[Freesurfer] Several faculty jobs at University of Chicago in Aging + Alzheimer's and related dementias

[Adam Martersteck]

External Email - Use Caution

*Apologies for cross-posting*

The University of Chicago's Department of Neurology is recruiting several
faculty members at any rank to join the Healthy Aging & Alzheimer’s
Research Care (HAARC) Center. We welcome candidates with research interests
that align with our mission including topics and methods such as digital
biomarkers, blood-based biomarkers, imaging biomarkers (MRI, PET),
large-dataset curation, social determinants of health, assessment of
cognition, memory, psychosocial wellbeing, functional outcomes,
neuropathologic, nonpharmacologic interventions, and implementation
science.

We are looking for (1) a tenure track faculty (any rank, with or without
tenure), (2) a non-tenure track faculty (any rank), (3) a behavioral
neurologist, and (4) a full professor of neuroimmunology to direct a
program in neuroinflammation.

Clinical neuropsychologists, behavioral neurologists, and cognitive
neuroscientists with an interest in contributing to a collaborative
multidisciplinary research center are encouraged to apply. We especially
welcome applicants from URM groups, which are African American, Latino,
Native American, Pacific Islanders, women, and individuals with
disabilities.

For more information see our website:
https://secure-web.cisco.com/10L7_lboSnfTgH5hrqe1sUZtGSywMbqb47r96NhJAp4tK2nOorN27NkJvDmmqD6on6dFVSd_UQlK9xq0TY-LKv7O0YwxSlCOYNEGg2vmxpRcpVwsp8eqiD7SGPeLZ7FJSrRZkuqTTXt2n13a-wyj53S_XcroxdWBdlPKgL8OqTJ27-EehXUjPQ2nmJ-plWeGk_imYOba3Ne7Kx1ue1PU00q7fmc7Mvl_UukLjfL0prukuobfkh3y5PW7BBhhMz-B0BAn2E1S5Z80D5mkeEu2qw7AUFqreSRcRHAxo4rcFPYm7sbRMMaTy6tPkqYLhJSs0rmM4PIxp4pggOIkLkwRsRg/https%3A%2F%2Fhaarc.center.uchicago.edu%2Femployment-opportunities
Tenure track faculty position: 
https://secure-web.cisco.com/1OeZ6fDc9_LaXQp8riD9fIo6-CzZ7ojZNXgL4wc93ARP8I8-gKxHdKzfAxE4r6NRmD3sKUgzyX48yXMfJ4WoPvcR70lbgbHT2jdMlhXQ0kNdHN56w88mPPRg9PjxVe8oyYwPJu2z8YlI_Y2G3OyWVmdOTVLO0rRh9sts_kgxCAOIJfPrT8tDkNyNzoFfylstNPa-BqNNCGKwbVgsC_DwXz2Z0UtWlvK9gH-H0rNEG8yDfYeYBOn5BJBPLK9VXtTW6a65F88a_M3YpEqSlD1AAMeM2v9xByHsayoTVZ7xQPZ2oZCQHfmNc5XEVhOF0vJCzNuZ2TGWrkaMfHAx19bsu4Q/https%3A%2F%2Fapply.interfolio.com%2F141590
Non-tenure track faculty position: 
http://secure-web.cisco.com/17J6yWYJ2zsoku90RYF2YU_thqO3lxxSRJXfK4HSbPzjCannkCOhzR7s5uZ6jgb2oHJVS2PYIzigvOx0tgGFEA4cDDIp_CPjc5YQxoPlCzuK6n8cCuPg5zjt24Uh6AeBfXe2PDTh-tE228rLVKFd2RkajbY6OBMk7VmTxztfHXMWTWvdq5pOjyHM91Ry9T_YrZil0A4rKMRv-hcxkZObvyYr-BXS9E-Oqo56Y3cvO4vdx6jj19zFodH7yfGPx8K4FxVNhHfGRG-R-Mk1DZRZNUyaj7vPpHxJvegwtoHe6EVKN5FWo_uLbzMcGcgGd1KJ2NpF3zk7lxEz8xHSNm5bPRQ/http%3A%2F%2Fapply.interfolio.com%2F141591
Behavioral neurologist: 
https://secure-web.cisco.com/1ZT7et8OCIVgBMktDPuQAx1nX2C27i0IwlduDjDBH2QFZffVyzLTqfD8x4GShtjcxO9SOXwjgxwDqQ99wjUxwVi1g3iE1kusOGa7RatrX_CSWOyYz4erkYK3s_eyp3SyzAciLD1N1qMIHbTXiiarFkjURr6UCGhBmL17ARIPCGEEhBWyhHrgTfc6f0n2CGb-PvYsSvx-uxgtZcvgWTJC6fVbQtPi6rRnZLWBRE0FAITqacs90PXCplpYpdrMkLR7jeM2N_6oXEBKgpzsdLlvMrWF73MjtAJ18k6i3okMqq1ERRhWEjZ3t_FiMIlqznWQiqYV1RWYn-l3MrK5l1cNZJw/https%3A%2F%2Fapply.interfolio.com%2F119788
Tenured full professor in neuroimmunology, with endowed chair:
https://secure-web.cisco.com/1aGaEvfSfHQUMYR0p_DyIC-4_q2Xse9-YUKKvf1BxySfjoOzdFh0reO4k1DoGB0wcpnrgNlXdYWH7FdbMyxTVK2-BEuUAWnPq8HbY39qxTChBfaUeN2WTE94tfjXYCspSexf3zkFEsQ-ZrFouNqM_e9GXgIq2FWjfUhH_ZS-tqxA58GDpjFCsUn6zjj1OFbVrWipbYErwpGWX8kQYHZhOJsf6pZdsEwahYNqD5f35h43w2SHKTv8A-880LQ3_7dJNTeCQ5d91xie-sXJXvrR1FdfeB-mHCVRIFUtYODq3xnGM6pHEPmDWl__wu7uaR4VS8JgPUxVEFXY1hv3Fb7HKLw/https%3A%2F%2Fapply.interfolio.com%2F140371

