Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs

2023-11-01 Thread Huang, Yujing 
Hi Maya,

I think you can pass extra parameters to mri_synthseg with recon-all option 
'-expert '.


  1.  Create file mri_synthseg.opt, and have this line in it
mri_synthseg -robust

  1.  Pass '-expert mri_synthseg.opt' to your recon-all

Can you reply to the list so other people can answer it too? Also can you keep 
previous exchanges?

Best,

Yujing

From: Maya Yablonski 
Sent: Wednesday, November 1, 2023 3:05 PM
To: Huang, Yujing 
Subject: Re: [Freesurfer] Using Synthseg segmentations to fix recon-all outputs


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Thanks! This seems to be working now. Can I set recon-all to use synthseg with 
the robust algorithm?
I tried the flag -robust as it appears for the command mri_synthseg, but that 
doesn't seem to be a recognized flag by recon-all.
Thanks!

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Re: [Freesurfer] Finding Intracranial volume

2023-11-01 Thread Mirsol Choi 
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Thank you Paul!

On Wed, Nov 1, 2023 at 3:33 PM Wighton, Paul 
wrote:

> Hi Peter,
>
> recon-all produces an estimate of ICV.   In aseg.stats there is a line
> that looks like:
>
> # Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total
> Intracranial Volume, 1696008.240403, mm^3
>
> You can read more about how it is computed at
> https://secure-web.cisco.com/1jljg6dkUgcWIVn7pjegiZm1C7K-LPzZxj3WP5JbiWaMqmbEdmAN3LEIHV65Yh-u6aVwJU3HxO34dyC0NzPsI2_KBOm8LgjyIOhK8fu5Xd-Svi9wPALxpmh_kvsXcbO365N6zYbK509nkCZF58iv7-yueDf7bRlFlVaa7vFBR_gWX6_rUVqZJjogo0Oj0WWfogxVckKBBb7ilATdRDyy638SXB8IUlaNTvPhPRyF135ckIUSpOUHwEtJ6VbKmZ-IeL3DYwC8Z7ncgO996v5ZZvCzJwoldXgcHBk5e42Ykchma6hd8PGQlWFc-JnHggT7vjT2Y6PMVHhOi-U4h71Fo6Q/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FeTIV
>
> -Paul
>
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Mirsol Choi <
> mir...@ualberta.ca>
> Sent: Wednesday, November 1, 2023 5:23 PM
> To: Freesurfer support list
> Subject: [Freesurfer] Finding Intracranial volume
>
> External Email - Use Caution
>
> Hi fellow freesurfers!
>
> I am a Masters student currently working with diffusion images.
>
> I would like to ask you experts how I can obtain ICV from my T1/T2 or
> diffusion images.
>
> Is there a certain output from recon-all that produces intracranial
> volume? Or is there a different command I must use?
>
> Thank you all so much for your time. I look forward to hearing from you.
>
> Peter
>
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Re: [Freesurfer] Finding Intracranial volume

2023-11-01 Thread Wighton, Paul 
Hi Peter,

recon-all produces an estimate of ICV.   In aseg.stats there is a line that 
looks like:

# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial 
Volume, 1696008.240403, mm^3

You can read more about how it is computed at
https://surfer.nmr.mgh.harvard.edu/fswiki/eTIV

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Mirsol Choi 

Sent: Wednesday, November 1, 2023 5:23 PM
To: Freesurfer support list
Subject: [Freesurfer] Finding Intracranial volume

External Email - Use Caution

Hi fellow freesurfers!

I am a Masters student currently working with diffusion images.

I would like to ask you experts how I can obtain ICV from my T1/T2 or diffusion 
images.

Is there a certain output from recon-all that produces intracranial volume? Or 
is there a different command I must use?

Thank you all so much for your time. I look forward to hearing from you.

Peter

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Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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[Freesurfer] Finding Intracranial volume

2023-11-01 Thread Mirsol Choi 
External Email - Use Caution

Hi fellow freesurfers!

I am a Masters student currently working with diffusion images.

I would like to ask you experts how I can obtain ICV from my T1/T2 or
diffusion images.

Is there a certain output from recon-all that produces intracranial volume?
Or is there a different command I must use?

Thank you all so much for your time. I look forward to hearing from you.

Peter
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[Freesurfer] NIH R25 Course : Training in Advancd Statistical Methods in Neuroimaging and Genetics, Salt Lake City, Utah, April 15-26, 2024. Extended deadline!

2023-11-01 Thread ROBERT CARY WELSH 
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Hi everybody,
We are pleased to announce that the application portal is still open for the 
NIH funded 2024 session of the course, “Training in Advanced Statistical 
Methods in Neuroimaging and Genetics”.

We hope you pass this email on to your local neuroimaging community.

The course will start on Monday, April 15, 2024 and finish on April 26, 2024 
and is to be held in person, in Salt Lake City, Utah, United States at the 
University Guest House Conference Center. Our course also includes an ongoing 
(throughout the year) continuing education portion.

The course is an intensive 2-weeks, about 8 hours per day of a mix of lectures 
and hands-on computer labs.

neurostatsbootcamp.org

Due to recently increased funding, we are pleased to announce we can drop our 
tuition this year to $2250 (from $3000). Strictly financial need scholarships 
will also still be offered.

Tuition includes hotel accommodations at the University Guest House (arrival on 
April 14 with departure on April 26), breakfast, lunch, day time snacks, three 
dinners out as a group, and the planned evening activities. All course 
attendees will arrange for their own transportation to Salt Lake City. The 
course cost does include a daily pass to the Salt Lake City Trax light 
rail/commuter system. (Please note that the course instructors' effort is 
supported by the NIH grant thus avoiding that cost being passed on to the 
course attendees. This course is strictly not-for-profit.)
Because of the limited size and advanced nature of the course, attendance is by 
application only – please make sure to fully read the website instructions. In 
general, applicants must be a US citizen, permanent resident, or working with 
an appointment at a US institution, though we do have the ability to 
accommodate 3 to 6 individuals that do not meet this criteria. We anticipate 
the total class size to be between 22 and 25 students.

There are opportunities for scholarships which can partially offset hotel 
accommodations. These are based on true financial need and you will be 
instructed how to apply if you are admitted to the course.

We look forward to seeing you in SLC in 2024!

Priority application deadline is Nov 1, 2023; decisions around Dec 5th.

Late application deadline is Dec 1, 2023; decisions by Jan 5th, 2024.

For more information email us at 
neurost...@g.ucla.edu or  
advancedstatisticscou...@utah.edu

Robert and Anna

--
Robert Welsh, PhD
Course Director, Training in Advanced Statistical Methods in Neuroimaging and 
Genetics
rcwe...@g.ucla.edu
robert.c.we...@utah.edu

Anna Docherty, PhD
Associate Course Director, Training in Advanced Statistical Methods in 
Neuroimaging and Genetics
anna.doche...@utah.edu

Christina Caldera
Course Administrator
neurost...@g.ucla.edu

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