Re: [Freesurfer] Mindboggle official software release and publication!

[Antonin Skoch]

Dear experts,

I was wondering what is your opinion on the fact, that, according to the 
mindboggle paper

http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005350

it is beneficial to use ANTS volume-based gray matter segmentation to refine 
gray matter segmentation in FreeSurfer.

I am not expert in ANTS but looking at the ANTS code it seems to me that the 
ANTS routine does not do anything more than the volume-based nonlinear 
registration to the template and intensity and probabilistic atlas-based voxel 
labeling. Therefore, the method is in principle identical to GCA volume-based 
labeling (mri_ca_register and mri_ca_label, part of recon-all) in FreeSurfer 
which also produces cortical gray matter mask, far not so precise as the 
segmentation based on pial and white surface estimation.

I think that FreeSurfer pipeline for estimation of white and pial surfaces is 
much more sophisticated and precise than any method using volume-based 
registration and volume-based labeling by intensity and anatomical priors. 

The FreeSurfer gray matter underestimation showed in figure 2 of the paper
http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005350#pcbi-1005350-g002
seems to me like either partial-volume effect or skull-strip error (which cuts 
out part of gray matter) which can be corrected by proper inspection and manual 
correction of brainmask.mgz. In contrast, the errors in presented ANTS gray 
matter segmentation in figure 2 are much more severe, spanning not only the 
blue encircled region.

I would very appreciate your expert opinion on this.

Regards,

Antonin Skoch




Announcing the official release of Mindboggle (http://mindboggle.info),
open source software  and data
 for analyzing the shapes of brain structures from
human MRI data (processed through FreeSurfer and optionally through ANTs).
The release coincides with a publication in PLoS Computational Biology that
documents and evaluates the software:Klein A, Ghosh SS, Bao FS, Giard J, Hame 
Y, Stavsky E, Lee N, Rossa B,
Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human
brains. PLoS Computational Biology 13(3): e1005350.
doi:10.1371/journal.pcbi.1005350


Cheers,
@rno


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Re: [Freesurfer] Mindboggle official software release and publication!

[Arno Klein]

Great question!  You can certainly run Mindboggle on FreeSurfer output for
earlier versions of FreeSurfer.  In fact, we did this for part of the work
described in the PLoS Computational Biology article:

"For this study we used FreeSurfer v5.1-derived labels and meshes, but the
recently released FreeSurfer version 6 is recommended because it uses
Mindboggle’s DKT-100 surface-based atlas (with the DKT31 labeling protocol)
by default to generate labels on the cortical surfaces, and generates
corresponding labeled cortical and non-cortical volumes (wmparc.mgz) [75
<http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005350#pcbi.1005350.ref075>
]."

I am certain you can run a FreeSurfer command to update the cortical labels
to be in accord with the DKT-31 labeling protocol (
http://journal.frontiersin.org/article/10.3389/fnins.2012.00171/full) and
the new DKT-100 atlas used in FreeSurfer.  I will leave it to others on
this list who have greater FreeSurfer expertise than I to recommend the
appropriate command.

Cheers,
Arno

On Fri, Feb 24, 2017 at 6:55 AM Ritobrato Datta <rida...@mail.med.upenn.edu>
wrote:

> Hi Arno,
>
> This is fascinating stuff. In my research, I have come across instances
> when I felt that a hybrid of ANTS and freesurfer would be very useful. Is
> this pipeline possible for data processed with the earlier versions of
> freesurfer say 5.1 ? FS6 just got released in Jan 2017 and I am sure for
> most ongoing studies, the data have already been processed in earlier
> versions of freesurfer.
>
> If there is a patch or script to update the data processed using earlier
> versions of freesurfer, that will save a lot of time than running
> everything from scratch in FS6.
>
> Please let us know.
>
> Best
>
> Rito
>
> - Original Message -
> From: Arno Klein <binarybot...@gmail.com>
> To: freesurfer@nmr.mgh.harvard.edu
> Sent: Thu, 23 Feb 2017 20:37:44 -0500 (EST)
> Subject: [Freesurfer] Mindboggle official software release and publication!
>
> Announcing the official release of Mindboggle (http://mindboggle.info),
> open source software <http://mindboggle.info/software.html> and data
> <https://osf.io/ydyxu/> for analyzing the shapes of brain structures from
> human MRI data (processed through FreeSurfer and optionally through ANTs).
> The release coincides with a publication in PLoS Computational Biology that
> documents and evaluates the software:
>
> Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B,
> Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human
> brains. PLoS Computational Biology 13(3): e1005350.
> doi:10.1371/journal.pcbi.1005350
> <http://doi.org/10.1371/journal.pcbi.1005350>
>
> Cheers,
> @rno
>
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Re: [Freesurfer] Mindboggle official software release and publication!

[Olivier Coulon]

Thanks to Docker, you can run it on a mac, it's all explained on the 
Mindboggle website.


Olivier

Shane Schofield a écrit :

Hello,

Thanks. Seems very interesting!
Is there any way to run this on Mac?

Cheers


--
Shane Schofield
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Re: [Freesurfer] Mindboggle official software release and publication!

[Shane Schofield]

Hello, 

Thanks. Seems very interesting! 
 
Is there any way to run this on Mac? 

Cheers 


-- 
Shane Schofield ___
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Re: [Freesurfer] Mindboggle official software release and publication!

[Ritobrato Datta]

Hi Arno,

This is fascinating stuff. In my research, I have come across instances when I 
felt that a hybrid of ANTS and freesurfer would be very useful. Is this 
pipeline possible for data processed with the earlier versions of freesurfer 
say 5.1 ? FS6 just got released in Jan 2017 and I am sure for most ongoing 
studies, the data have already been processed in earlier versions of 
freesurfer. 

If there is a patch or script to update the data processed using earlier 
versions of freesurfer, that will save a lot of time than running everything 
from scratch in FS6. 

Please let us know. 

Best

Rito
 
- Original Message -
From: Arno Klein <binarybot...@gmail.com>
To: freesurfer@nmr.mgh.harvard.edu
Sent: Thu, 23 Feb 2017 20:37:44 -0500 (EST)
Subject: [Freesurfer] Mindboggle official software release and publication!

Announcing the official release of Mindboggle (http://mindboggle.info),
open source software <http://mindboggle.info/software.html> and data
<https://osf.io/ydyxu/> for analyzing the shapes of brain structures from
human MRI data (processed through FreeSurfer and optionally through ANTs).
The release coincides with a publication in PLoS Computational Biology that
documents and evaluates the software:

Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B,
Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human
brains. PLoS Computational Biology 13(3): e1005350.
doi:10.1371/journal.pcbi.1005350
<http://doi.org/10.1371/journal.pcbi.1005350>

Cheers,
@rno
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dispose of the e-mail.

[Freesurfer] Mindboggle official software release and publication!

[Arno Klein]

Announcing the official release of Mindboggle (http://mindboggle.info),
open source software  and data
 for analyzing the shapes of brain structures from
human MRI data (processed through FreeSurfer and optionally through ANTs).
The release coincides with a publication in PLoS Computational Biology that
documents and evaluates the software:

Klein A, Ghosh SS, Bao FS, Giard J, Hame Y, Stavsky E, Lee N, Rossa B,
Reuter M, Neto EC, Keshavan A. (2017) Mindboggling morphometry of human
brains. PLoS Computational Biology 13(3): e1005350.
doi:10.1371/journal.pcbi.1005350


Cheers,
@rno
___
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The information in this e-mail is intended only for the person to whom it is
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