-- 

*Adam Martersteck, PhD *
*(he/him)**Assistant Professor of Neurology* | The University of Chicago,
Healthy Aging & Alzheimer's Research Care (HAARC) Center
*Address *| 850 East 58th Street | Chicago, IL 60637
*Phone *| 773-795-1683

*Email *| marterst...@uchicago.edu
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[Freesurfer] Invitation to free symposium “What is brain connectivity?”

[Rullmann, Michael]

Dear colleagues,

 

On behalf of the  

 Molecular Connectivity Working Group, I am delighted to invite you to our next 
hybrid symposium with the title “What is brain connectivity?”, bringing 
together leading experts in the field of fMRI, DWI, EEG, and molecular imaging. 
 

 Registration is free (but places are limited - only 15 places left for 
in-person registration at the moment!).

 

 Date: May 3, 2024
 Time: 9:00 am - 1:00 pm CEST

    Virtually + @TranslaTUM, University Hospital “Klinikum rechts der Isar”, 
Ismaninger Str. 22, Munich 

 

Key Highlights:

·   Recognized experts

·  欄 Networking opportunities

·   Virtual and on-site hybrid event 

·    No registration fees


Goal

The symposium aims to identify a common denominator across modalities in the 
definition of macroscale brain connectivity. The event is supposed to provide a 
baseline for follow-up debates on standardized nomenclature for molecular 
connectivity.

 

 For more information visit:  

 tinyurl.com/MCWGMunich2024

 

Registration:

Registration for the symposium is open and free but obligatory. Places are 
limited so do not miss out on the opportunity to be a part of this event by 
securing your spot  

 here. 

 

NB: in-person registration closes on April 14th!


Thanks to the sponsors  

 Deutsche Forschungsgemeinschaft (DFG) - German Research Foundation,  

 Bruker (PMOD),  

 Curium Pharma,  

 Technical University of Munich for the support.

 

Who we are

The  

Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

[Rullmann, Michael]

You can just google those values for each scanner.

For example:

https://secure-web.cisco.com/1XqX9-a2LU-Yqo_eubkdqqmahVQPBMg1MvLiOSxV5SHgUNoohax6i_xqsuxgNWaGaYEFJOxJsV11MLT6HHPiItNJeCGcOpVrw3hkNph4i7cDnF6mIPBYXYS_7UwBKXePxqIoeUnn502yqPymKl-jCG3IF8rs4QJ23ue3hl1wCnMbVuMOqrbLmfa5WYv5SNbb9oJgRSyufzcncChaZUVs3DVHDzh_jFTwhKsxhutEHCAMvsT8v5R66-1qPhIKS_Y36ul2LwJnGJl5TNlrFnilUI5NJsunm5q7r9WSLf6AlvdPgxeuprMIa2pTRRORkGG3w/https%3A%2F%2Fwww.google.com%2Fsearch%3Fq%3Dnema%2Bfwhm%2Bsiemens%2BmMR

 

