[Freesurfer] Neuroimaging postdoctoral fellowship at Stanford University, USA

2023-02-27 Thread Mira Michelle Raman 
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Dear FreeSurfer community,

The Brain Imaging, Development, and Genetics (BRIDGE) lab, part of Stanford 
University’s Division of Brain Sciences, is seeking two full-time Postdoctoral 
Fellows in brain imaging and/or human genetic modeling. Ideal candidates will 
have a solid neuroscience, neuroimaging, and/or human genetics background.

BRIDGE focuses on neuropsychiatric disorders, specifically those associated 
with RASopathies, such as Noonan syndrome and neurofibromatosis 1 (NF1). In our 
NIH-funded research, we employ three unique approaches: 1. Taking a 
genetics-first approach, we study children with known genetic conditions who 
exhibit attention problems, irritability, and deficits in social cognition. The 
approach differs from traditional research, which begins with the child's 
symptoms. 2. We apply in-depth phenotyping of the child's brain, genes, and 
behavior using brain imaging, genetic testing, and behavioral assessment. 3. We 
use large publicly available data sets (>10K children) focusing on child brain 
and behavioral development. Our goal is, therefore, to uncover how genetic 
variation and its associated downstream pathways affect children's 
developmental disorders.

If interested, please see the official posting for additional details at
https://secure-web.cisco.com/1KzHM6M8eHNAqniwUwClGLco44e39zsXfqSw4bO6Ms6b1qUuvuo4MY973iIY7fnvySfyX8tVQzqJglrrCBZxiqaq6C4puOdoSBdUDsJOOZd8556hJJ2PfQeoOWRTUpZiRaioaERFk1H5LLCHBhLJLzgUYlBbEsNOBuRB9NGjiRnhesMqcepiIajAU-kPOXPom_5NnIDQ12qLxXyBBn4SbNXWiio_dFOK1NRpqV0k0oGBN_ck36BrGEF97oUCSjhOD5tDpNUniZXwh7EkOnjuxmfSBHrkFuMUqcAf57wGLm7Y0Kt5HTYrILM5hBChxyrc1AQlFZrrXj1GiJ8ogfjUaeg/https%3A%2F%2Fpostdocs.stanford.edu%2Fprospective%2Fopportunities%2Fopen-postdoctoral-position-faculty-mentor-tamar-green

Thank you,
Mira Raman, Research Data Analyst
BRIDGE, Stanford University


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[Freesurfer] Consequences of using -notal-check / using a poor talairach transformation

2023-02-27 Thread Tyler Ward 
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Hi Freesurfer developers,

I am processing several thousand MRIs through Freesurfer and have come
across >200 cases where recon-all failed due to the automated talairach QA
check. In these cases, I do see some which have bad transformations and
others which look acceptable to me. After freesurfer runs, we review the
cortical ribbon from the aparc+aseg file to the quality of the
parcellation.

My question: what problems might arise from using the "-notal-check" on all
our freesurfer runs which would not be caught by looking at the
parcellation?

I am also wondering if you have the "RLB700_preprocessing_statistics.pdf"
document which the code references

> # now run Avi's QA check on the results found in talairach_avi.log
> # see document RLB700_preprocessing_statistics.pdf for details
>

Thanks for your time,
Tyler
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Re: [Freesurfer] Freeview displaying images in the wrong orientation

2023-02-27 Thread Nathan Kindred (PGR) 
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That worked, thank you so much!

Best,
Nathan

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wang, Ruopeng 

Date: Monday, 27 February 2023 at 15:38
To: Freesurfer support list 
Subject: Re: [Freesurfer] Freeview displaying images in the wrong orientation
Freeview by default will display the image in its original pixel space, without 
re-sampling. You can try the -r flag to enable the resampling like this:

freeview foo.mgz -r -cubic

Ruopeng


On Feb 27, 2023, at 7:04 AM, Nathan Kindred (PGR) 
mailto:n.kindr...@newcastle.ac.uk>> wrote:

External Email - Use Caution

Hi,

Apologies for the delay, please find attached a screenshot of an example image 
in orient_mri and the same image in freeview.

