[Freesurfer] Job posting: SRA at UCSD

[Wang, Xin]

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Hi there,

Could you help to post this job advertisement for our lab as below, please? 
Thank you so much.
Please let me know if you need more.

Best,
Xin Wang

Imaging Researcher

This position will work a hybrid schedule which includes a combination of 
working both onsite and remote.
DESCRIPTION
The research project will involve multiple neuroimaging studies examining 
biomarkers of brain aging and dementia. These studies will be partially 
conducted in collaboration with the UC San Diego Shiley-Marcos Alzheimer’s 
Disease Research Center. These studies will employ structural, diffusion and 
contrast MRI, amyloid and tau PET, neuropsychological testing, and blood and/or 
CSF biomarkers, among other tools, to better understand how brain 
microstructure, vascular integrity, and neuropathology, relate to disease risk 
and cognitive decline in Alzheimer’s disease or related dementias.
Under the supervision of the project PIs (Drs. Reas and Banks), the incumbent 
will serve as a research project associate for multiple research protocols 
assessing neuroimaging biomarkers of dementia. Incumbent is responsible for 
organizing and managing brain imaging research data. Incumbent will manage 
Linux based workstations for post processing/data manipulation, and data 
analysis as well as create, maintain and update research databases. Provide 
support in project administration and publication preparation of imaging 
research. May provide assistance and have direct communication with subjects 
and families involved in research projects.
MINIMUM QUALIFICATIONS
· Bachelor's degree (psychology, neuroscience, biology, cognitive 
science, statistics, computer science or related field preferred) or equivalent 
work experience.
· Proven knowledge of human subjects research policies and procedures. 
Knowledge of the human subject consent process, and federal government 
regulations pertaining to consenting of subjects. On-line training certificate 
(acquired on job). Knowledge of IRB, and sponsored research requirements.
· Experience in a clinical trials research environment including basic 
understanding of persons with dementia, preferred experience with MRI in order 
to recruit, schedule, and test patients for clinical study subjects.
· Thorough working knowledge of medical and scientific terminology.
· Knowledge of statistical analysis of quantitative brain imaging data 
measures using SPSS, Matlab, and other statistical programs and prefer skills 
in coding.
· Strong experienced with computers (Personal computer and Macintosh). 
Skill with personal computers, word processing, spreadsheet, e-mail software, 
databases, etc. Specifically Linux OS and the Microsoft office suite (excel, 
access, powerpoint, word, etc).
· Proven ability to determine sources of clinical data, analyze the 
data and information obtained, in order to create documents and to propose 
solutions to issues and to help in developing standardized operational 
procedures.
· Proven ability in researching clinical data in preparation for grant 
applications and technical manuals, staying abreast of new research 
developments. Ability to abstract information from protocol and investigator 
brochure, which requires summarizing large quantities of data.
· Skill in assembling written narrative information using word 
processing software for documenting image analysis procedures and tracking data.
· Excellent interpersonal skills with the ability to use tact and 
diplomacy with subjects (including patients with cognitive impairment), their 
families, faculty and institutional staff, as well as when representing the 
agency in the community.
· Ability to collaborate and communicate effectively and diplomatically 
at all organizational levels, both verbally and in writing. Ability to work 
professionally and effectively with a diverse population, including the 
business community, academicians, staff and students.
· Excellent record keeping, database management, detail oriented, 
logical, methodological approach to problem solving, strong process 
orientation, strong administrative and organizational skills with demonstrated 
ability to prioritize assignments, maintain workflow, and work productively in 
meeting critical deadlines and milestones.
PREFERRED QUALIFICATIONS
· Working knowledge of UCSD Human Research Protections Program policies 
and Procedures.
SPECIAL CONDITIONS
· Employment is subject to a criminal background check and 
pre-employment physical.

If anyone is interested in this position, you could contact Dr. Reas 
(er...@health.ucsd.edu ) and Dr. 
Banks(sba...@health.ucsd.edu ) for further 
detail.



