Re: [Freesurfer] Shift in cortical parcellation, issues with previously suggested solution

[Fischl, Bruce]

What is the output of the first command? And if you bring up the ?h.sphere.reg 
does it align better with the atlas? You can use mrisp_paint or just look at 
fsaverage on the sphere

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Trolle, Carl
Sent: Wednesday, August 3, 2022 9:25 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Shift in cortical parcellation, issues with 
previously suggested solution

Thank you for the help and for getting back to me,

After using the custom-fill option and labelling the central sulcus (yellow), 
I've been running the following code:
"mris_register -L subject/label/?h.central_sulcus.label 
$FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs S_central
subject/surf/?h.sphere 
$FREESURFER_HOME/average/?h.average.curvature.filled.buckner40.tif 
subject/surf/?h.sphere.reg".

Which is followed by
"mris_ca_label subject ?h subject/surf/?h.sphere.reg 
$FREESURFER_HOME/average/?h.destrieux.simple.2009-07-29.gcs 
subject/label/?h.aparc.a2009s.annot" or "recon-all -make all -subject". For 
some reason, I don't see any difference in the subject Destrieux-labelling (the 
incorrect shift is still there) and I suspect that I'm not doing this 
correctly. Would it be possible for you to check if I'm using the wrong syntax 
or if I might have missed out on some parts necessary for this solution to work?

Kind regards,

Carl

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[Freesurfer] adding volume to aparc aseg

[Benjamin Deck]

External Email - Use Caution

Hi there,

I have extracted an ROI mask for the subthalamic nucleus from MNI space and
registered this with the subject's native space orig.mgz

I would like to append this to the subject's automated segmentation from
aparc+aseg.mgz. So I can use this segmentation as an atlas file for some
later analyses.

How should I go about doing this?

Thanks,
Ben


-- 
*Benjamin L. Deck*
*Doctoral Student*
*Applied Cognitive and Brain Sciences*
*Department of Psychological and Brain Sciences*
*Drexel University*


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[Freesurfer] Post-doctoral position at University of Pittsburgh in population neuroscience

[James Hengenius]

External Email - Use Caution

*Dear All, please see the opportunity for a Post-Doctoral Associate
position:*



*Link to apply*: Job Description - Post Doctoral Associate (ROSANO)
(21008433) (taleo.net)


https://secure-web.cisco.com/1ZOanogXZkLzkQnqrC_mxzi3jWIx4w7dKQBsNZA5Sfk_8PR6qgOJN1XCVC6zGz0ApudW2om-d8nB2h6koYhw-aiZLferhAa1W7EuFhbwQtavpveNckdyWYzoGcW3RoD6z730ecSTWoGHRlEFX08tM4NWuzrlQn3_jaJPZmlRxEwMk1ckRY-FvBPOMM_dbpqTLkUD8UK487rjGMXz38cEr3Lqj3MYSxp3l0iQU2Pk2h7NfwFJ76NuDh3U0yZ26RHjwnY_vAh-fBlmxhxiFIJ2_WZVeNWj74JKvYGdszvB6_9HMnFn0uThxiOQ158mEp77IsBpSOKKs31Af_tzWbeGL8mgK5Oi0iv9Rm090-IEV6Gw/https%3A%2F%2Fcfopitt.taleo.net%2Fcareersection%2Fpitt_faculty_external_pd%2Fjobsearch.ftl%3Flang%3Den%26portal%3D24100023232


position # 21008433



*Post-Doctoral Associate* (with Dr. Caterina Rosano)

GSPH-Epidemiology - Pennsylvania-Pittsburgh - (21008433)

Post-Doctoral Associate; Graduate School of Public Health (GSPH),
Department of Epidemiology


The Postdoctoral Associate will join a cross-institutional research team
focused on the intersection of epidemiology, neuroscience, neuroimaging,
causal inference, and machine learning. The Postdoctoral Associate is
expected to take a leadership role in ongoing research projects, including
developing novel and important research questions, analyzing data, writing
manuscripts, and meeting with mentors. The candidate will be encouraged to
develop their own personal goals within the context of the existing
research program, and will work with mentors to achieve these goals.



*Duties and responsibilities*: All activities below will be performed
independently and then reviewed by the mentors for discussion and revisions.



-Develop short-term (6 months) and longer-term (1-2 years) career goals.

-Develop important and novel research questions within the context of the
research program.

-Analyze neuroimaging and epidemiological data

-Interpret results.

-Write manuscripts based on research findings.

-Provide some mentorship to Ph.D. students and contribute to their
manuscripts as appropriate.



*Expectations: *The Postdoctoral Associate will have a Ph.D. in
epidemiology, biostatistics, neuroscience, or another area of public
health. They will also have experience in causal inference and/or machine
learning. The Postdoctoral Associate is expected to produce 3 to 4
first-authored papers per year and co-author manuscripts that come out of
the research group, as appropriate, as well as submit one or more abstracts
to scientific meetings each year. They will attend weekly mentorship
meetings and biweekly research team meetings, and provide input on other
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*Opportunities:* Attendance of several annual meetings, including the
society of neuroscience, Human Brain Mapping, Gerontological Society of
America.