Best,
Nathan

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Date: Wednesday, 22 February 2023 at 14:24
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview displaying images in the wrong orientation
⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.

Can you send us a screenshot or even better, a sample image file?

Ruopeng

> On Feb 22, 2023, at 7:34 AM, Nathan Kindred (PGR) 
> mailto:n.kindr...@newcastle.ac.uk>> wrote:
>
>External Email - Use Caution
>
> Hi,
>
> When I am displaying certain images in freeview the orientation does not 
> match what is displayed in both orient_mri and SPM. The coronal and 
> horizontal views seems to be okay but the midsagittal view is often wrong 
> with the front of the brain tilted up. How do I get freeview to display the 
> images in the correct orientation?
>
> Thanks,
> Nathan
>
>
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Re: [Freesurfer] Freeview displaying images in the wrong orientation

2023-02-27 Thread Wang, Ruopeng 
Freeview by default will display the image in its original pixel space, without 
re-sampling. You can try the -r flag to enable the resampling like this:

freeview foo.mgz -r -cubic

Ruopeng

On Feb 27, 2023, at 7:04 AM, Nathan Kindred (PGR) 
mailto:n.kindr...@newcastle.ac.uk>> wrote:


External Email - Use Caution

Hi,

Apologies for the delay, please find attached a screenshot of an example image 
in orient_mri and the same image in freeview.

Best,
Nathan

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Wang, Ruopeng 
mailto:rwa...@mgh.harvard.edu>>
Date: Wednesday, 22 February 2023 at 14:24
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Freeview displaying images in the wrong orientation
⚠ External sender. Take care when opening links or attachments. Do not provide 
your login details.

Can you send us a screenshot or even better, a sample image file?

Ruopeng

> On Feb 22, 2023, at 7:34 AM, Nathan Kindred (PGR) 
> mailto:n.kindr...@newcastle.ac.uk>> wrote:
>
>External Email - Use Caution
>
> Hi,
>
> When I am displaying certain images in freeview the orientation does not 
> match what is displayed in both orient_mri and SPM. The coronal and 
> horizontal views seems to be okay but the midsagittal view is often wrong 
> with the front of the brain tilted up. How do I get freeview to display the 
> images in the correct orientation?
>
> Thanks,
> Nathan
>
>
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Re: [Freesurfer] PETsurfer: PVC without psf of the scanner

2023-02-27 Thread Federica Di Antonio 
External Email - Use Caution

Thank you so much!



Il giorno gio 15 dic 2022 alle ore 16:24 Douglas N. Greve <
dgr...@mgh.harvard.edu> ha scritto:

> I have something called the adaptive GTM that is currently a "hidden"
> feature in mri_gtmpvc as it has not been published yet. You can try it by
> adding the following flags --opt 1 --opt-tol 4 10e-6 .02 --opt-seg-merge
> When this is done, there will be a file called gtmdir/aux/opt.params.dat
> The value in that file with be the fwhm. Run mri_gtmpvc again passing that
> value as the --psf
> Again, this has not been fully evaluated so use at your own risk.
>
>
> On 12/12/2022 3:10 AM, Federica Di Antonio wrote:
>
> External Email - Use Caution
>
> Dear experts,
>
>
>
> Few weeks ago i wrote to this mailing list but I didn't receive any
> answer, so I'll try again:
>
>
> mri_gtmpvc --i pet.nii.gz --reg template.reg.lta --psf FWHM --seg gtmseg.mgz
>
>  --default-seg-merge  --auto-mask 1 .01 --mgx .01 --o gtmpvc.output
>
>
> If I put psf to 0, there is no PVC, and the same happens if I don’t put that 
> flag at all.t all
>
> Is able mri_gtmpvc to evaluate the fwhm without receiving it from the user?
>
> I apologize for the repetition,
>
> Thanks for your patience,
>
> Federica
>
>
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>  .
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