Second result links directly to the Siemens website:

https://secure-web.cisco.com/1nbS9Vytnf798M-69hNgHUf9LyYJC4rkYI4w5c0QOt-Xd4n6mwlq-btGz5Nj6v4ciYO_m8LlBQQmPrMl26Bs9lG3WStwV-7GPVAEy2ABiy2zfNI3I5OvfjkMHzooOZUki5sPe70e6vm9lnb51h06HiA5lDgoO13QgqMhiNFRuUZoRp9usrCq8-ewf48IariB6LLxHlZyS_3jiTYj9KtBx_v6vfDFLq3M8hsUxnj2ar-P46i2JcRsfMLIUJQXlTCyTB0lp3-DbVtYFhsa6nvALJmqd3uEhHoM8B1VGbT5p9jT3FoMvds59LWkwoi0nHslf/https%3A%2F%2Fwww.siemens-healthineers.com%2Fmagnetic-resonance-imaging%2Fmr-pet-scanner%2Fbiograph-mmr

 

There, it is stated:

Transverse spatial resolution (NEMA 2012)

FWHM @ 1 cm : 4.6 mm

 

 

You can also determine the parameters yourself by following the NEMA standards.

 

Best

Michael

 

 

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 Im Auftrag von WONG Wan Wa
Gesendet: Dienstag, 9. April 2024 12:03
An: Freesurfer support list 
Betreff: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET 
data with single frame?

 

WARNUNG: Diese E-Mail kam von außerhalb der Organisation. Klicken Sie nicht auf 
Links oder öffnen Sie keine Anhänge, es sei denn, Sie kennen den Absender und 
wissen, dass der Inhalt sicher ist. 

 

External Email - Use Caution

How to determine the PSF?

  _  

From: freesurfer-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of WONG Wan Wa 
mailto:angelw...@ust.hk> >
Sent: Friday, April 5, 2024 12:14 PM
To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu> >
Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET 
data with single frame? 

 

External Email - Use Caution

Any idea about the PSF?

  _  

From: freesurfer-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of WONG Wan Wa 
mailto:angelw...@ust.hk> >
Sent: Tuesday, April 2, 2024 12:36 PM
To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu> >
Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET 
data with single frame? 

 

External Email - Use Caution

Hi Douglas,

 

Here is the information given by the technician from the PET center:

 

There are a total of 3 machines used for PIB PET/CT or PET/MR scans

 

1.  PET/CT1 ( mCT)(contain "mCT" in the pet series)

Manufacturer: Siemens
ManufacturersModelName: Biograph128_mCT

recon method : TrueX + TOF (ultra HD-PET)

iteration: 5 subset:21 matrix: 400x400

zoom: 2.0  Gaussian filter FWHM: 2.0mm

 

2.  PET/CT2 (Vision)(contain "Vis" in the pet series)

Manufacturer: Siemens
ManufacturersModelName: Biograph128Edge_Vision 600

recon method:  TrueX + TOF (ultra HD-PET)

iteration: 8 subset: 5 matrix: 512x512

zoom: 2.0  Gaussian filter FWHM: 2.0mm

 

4.  PET/MR (mMR)

Manufacturer: Siemens
ManufacturersModelName: Biograph_mMR

recon method: HD-PET

iteration: 5 subset: 21 matrix: 344x344

zoom:2.0 Gaussian filter FWHM:2.0mm

 

Thanks,

Angel

 

  _  

From: freesurfer-boun...@nmr.mgh.harvard.edu 
  
mailto:freesurfer-boun...@nmr.mgh.harvard.edu> > on behalf of Douglas N. Greve 
mailto:dgr...@mgh.harvard.edu> >
Sent: Saturday, March 30, 2024 5:23 AM
To: freesurfer@nmr.mgh.harvard.edu   
mailto:freesurfer@nmr.mgh.harvard.edu> >
Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET 
data with single frame? 

 

That 2mm for the gaussian is just the post-processing filter and does not 
represent the full amount of partial volume effect. What kind of scanner is it? 

On 3/22/2024 12:42 AM, WONG Wan Wa wrote:

External Email - Use Caution

Hi Douglas,

 

Thanks for your clarification. This is my first time to run PetSurfer. We did 
want to normalize by cerebellar grey matter, and I will add the "--rescale 8 
47". I just copied "6" from the example command. I know "6" should be the FWHM 
of the point-spread function (PSF) of the scanner as measured in image space. I 
did ask the technician at the PET centre, and he replied that the 
reconstruction method was "OP-OSEM 8i21s" and the filter was "XYZ gaussian 
2.00". Can I use "2" for psf in the command?

 

Thanks,

Angel

 

  _  

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

[Freesurfer] vertices are -1 when using vol2label

[Sam W]

External Email - Use Caution

Hello!
I'm trying to convert the cerebellum cortex in the aparc+aseg.mgz into a
label so I tried:

mri_vol2label --c bert/mri/aparc+aseg.mgz --id 8 --l lh.cerebellum.label

but the resulting output file only has -1 as vertices. Is there anything
wrong with the command above?