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Re: [Freesurfer] Wrong thickness values with mris_anatomical_stats

[lqcheng2017]

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Hi Yulin and Bruce, 
Thanks for your quick replies. I tested FS v6.0 and v7.2 with the following command, and got the same results. mris_anatomical_stats -thr3 -mgz -f ./lh.aparc.stats -b -a $SUBJECTS_DIR/100307/label/lh.aparc.annot 100307 lh whiteusing thickness file -mgz.
computing statistics for each annotation in /dat03/data/HCP1200_FS//100307/label/lh.aparc.annot.
reading volume /dat03/data/HCP1200_FS//100307/mri/wm.mgz...
reading input surface /dat03/data/HCP1200_FS//100307/surf/lh.white...
Using TH3 vertex volume calc
Total face volume 245583
Total vertex volume 241389 (mask=0)
reading input pial surface /dat03/data/HCP1200_FS//100307/surf/lh.pial...
reading input white surface /dat03/data/HCP1200_FS//100307/surf/lh.white...
error: No such file or directory
error: MRISreadCurvature: could not open /dat03/data/HCP1200_FS//100307/surf/lh.-mgz

table columns are:
    number of vertices
    total surface area (mm^2)
    total gray matter volume (mm^3)
    average cortical thickness +- standard deviation (mm)
    integrated rectified mean curvature
    integrated rectified Gaussian curvature
    folding index
    intrinsic curvature index
    structure name

atlas_icv (eTIV) = 1512540 mm^3(det: 1.287970 )
 1297908   2459  0.000 0.000 0.096 0.0159 0.9  bankssts
  928588   1875  0.000 0.000 0.130 0.025   12 1.0  caudalanteriorcingulate
 3498   2347   6757  0.000 0.000 0.116 0.024   32 3.7  caudalmiddlefrontal
 2196   1350   2877  0.000 0.000 0.145 0.036   34 3.6  cuneus
  657427   1942  0.000 0.000 0.135 0.0479 1.5  entorhinalBest,Luqi


 





 

On 4/12/2022 21:41，Huang, Yujing wrote： 




Hi Luqi,
 
I’m wondering how you ran mris_anatomical_stats. Can you send the command?
 
I noticed 2 things in the error output:

The filename has a ‘-‘ after the ‘.’lh files should not have ‘mgz’ extension
 
Best,
 
Yujing
 


From: freesurfer-boun...@nmr.mgh.harvard.edu 
On Behalf Of lqcheng2017
Sent: Tuesday, April 12, 2022 9:09 AM
To: freesurfer 
Subject: [Freesurfer] Wrong thickness values with mris_anatomical_stats


 
External Email - Use Caution



Dear experts,



 


I thied to calculate measures using mris_anatomical_stats. All the measures seems right excepted that the thickness is 0. I noticed a error as follows: 


 


MRISreadCurvature: could not open /dat02/subjects/sub001/surf/lh.-mgz



No such file or directory



 


Could you have any ideas to solve the problem? 


 


Thank you very much.



 


Best,



Luqi


 






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[Freesurfer] Failed to load MRI error

[HYE JUNG YOUN]

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Dear freesurfer devleopers,

 

I am experiencing an error while loading freeview using the following code: 



 

This always worked for me but now when I try to load and view it, a message
"failed to load MRI" pops up on freeview after loading T1.mgz. 

 

>From the terminal it says: 

error:
mghRead(/Applications/freesurfer/7.2.0/subjects/211025/1079_4/mri/wm.mgz,
-1): read error

MRIread failed: Unable to read from
/Applications/freesurfer/7.2.0/subjects/211025/1079_4/mri/wm.mgz

 

Also, when I check the mri containing file, eg: 1079_4 folder, after loading
freeview, the folder contains automatically generated -v and -f file. 



I have seen a few similar errors on google and mail archive but they did not
solve my issue. 

I would very much appreciate any solution to this. 

 

Thank you in advance. 

 

Best, 

HJ

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[Freesurfer] rerunning on 7.2 with edited brainmask using hi-res

[Alexopoulos, Dimitrios]

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We are running some hi-res 0.8mm3 isotropic data through FS 7.2 using the 
following command.
recon-all -s subj -all -hires

We are adding back brain which has been removed by the masking process by 
cloning the T1/brainmask images in freeview and adding back voxels.
A revised brainmask.mgz is saved.

Can/should the same command be used to rerun using hi-res data?

Jim




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[Freesurfer] Beta values (resubmitting)

[Laura Willers de Souza]

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Hey! I'm resending this email because I think it got lost on the list.


Hello FreeSurfer Developers,



I'm extracting beta values ​​from some analyzes and I would like to know if I'm 
extracting and interpreting these values ​​correctly.



To extract the beta values ​​I used this command:

mri_segstats --seg 
lh.cortisol_CSF.glmdir/cortisol_CSF_slope/perm.th20.neg.sig.ocn.mgh --i 
lh.cortisol_CSF.glmdir/beta.mgh --excludeid 0 --avgwf 
lh.cortisol_CSF.beta.clusters.dat



The model consists of 1 group and 1 covariate.

