[Freesurfer] Exciting Postdoc Position at UCLA

2022-06-13 Thread Arpana Annie Gupta 
External Email - Use Caution

Dear Freesurfer Community,

We are looking for a postdoc fr this exciting position (2-3 years)- details 
below

https://secure-web.cisco.com/1wp5qnfMl6kH8tGZQqKIFBkrm-7MMorOxY-JjeSnDeCwRfA77onXGUvP5p6yJ22_O-4qJCxzoc1RNtNoCL-6kq1NXxZZM7y83Rdxnk87FRF_TEJa6wWHtbFVHcJ8THdYXsbumBsEEhosUDh--GyU70SquVkqESD3jvVr1L83mPMVEbrLDjgyWJG2gzpr6-Vdq1FYHauUNwETVoVEdtFD_DyDvAWA4rOX6pfbIju9Gs6_VsXj9_o9FukoXJ07g-BElrWgXiqnkydi-9ZBBqtQn6wJ3apzExZAsIOW9F32SVbxlUNiDdcUFkvWdclSOegB9B1CmyHGPAnX8MFEixvrv7A/https%3A%2F%2Fwww.uclahealth.org%2FMedicine%2Fdigestive-diseases
 


Thanks
Annie


The Center for Neurobiology of Stress and Resilience in the Division of 
Digestive Diseases at the University of California Los Angeles is seeking a 
full time Post-Doctoral Research Fellow for a U54-funded project studying 
sex-related differences in the brain-gut-microbiome interactions related to 
visceral pain. This project is focused on the sex-specific effect of gut 
microbial metabolites, and estrogen levels on ascending arousal pathways 
originating in distinct brainstem nuclei to change the activity and 
connectivity of brain networks involved in symptom generation in irritable 
bowel syndrome.

As a part of an multidisciplinary research team the fellow will apply advanced 
computational, neuroimaging, biostatistical, and bioinformatics approaches to 
assess the interaction between various levels of biological data (e.g., 
microbiota, metabolites, sex hormones, multimodal brain and brainstem imaging 
data), clinical variables (symptom severity, widespread pain) and sex.

There will be opportunities to develop translational and clinical neuroscience 
research skills (e.g., target discovery, individualized treatment development 
and biomarker/predictor development), in addition to state-of-the-art 
analytical skills to address basic and pathophysiological systems biology 
questions.

The G Oppenheimer Center for Neurobiology of Stress and Resilience (CNSR) is an 
interdisciplinary, translational Center funded by the National Institutes of 
Health, and by philanthropic support. The overall research goals of the CNSR 
are to better understand the interactions between mind brain and body in health 
and disease, and to develop novel management strategies for optimal health and 
for complex chronic disorders.

Center investigators are conducting clinical, translational and basic research 
with human populations, using interventions (e.g., diet, cognitive behavioral 
therapy) alongside deep phenotyping including neuroimaging, mutli-omics 
profiling (gut microbiome, metabolomics, inflammatory biomarkers, psychosocial 
and behavioral assessments. You will work directly with Arpana “Annie” Gupta, 
PhD and Jennifer Labus, PhD and an array of faculty collaborators across UCLA, 
and beyond.

There will be many opportunities to lead high impact publications starting on 
day one, working with existing rich and unique datasets in addition to creating 
new ones. Extensive mentorship will be provided to facilitate the transition to 
an independent research career.

Duties and Responsibilities:

The Post-Doctoral Fellow’s responsibilities will include, but are not limited 
to:

Develop longitudinal multimodal MRI data analysis streams (functional 
connectivity, task-based fMRI, diffusion tractography and volumetrics).
Analyze complex multi-omics datasets including imaging, gut microbiome, 
metabolomics, behavioral and clinical data.
Prepare and submit manuscripts
Mentor graduate and undergraduate students
Be inquisitive, curious and publish!
Required Qualifications:

Ph.D. in Neuroscience, Neuropsychology, Bioinformatics, Biostatistics, 
Engineering, Computer Science or a related field.
Strong proficiency and independence with various neuroimaging analysis 
platforms, multivariate modeling strategies and network connectivity analyses.
Established quantitative and statistical skills, including strong programming 
skills and comfort with diverse computing environments. Experience with R, 
Linux, Matlab or Python preferred.
Background in systems/cognitive neuroscience, neuroanatomy and 
psychological/clinical constructs.
A demonstrated capacity to drive first author publications.
Excellent communication and writing skills, motivated and driven to publish.
Preferred Qualifications:

Connectomics network analysis and machine learning modeling confer a very 
significant advantage.
Management/coding of neuroimaging databases (XNAT or others).