Presentation of results in those scientific meetings, to the Epidemiology
Department, to visiting experts, and to our research team;



Participation in career development 

[Freesurfer] Using averaged T1-images to calculate cortical thickness

[Trolle, Carl]

Hello dear FreeSurfer team,


We are undertaking a multicenter study analyzing cortical thickness of controls 
and persons with a neurological condition. Unfortunately, there are issues with 
motion artifacts and image quality. To counter this, we’ve created averaged 
T1-images by combining one axial and one sagittal image in SPM for one of the 
study sites. Also, we are using recon-all with the optional T2- and T2-pial 
flags. Our impression is that the image quality has improved with the averaged 
images as compared to the non-averaged ones.

Do you have any thoughts on this method or if combining images this way might 
cause issues when trying to calculate and compare cortical thicknesses? The 
averaged T1-images are only created for one of the study-sites and we plan on 
using study site as a covariate in our model. Will be happy to post images or 
logs if those may be helpful

Kind regards,

Carl

FreeSurfer version: freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551
Platform: CentOS Stream 8

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[Freesurfer] postdoc

[Thomas Yeo]

External Email - Use Caution

Hi Everyone,

I am looking for a postdoc to start this year or 2023. Candidates should
have a PhD in neuroscience, machine learning or related fields.

Research topics are quite flexible and can include can include developing
machine learning algorithms for predicting disease progression from
large-scale brain imaging data, individual-specific brain network
organization, multi-modal fusion/prediction (e.g., relating brain imaging
with wearable & smartphone data), neural mass modeling, deep phenotyping,
brain network dynamics and naturalistic paradigms. I am particularly
interested in applications to aging, Alzheimer’s disease dementia and
neurodevelopment.

Lab website can be found here 
(https://secure-web.cisco.com/163_oJDbnYF8kJLTi8C6K0GEnoNtFGd19DY-CEBe1pYtwKc5u_lOCaszWX1ur1DNvrMAXvVuSTBu0hNERfcbfbY4IaurnedCTIKybzAqNKHd38znjhFcer6rqxyC0O4Lf7g5ti4RHZsp6r3Gqo6gSVd_qR-F-psaG_3T8Szj_HZOjPoPHDHmA51T2ercEiqPBy_c9uoCKKlcaxGEs8-LyhRlxDyOxhuYIik8VNKmeF9uNWMFG63p0Sy99gVYQmZime2gXDvul8deJDMwUSBNurbs9Fjb31-L4_nOG2-ym-D7FMaMNRVK2jUrVfsXLIIA8onWaWh2AiGIJlCRJcKMcLg/https%3A%2F%2Fsites.google.com%2Fview%2Fyeolab%2Fhome).
Interested candidates can email their CV to me.

Thanks,
Thomas
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Re: [Freesurfer] postdoc

[Thomas Yeo]

External Email - Use Caution

Hi Everyone,

Apologies for sending this email twice, but interested candidates should
email me at yeoye...@gmail.com (rather than my MIT email).

Regards,
Thomas

On Thu, Aug 4, 2022 at 11:25 AM Thomas Yeo  wrote:

> Hi Everyone,
>
> I am looking for a postdoc to start this year or 2023. Candidates should
> have a PhD in neuroscience, machine learning or related fields.
>
> Research topics are quite flexible and can include can include developing
> machine learning algorithms for predicting disease progression from
> large-scale brain imaging data, individual-specific brain network
> organization, multi-modal fusion/prediction (e.g., relating brain imaging
> with wearable & smartphone data), neural mass modeling, deep phenotyping,
> brain network dynamics and naturalistic paradigms. I am particularly
> interested in applications to aging, Alzheimer’s disease dementia and
> neurodevelopment.
>
> Lab website can be found here 
> (https://secure-web.cisco.com/1b9gsm4fyGptbthNcW5MCGEzln1ZTqhkpinc48hpfFC50MfdDumIF5X_gknE4uWf52c9v5K55Xj-MgIBbUl6WSN1qFM4Lkf0jRMtqo8QYnlJ7SIYWByy4IWwHJmp7tM7_PJa6D6lgJ046spPMU7O7KDeByt7nGBWUojvMWqJLf-MZGh7clsxhT_UNbdc9l-tI03oYcvGtp_kQUFP_z5TVhcmp-M8L3O-b0LthBa2Wc21Qe5tqV2HO4MnZ9UlDJINiG-0MrHc6uf8Dl4OGwfJW7-ULB4fO92hCu-DtoFX1xIaq6apRxGPkUZLpgbl6dMdjtFHi-WtUO47kcCsuiebvuw/https%3A%2F%2Fsites.google.com%2Fview%2Fyeolab%2Fhome).
> Interested candidates can email their CV to me.
>
> Thanks,
> Thomas
>
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