I used the contrasts for intercept and slope.

The fsgd file looks like this:



GroupDescriptorFile 1

Title cortisol_CSF

Class Main

Variables  cortisol_CSF

Input   011_S_0003_S9128   Main2.397895273

Input   022_S_0004_S9233   Main2.772588722

Input   011_S_0005_S9137   Main3.044522438

Input   011_S_0008_S9196   Main2.397895273

Input   011_S_0010_S8800   Main2.151762203

... (n=300)


The beta values ​​extraction file contains 2 lines (image below).

[cid:69d5a8c2-68b8-43ac-85f3-0448f1e3a0b5]

  *Would the first line be the beta value for the intercept and the second 
line for the slope?
  *   Thus the glm equation for the 1st cluster would be:cortical thickness 
= 2.57 - 0.12X + n

Is this correct?


Thank you very much in advance.


Laura Willers de Souza

Master Student in Biochemistry

Zimmer Lab - Federal University of Rio Grande do Sul

- Porto Alegre/RS - Brazil

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[Freesurfer] Postdoctoral Researcher in Neuroimaging at Karolinska Institute, Stockholm, Sweden

[Joana Braga Pereira]

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Dear all,

We are looking for a Postdoc to work in an interdisciplinary and
internationally competitive environment at Karolinska Institute, one of the
top medical universities in the world and the home for the Nobel Prize in
Medicine.

We combine imaging analyses, statistical tools, machine learning
algorithms, biofluid assays and genetics to study brain aging and the
earliest signs of Alzheimer’s and Parkinson’s diseases.

This project will be carried out under the supervision of Associate
Professor Joana B. Pereira and it will involve analyzing cross-sectional
and longitudinal imaging data, combining clinical measures and
cerebrospinal fluid biomarkers, as well as writing manuscripts and
presenting results in international conferences. The fellow is expected to
be independent, develop his or her own projects, supervise students and
show an interest in approaches based on graph theory. In addition, he/she
will have the opportunity to develop new skills, analyze large datasets,
apply for grants and develop a wide network of collaborations.

The ideal candidate should have the following qualities:
- A PhD in neuroimaging, computational science, neuropsychology, physics,
statistics or a related field;
- Experience in statistical techniques, programming, or scripting;
- Experience with structural MRI, DTI, fMRI or PET imaging analyses;
- Clinical or research experience with aging and/or neurodegenerative
disorders.
- Excellent record of scientific publications.

The Postdoctoral studies will be performed for 1 year, with possible
extension for an additional year.

To apply please go to: 
https://secure-web.cisco.com/1_02gjVybcT6ODyv8ExuxWUpg_0WuTiWWNMhc561CKQhUuGTQnBJhWGRfGhBljRExkgHPvmU4XWqCRjiasgHuK_MNoz1UVEMtShOAmxOVnjD2WVXjzcVaXuQmJwSIIOmwQvJ6qV4cVJjnHGB1GSAPmmakbLqSQdqmF3lk6bV3HMfLGBlLsPv1f3e4dtwF-x0UurehXA3JWhiBtyRTp4flXJWTkIpny3jnYbcF1iSTye1pHxmArKibq6rgLayhD3Htrd3Cbd8dPlpgkHjvBHbH6UiH58CF429BIY0bqo_XaVjSeZ9wH-gv2awtRv_mQika3fT5QdupGMeiFDOEKPkB7A/https%3A%2F%2Fki.varbi.com%2Fen%2Fwhat%3Ajob%2FjobID%3A489190%2F

(Deadline: 29/04/2022)

For further information or general inquires, please contact Joana B.
Pereira at jbragapere...@gmail.com or joana.pere...@ki.se.

Best wishes,
Joana
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Re: [Freesurfer] Wrong thickness values with mris_anatomical_stats

[Fischl, Bruce]

Hi Luqi

You need to send us the complete command line you ran and the entire output of 
the command, plus the FS version number you are using.

Cheers
Bruce


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of lqcheng2017
Sent: Tuesday, April 12, 2022 9:09 AM
To: freesurfer 
Subject: [Freesurfer] Wrong thickness values with mris_anatomical_stats


External Email - Use Caution
Dear experts,

I thied to calculate measures using mris_anatomical_stats. All the measures 
seems right excepted that the thickness is 0. I noticed a error as follows:

MRISreadCurvature: could not open /dat02/subjects/sub001/surf/lh.-mgz
No such file or directory

Could you have any ideas to solve the problem?

Thank you very much.