Arpana "Annie" Gupta, Ph.D.
Associate

[Freesurfer] mri_aparc2aseg bad incorrect ROIs

2022-06-13 Thread Benjamin Deck 
External Email - Use Caution

Hi Freesurfer experts,

I am attempting to turn my surface-based parcellation into a segmentation
file using the following command:

mri_aparc2aseg --s sub-DAEK --annot yeo2011 --annot-table
sub-DAEK_yeoLUT.txt --threads 6 --rip-unknown --volmask

However, when I load the resulting volume using my custom LUT the ROIs get
labeled to the white matter and subcortical structures leaving the grey
matter unlabeled.

When I examine the annotation files, they look appropriate and there isn't
any overlap.

Do I need to include the subcortical structures in my custom LUT to avoid
this from happening or is there a better solution?

Thank you!

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


Virus-free.
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Re: [Freesurfer] Trac-all error assistance

2022-06-13 Thread Yendiki, Anastasia 
Hi Emmanuel - Not sure if you saw my earlier response, but the infant stream is 
under construction and not currently supported.

Anastasia.

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Emmanuel Rodríguez Silva 

Sent: Monday, June 13, 2022 12:39 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Trac-all error assistance


External Email - Use Caution

Hello, freesurfer developers
I was running the trac-all command for infant images. But I got an error during 
the cst processing. I've already checked the mailbox to find similar issues, 
but it seems that there are several logic errors. I will appreciate any 
assistance on this matter. I' m attaching my trac-all.log file for reference. 
Thank you.

This is the exact error:

terminate called after throwing an instance of 'std::logic_error'
  what():  basic_string::_S_construct null not valid
Abort (core dumped)

best,
Emmanuel from Mexico

--
Saludos cordiales
Emmanuel Rodríguez Silva


Contacto: (044) 55 59 97 76 18

Licenciado en Manejo Sustentable de Zonas Costeras
UNAM
[https://secure-web.cisco.com/1cNbEZQlhdfIEUxiqcxEsMm9hLKF76H8fbAIIAl4-Gj9OVh67QLId37gMusA7k5OI3h7TMVzBG4eneoNwE1xilPCKmzqIUY3efr61fcjchJNuBxkOPfXFKv0i7rkOh4ZWUy2XYa2mDXj6Mdb0Ay0YwB-9hjDm8bmbiGOk6YOv0U2dRGBeEel9hSEPXkHfuO4ywdWy6FFbMD-xAnDTwVnAjYqApi1stC69qZmMNI8zIS_0i7J6vxEkV9Id5bPSTl6l5NvZMPDQq_Nj6NT-VPymtJ0my5FW3pAUkaApSWaQ2s4JTTHHpKQd7eMZtbmcGzgb9is_z2viNqr3ddcK2BSiRg/https%3A%2F%2Fdocs.google.com%2Fuc%3Fexport%3Ddownload%26id%3D0B5vV8VGxH26nNzd4YTc2bHFqRjQ%26revid%3D0B5vV8VGxH26nNjY3OWIxM2FzbHdtY3RDeFRkZmNHYVJwbFlBPQ][https://secure-web.cisco.com/10x58ceCV8utm8rOGTRKLQFTN5kgOzUu2_gLdMiSeLdX49Jb32I3U0aa6X_4EbnwslLQLkg1QkK_Mo17y6-RIv9Km8avPsXGKpMbo6b1TirHMx27UYBoMAGYSa1YZURMbWNk6NJOXsS2XStLWsGUtjGpl7avP1tawvfiePNuEJUITupS6eqNfjUCZVTni2DlVEG_2k29AbbxTSWFkns4qR-39zFXdpiK3QRKqdvZhq_xy9lR23lXMxGF5fRmyT2Fx5dFpCgnVtzB2q7zphL7P8A5W5LGfsEqQYqfmhp3UhFG6G8ds8i8g0--6o0r2JGVP7vMdrfDl4CC2ZdfEKY65lg/https%3A%2F%2Fdocs.google.com%2Fuc%3Fexport%3Ddownload%26id%3D0B5vV8VGxH26nNTJyNXVVcm9TYk0%26revid%3D0B5vV8VGxH26nSmhYSGdtU1ZkUy9oSExhY3JSZENITTJVWnlNPQ]
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[Freesurfer] Trac-all error assistance

