
-----Original Message-----
From: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Lilla Zollei
Sent: 06 July 2017 21:43
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] recon-all on newborn
It is not only the atlas but the tools that are different.
Lilla
On Wed, 5 Jul 2017, Das S. wrote:
...
Dear Lilla,
In that case you mean if I have my own atlas specific to neonates then I can follow these steps of auto recon.
If you give me little more details will be easy for me to understand the gap.
many thanks
Sarbani
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu
[freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei
[lzollei@nmr.mgh.harvard.edu]
Sent: 05 July 2017 22:32
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all on newborn
We use a similar pipeline but with different atlases and processing
steps for the newborns.
Lilla
On Wed, 5 Jul 2017, Das S. wrote:
...
Thanks for the reply. If you let me know, among the below list of steps of current recon-all, currently which is not suitable to perform on neonates MRI image, will really appreciate.
Autorecon Processing Stages:
   Motion Correction and Conform
   NU (Non-Uniform intensity normalization)
   Talairach transform computation
   Intensity Normalization 1
   Skull Strip
   EM Register (linear volumetric registration)
   CA Intensity Normalization
   CA Non-linear Volumetric Registration
   Remove Neck
   LTA with Skull
   CA Label (Volumetric Labeling, ie Aseg) and Statistics
   Intensity Normalization 2 (start here for control points)
   White matter segmentation
   Edit WM With ASeg
   Fill (start here for wm edits)
   Tessellation (begins per-hemisphere operations)
   Smooth1
   Inflate1
   QSphere
   Automatic Topology Fixer
   Final Surfs (start here for brain edits for pial surf)
   Smooth2
   Inflate2
   Spherical Mapping
   Spherical Registration
   Spherical Registration, Contralateral hemisphere
   Map average curvature to subject
   Cortical Parcellation - Desikan_Killiany and Christophe (Labeling)
   Cortical Parcellation Statistics
   Cortical Ribbon Mask
   Cortical Parcellation mapping to Aseg
BW
S Das
________________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu
[freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Lilla Zollei
[lzollei@nmr.mgh.harvard.edu]
Sent: 04 July 2017 22:04
To: Freesurfer support list
Subject: Re: [Freesurfer] recon-all on newborn
Hi S Das,
We are trying to release the infant pipeline by the end of the summer.
Lilla
On Tue, 4 Jul 2017, Das S. wrote:
...
Dear Freesurfer expert,
I want to perform recon-all pipeline on neonates data.Can I do so?
I was going through some mail archives and there it is said that on T1 image of neonates data we can't perform recon-all.
But again there is another paper where it says Freesurfer can perform segmentation of neonates image.
Any input will be appreciated.
Thanks
S Das

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