Best,
Luqi

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Re: [Freesurfer] Wrong thickness values with mris_anatomical_stats

[Huang, Yujing]

Hi Luqi,

I’m wondering how you ran mris_anatomical_stats. Can you send the command?

I noticed 2 things in the error output:

  1.  The filename has a ‘-‘ after the ‘.’
  2.  lh files should not have ‘mgz’ extension

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of lqcheng2017
Sent: Tuesday, April 12, 2022 9:09 AM
To: freesurfer 
Subject: [Freesurfer] Wrong thickness values with mris_anatomical_stats


External Email - Use Caution
Dear experts,

I thied to calculate measures using mris_anatomical_stats. All the measures 
seems right excepted that the thickness is 0. I noticed a error as follows:

MRISreadCurvature: could not open /dat02/subjects/sub001/surf/lh.-mgz
No such file or directory

Could you have any ideas to solve the problem?

Thank you very much.

Best,
Luqi

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Re: [Freesurfer] recontruction of an elephant brain

[Malav Shah]

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Hi Douglas, 
thank you so much for your suggestions. 
Your understanding of my task is very precise, and I would love to move in the 
direction you recommend. I would appreciate a bit more detailed guidance. 
Would you have a little bit of time to spare for me in those regards? 

Looking foward, 
Malav Shah 


From: "Douglas N. Greve"  
To: "freesurfer"  
Sent: Saturday, April 9, 2022 10:18:18 PM 
Subject: Re: [Freesurfer] recontruction of an elephant brain 

Lot's of people have adapted FS to non-human brains, just google it. For 
surface analysis, you need to get the "subcortical mass" -- the equivalent to 
the filled.mgz. This is the cerebral white matter + subcort gray structures. 
Once you have that, you might be able to run mris_place_surfaces. I'd have to 
walk you through the options to use or not. 

On 4/8/2022 6:01 AM, Malav Shah wrote: 




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Hi Lilla, 

Thank you so much for your feedback. 

I completely understand the tool's bias for human brains. As you said, the 
elephant brain images are not well understood so far. We aim to take initial 
steps in that direction, starting with small goals like WM-GM seperation, 
cortical thickness measurements, and surface visualisation with flattening. Do 
you think it can be achieved with FreeSurfer's volume-based analysis pipeline? 
We would be more than happy to collaborate on that. 

Looking forward to hearing from you :) 
Thanks and regards, 
Malav Shah 



From: "Zollei, Lilla,Ph.D." [ mailto:lzol...@mgh.harvard.edu | 
 ] 
To: "freesurfer" [ mailto:freesurfer@nmr.mgh.harvard.edu | 
 ] 
Sent: Wednesday, April 6, 2022 8:29:33 PM 
Subject: Re: [Freesurfer] recontruction of an elephant brain 

Hi Malav, 

Freesurfer is guided by an atlas that was built from human adult brain images. 
In the past though, we did have collaborators who have tried some modified 
versons of the pipeline to work on non-human data. Here are some pointers: 

[ 
https://secure-web.cisco.com/1149bxkRGOm5AzvVYmA-Bxc160t7HU-wHF-xUFdBZaQ-CBDMhfyoMiEkF7LgJIJ_w2ZHvZc48UMSj3dntsS0oSNQ8vdQc73Jlmd34JnP5adcUaLvPSYD34MknD4RGJCciLXDv6LLLWHftORNu5-I2UJ9s-3vmM0xvwEOg_rP6R_H06ZkjIIqqSlghgO6dQWO2TD0avKyXnSU_eDy0zm0jtaUQQo_9wjJxYXzzbruHepTSyu0mPr2m1plsCrh1oqcnOIO52xQ59mJxjJHGSSG0NSkfLM9x7-WkZswQgb9jyx13SmLAfd8qay-lglviBvnwJnizBfEJwrJyEuIJ53mdzQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FMonkeyData
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 ] 

As far as I know elephant brain images have not yet been processed. G ood luck, 
Lilla 


From: [ mailto:freesurfer-boun...@nmr.mgh.harvard.edu | 
freesurfer-boun...@nmr.mgh.harvard.edu ] [ 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu | 
 ] on behalf of Malav Shah [ 
mailto:malav.s...@bccn-berlin.de |  ] 
Sent: Wednesday, April 6, 2022 1:10 PM 
To: [ mailto:freesurfer@nmr.mgh.harvard.edu | freesurfer@nmr.mgh.harvard.edu ] 
[ mailto:freesurfer@nmr.mgh.harvard.edu |  ] 
Subject: [Freesurfer] recontruction of an elephant brain 


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hi, 
I am trying to reconstruct elephant brain MRI. I am wondering if FreeSurfer can 
manage this, or does the recon-all command has an inherent bias for human data. 
Does anyone have an experience using FreeSurfer with a non-human mammal for 
such purposes? 