Best regards,
Sam
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Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET data with single frame?

[WONG Wan Wa]

External Email - Use Caution

How to determine the PSF?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of WONG Wan Wa 

Sent: Friday, April 5, 2024 12:14 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET 
data with single frame?


External Email - Use Caution

Any idea about the PSF?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of WONG Wan Wa 

Sent: Tuesday, April 2, 2024 12:36 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET 
data with single frame?


External Email - Use Caution

Hi Douglas,

Here is the information given by the technician from the PET center:

There are a total of 3 machines used for PIB PET/CT or PET/MR scans


  1.  PET/CT1 ( mCT)(contain "mCT" in the pet series)

Manufacturer: Siemens
ManufacturersModelName: Biograph128_mCT
recon method : TrueX + TOF (ultra HD-PET)
iteration: 5 subset:21 matrix: 400x400
zoom: 2.0  Gaussian filter FWHM: 2.0mm


  1.
PET/CT2 (Vision)(contain "Vis" in the pet series)
Manufacturer: Siemens
ManufacturersModelName: Biograph128Edge_Vision 600

recon method:  TrueX + TOF (ultra HD-PET)
iteration: 8 subset: 5 matrix: 512x512
zoom: 2.0  Gaussian filter FWHM: 2.0mm


  1.  PET/MR (mMR)

Manufacturer: Siemens
ManufacturersModelName: Biograph_mMR
recon method: HD-PET
iteration: 5 subset: 21 matrix: 344x344
zoom:2.0 Gaussian filter FWHM:2.0mm

Thanks,
Angel


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas N. Greve 

Sent: Saturday, March 30, 2024 5:23 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET 
data with single frame?

That 2mm for the gaussian is just the post-processing filter and does not 
represent the full amount of partial volume effect. What kind of scanner is it?

On 3/22/2024 12:42 AM, WONG Wan Wa wrote:

External Email - Use Caution

Hi Douglas,

Thanks for your clarification. This is my first time to run PetSurfer. We did 
want to normalize by cerebellar grey matter, and I will add the "--rescale 8 
47". I just copied "6" from the example command. I know "6" should be the FWHM 
of the point-spread function (PSF) of the scanner as measured in image space. I 
did ask the technician at the PET centre, and he replied that the 
reconstruction method was "OP-OSEM 8i21s" and the filter was "XYZ gaussian 
2.00". Can I use "2" for psf in the command?

Thanks,
Angel


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Thursday, March 21, 2024 9:44 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET 
data with single frame?

Yes, though that will normalize by the pons. If you want to normalize by 
something else, you will need to specify it with --rescale. Eg, if  you want to 
normalize by ceberbellar gray matter, add
--rescale 8 47
Where did you get "6" from for the psf?

On 3/20/2024 10:57 PM, WONG Wan Wa wrote:

External Email - Use Caution

Hi Douglas,

Thanks for your reply. We used different tracers for diagnosis of AD or other 
neurodegenerative diseases, including PIB, FDG, Flutemetamol and TAU. If an SUV 
analysis is used, is it done by mri_gtmpvc? Is there any subsequent analysis 
needed?

This is my mri_gtmpvc command:
mri_gtmpvc \
  --i 
$SUBJECTS_DIR/sub-QM001/pet/sub-QM001_ses-001_trc-C11PIB_rec-05MINS_run-001_pet.nii.gz
 \
  --reg 
$SUBJECTS_DIR/sub-QM001/pet/sub-QM001_ses-001_trc-C11PIB_rec-05MINS_run-001_pet.reg.lta
 \
  --psf 6 \
  --seg $SUBJECTS_DIR/sub-QM001/mri/gtmseg.mgz \
  --default-seg-merge  \
  --auto-mask 1 .01 \
  --mgx .01 \
  --o $SUBJECTS_DIR/sub-QM001/pet/gtmpvc.output

Is this command okay?

Thanks,
Angel


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 

 on behalf of Douglas N. Greve 

Sent: Wednesday, March 20, 2024 11:27 PM
To: freesurfer@nmr.mgh.harvard.edu 

Subject: Re: [Freesurfer] PetSurfer: Can kinetic modeling be applied to PET 
data with single frame?

you cannot apply kinetic modeling to one frame. What is you ligand? For a one 
frame acquisition, you usually use an SUV analysis.

On 3/20/2024 12:03 AM, WONG Wan Wa wrote:

External Email - Use Caution

Hi experts,

As stated in the subject, can kinetic modeling be applied to PET data with only 
one frame? Or we just stop at