2022-06-13 Thread Emmanuel Rodríguez Silva 
External Email - Use Caution

Hello, freesurfer developers
I was running the trac-all command for infant images. But I got an error
during the cst processing. I've already checked the mailbox to find similar
issues, but it seems that there are several logic errors. I will appreciate
any assistance on this matter. I' m attaching my trac-all.log file for
reference. Thank you.

This is the exact error:

terminate called after throwing an instance of 'std::logic_error'
  what():  basic_string::_S_construct null not valid
Abort (core dumped)

best,
Emmanuel from Mexico

-- 
Saludos cordiales
Emmanuel Rodríguez Silva


Contacto: (044) 55 59 97 76 18

Licenciado en Manejo Sustentable de Zonas Costeras
*UNAM*
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[Freesurfer] 7z passcode

2022-06-13 Thread Lindner, Thomas 
External Email - Use Caution

Hello,


I try to install FreeSrufer in the Virtual Box and wanted to inquire for the 
passcode for the archive.


I already got a license.


Best,


Thomas


PD Dr. habil. Thomas Lindner
MRT Physik
Universitätsklinikum Hamburg-Eppendorf
Klinik und Poliklinik für Neuroradiologische Diagnostik und Intervention
Martinistraße 52
Gebäude West 14, Raum 57
20251 Hamburg
Telefon: +49 (0) 1522 281-6068
Fax: +49 (0) 40 7410-40114
t.lind...@uke.de
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_

Universitätsklinikum Hamburg-Eppendorf; Körperschaft des öffentlichen Rechts; 
Gerichtsstand: Hamburg | 
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Vorstandsmitglieder: Prof. Dr. Burkhard Göke (Vorsitzender), Joachim Prölß, 
Prof. Dr. Blanche Schwappach-Pignataro, Marya Verdel
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[Freesurfer] mri_vol2surf with --projopt

2022-06-13 Thread Kamiya Kouhei 
External Email - Use Caution

Dear FreeSurfer experts,

I have a question on the usage of mri_vol2surf's option, "--projopt". What
I want to do is to map the diffusion scalar value (like mean diffusivity
[MD]) to the cortical surface. Though mri_vol2surf with --projfrac 0.5
worked pretty well, I also tried with --projopt which I assumed to yield
better dealing with the partial volume effects.

However, when I run with --projopt, I encountered the following errors.
...
error: GM estimation at vno 31257 couldn't find enough samples
error: GM estimation at vno 31258 couldn't find enough samples
...

It looks the code tells me there is not enough data to solve the problem.
Could you please instruct me what should I do to use mri_vol2surf with
--projopt ?


My diffusion maps are in 1.7mm isotropic voxel and aligned with anatomical
T1w with BBregister, and I used the code as below.



tkregister2 --mov ${SUBJECTS_DIR}/${subject}/mri/norm.mgz --s ${subject}
--regheader --reg regheader.subject.dat --noedit
mri_compute_volume_fractions regheader.subject.dat
${SUBJECTS_DIR}/${subject}/mri/norm.mgz pvf
  # this gave me pvf.wm.mgz, pvf.csf.mgz, pvf.cortex.mgz, which are in 1mm
voxel

mv pvf.cortex.mgz pvf.gm.mgz
  # rename to pvf.gm.mgz to be compatible with the file name that appears
in mri_vol2surf code

mri_vol2surf --mov MD.nii.gz --regheader ${subject} --hemi lh --surf white
--projopt pvf --o lh.MD_pvf.GM.mgz




Respectfully yours,

Kouhei Kamiya
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