I have some hopes with this idea, because I am not trying to achieve 
parcellation or segmentation. Rather, we want to separate White matter from 
grey Matter, and t

[Freesurfer] Wrong thickness values with mris_anatomical_stats

[lqcheng2017]

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Dear experts,


I thied to calculate measures using mris_anatomical_stats. All the measures seems right excepted that the thickness is 0. I noticed a error as follows: MRISreadCurvature: could not open /dat02/subjects/sub001/surf/lh.-mgz
No such file or directory
Could you have any ideas to solve the problem? 
Thank you very much.


Best,
Luqi

 



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Re: [Freesurfer] parallel make_average_subject

[falk.luesebr...@med.ovgu.de]

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Hi Marina,


whenever I want to parallelize something which doesn't have a built in 
function, I'm using GNU parallel. Just google for it. The documentation is 
quite good.


Best,

Falk


...

[http://secure-web.cisco.com/1ZOQLXeEUYkEe-uLh_AhkGhdRee6u0HM4FgGRlgF7MqTQ2qnbOHrqhOwmAHjbzNqknHgOQ3ikU_MokLPD2LGdD2xgMxp6devAWGOLfKWxhGvZYnj5jQx3TKLNdCuhN_ZeEKms_Lla_yvkdQrf4FsJnVyAAbza9n6nx6VZoLe7tsiye--TJTLgZye5WkuPA8zp7CfnsfwjC93ZvXasDk-IIz5wDknm4AQlXXC_a93P9uOhe8EQOOrfGk5_OG01Zna1rKjcSLKqr4YJ_UMCr1veLOpEuEx6gHH58wMQPWNtmH9m9_8Vn3t-sHBByWOIFliA/http%3A%2F%2Fwww.med.ovgu.de%2Funimagdeburg_mm%2Fummd_focus.gif]
Universitätsklinik für Neurologie

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Telefon: +49-391-6117-512

falk.luesebr...@med.ovgu.de
http://secure-web.cisco.com/1gW_0xbMsYzzwqiqr-9YoZRlkYpY9CW9WVS2Yzi0N8B9CbPFkgvp1dDx6o7Rl9B7o9NA2dh7vPrECJz03zw23Y8B3erBHtMsrh7gQoTkxmDgla-u9eNIrR-PSiSgojYSbvSNxYMWnF5mlu3vV2dQWlpS7HsxnbNWqinHRWNvEF4YFHGgbKnJ5biGO_Ym_dwTfQ6_lTOzDTbs1VsK965XdWpPJGx5KPx8-eGAde51Bl8WQ6YsNmb6uT7w4Bz3DSqioksQbF4e-qyFF8INCE2iR0OJMEWxs69RO2Ca9K1sljwKHcKC_1XhJuM-r0lZg7FAI/http%3A%2F%2Fwww.kneu.ovgu.de%2Fkneu.html

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Marina Fernández 

Gesendet: Montag, 11. April 2022 15:54:13
An: freesurfer@nmr.mgh.harvard.edu
Betreff: [Freesurfer] parallel make_average_subject


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Dear experts,

I would like to create an average subject from a very large population. I am 
going to compute it on a computer with a lot of threads and I would like to 
know if it is possible to parallelize the make_average_subject function to try 
to shorten the computation time. I have tried to add the -openmp flag but I get 
the error that the flag is unrecognized.
How can I solve this?

Thank you in advance.

Best regards,
Marina






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Re: [Freesurfer] Pass code

[fsbuild]

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Sending the info to your email shortly.
- R.

On Apr 12, 2022, at 04:33, Wei  
wrote:External Email - Use 
CautionDear professors,I have 
downloaded the FreeSurfer Vitrual VM images and a pass code is needed for this 
7z archieve.. Would you please send me the pass code for 
help?wzh ___Freesurfer mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer​
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[Freesurfer] Pass code

[Wei]

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Dear professors,


I have downloaded the FreeSurfer Vitrual VM images and a pass code is needed 
for this 7z archieve. Would you please send me the pass code for help?
wzh___
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[Freesurfer] Pass code for FreeSurfer VitrualBox VM Images

[Wei]

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Dear professors,
I have downloaded the FreeSurfer Vitrual VM images and a pass code is needed 
for this 7z archieve. Would you please send me the pass code?
wzh___
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