Re: [Freesurfer] Standalone freeview

2022-07-05 Thread Wang, Ruopeng 
There is only a stand-alone version for macOS. You can download it from here:

https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview

You’ll still need to install a license file properly. 

Best,
Ruopeng 

> On Jul 5, 2022, at 5:19 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) 
>  wrote:
> 
> External Email - Use Caution
> 
> Hi developers,
> 
> I have some colleagues who have been assigned to quality check brain scans 
> remotely on their laptops (macs), and they have space constraints. Is there a 
> stand alone freeview-only installation that doesn't require the ~10gb needed 
> for the entire freesurfer suite? 
> Sorry if this question has already been asked. 
> Victor Zeng
> Beth Israel Deaconess Medical Center
> Keshavan Lab
> --
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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[Freesurfer] Fwd: Passcode for the VM

2022-07-05 Thread MANUEL RUOCCO 
External Email - Use Caution

Hello,

I would like to ask for the passcode for the VM file containing
FS_7_2_0_ubuntu_18_04_06.ova.7z. Thank you for your assistance.
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[Freesurfer] Standalone freeview

2022-07-05 Thread Zeng, Victor (BIDMC - Keshavan - Psychiatry) 
External Email - Use Caution

Hi developers,

I have some colleagues who have been assigned to quality check brain scans 
remotely on their laptops (macs), and they have space constraints. Is there a 
stand alone freeview-only installation that doesn't require the ~10gb needed 
for the entire freesurfer suite?
Sorry if this question has already been asked.
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
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[Freesurfer] Postdoc Position in Cognitive Neuroscience at Tulane University

2022-07-05 Thread Ben Deen 
External Email - Use Caution

The Social Memory Lab, directed by Dr. Ben Deen, is seeking a Postdoctoral
Fellow. The lab studies social perception, cognition, and memory, with the
goal of characterizing the cognitive and neural basis or our ability to
understand other people. We use behavioral and neuroimaging (fMRI) methods
in humans, with a focus on precision imaging of functional organization in
individual brains. Specific research projects within that scope are
flexible and dependent on the interests of the candidate. Fellows will have
the opportunity to conceive of and design research studies, lead and
participate in data collection and analysis, mentor graduate and
undergraduate lab members, write fellowship and grant proposals, and
present their results at scientific conferences.



*REQUIRED EDUCATION AND EXPERIENCE:*

1.PhD in psychology, neuroscience, or a related field





*REQUIRED KNOWLEDGE, SKILLS, ABILITIES/COMPETENCIES*

1.Ability to communicate effectively with lab members, university
staff, and volunteers

2.Experience with behavioral and/or neuroimaging research with human
participants

3.Proficiency coding in Matlab, Python, or R





*PREFERRED QUALIFICATIONS:*

1.Experience with fMRI data collection and analysis

2.Strong publication record in psychology and/or neuroscience





Interested candidates may apply online at 
http://secure-web.cisco.com/1MoQV-Z4F4SEZC3oVL8Qnleak3C0d8YKf-cog-cSxWXfCBn9GZBZAhGFdzVb2U980ucLmmFLtyNWDmabAF3vZ7ZzHwdSWjsuq863YdBtYUBRxSGnZBznQoSmsb96nX-13zIbM6zoUzuDE3SsrXXYen00E39IhZ1skR6FBOEsBm7R-gYJcut9oaSlDisDFD11SaKzOTr-o3WjQUVlhrgjBbZJyBvd2hdZuCVEXLCQxHgngejyb07t8NdD60n0Rg7MrK4IOXGJ0pXimaKskUBRDfx6HbK1YBLUuen7NLJFxwThCpu3Z4i43ddzlkrPCToKMPzY1ln33fewKHfjVnO-1lA/http%3A%2F%2Fapply.interfolio.com%2F108286
or email bd...@tulane.edu with any questions about the position.
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[Freesurfer] Research Technician Position in Cognitive Neuroscience at Tulane University

2022-07-05 Thread Ben Deen 
External Email - Use Caution

The Social Memory Lab, directed by Dr. Ben Deen, is seeking a Laboratory
Research Technician who will contribute to multiple aspects of research
projects studying social perception, cognition, and memory, using
behavioral and neuroimaging (fMRI) methods. The Laboratory Research
Technician will work as part of a team comprised of postdoctoral fellows,
graduate students, and undergraduate research assistants, and will
coordinate day-to-day operations of the lab. Major responsibilities include
participant recruitment, collection of behavioral and fMRI data, data
analysis using Matlab or Python, and administrative duties. Other tasks
will be commensurate with the experience and interests of the technician.
The position requires excellent communication and organizational skills, a
high degree of independence, and an interest in cognitive neuroscience.



*REQUIRED EDUCATION AND EXPERIENCE:*

1.Bachelor’s degree in psychology, neuroscience, computer science, or a
related field

2.Previous experience working in a research lab



*REQUIRED KNOWLEDGE, SKILLS, ABILITIES/COMPETENCIES*

1.Ability to communicate effectively with lab members, university
staff, and volunteers

2.Ability to perform daily tasks in a highly organized fashion, with
attention to detail

3.Strong time management skills and ability to effectively manage
multiple assignments

4.Willingness to work flexible hours, including evenings and weekends
as needed

5.Desire to acquire new skills and competencies in a dynamic research
atmosphere

6.Proficiency in computer skills, including Microsoft Office
applications



*PREFERRED QUALIFICATIONS:*

1.Proficiency coding in Matlab, Python, or R

2.Demonstrated interest in cognitive neuroscience research



Interested candidates may apply online at
https://secure-web.cisco.com/1wldJZ_Nw3f2XASAdXti-afFK0hYTKcIYRrtzeeaSycTIGhw_J5XPTYhpNahuH8jMJ3vykfAu_42XHEvuk2pyieZcLBvlyj7l0AD3P1cV3Raz6golL7gzGn1-K7frf8sxTzaj55rNGmEkR7SSAcHj7OSNm6FagZg5HDpfchTCeZ1zfRCYPTIbgY5_90PpMC21nS-aFsWYctrVVq2kW63rtoD2E1w0iwT9YApFRAmlV5mK473pijTkFDopjImmsNtX0oYVL3VcCCVbGJY_0ECnA110QRvoiBrDS5Op5kbxDAwEZ6rVvVrP8Nwth9N1nY89/https%3A%2F%2Fjobs.tulane.edu%2Fposition%2FIRC23869
 or email bd...@tulane.edu with
any questions about the position.
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[Freesurfer] Cohen's D from selxavg3-sess output

2022-07-05 Thread Caspar M. Schwiedrzik 
External Email - Use Caution

Hi!
I would like to compute Cohen's D for individual subjects.
I was wondering whether I can use the output from selxavg3-sess for this:
ces./rstd
Or does this only work with gamma and rstd after mri_glmfit?

Thank you, Caspar
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Re: [Freesurfer] How to project SPM image

2022-07-05 Thread Fischl, Bruce 
Hi Rachel

I'll leave bbreg command lines to others (Doug?), but in general you don't want 
to base the registration on the inflated since it doesn't have a meaningful 
location within the volume. I would use the standard bbreg command, then use 
mri_vol2surf to paint what you want onto the surface. Once it is on any surface 
for a subject you should be able to display it on any other surface for that 
same subject (and same hemisphere).
Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Rachel Wagner
Sent: Tuesday, July 5, 2022 12:17 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] How to project SPM image


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Thank you, that would work very well! I'm trying this code without success, am 
I missing a component to display on an inflated surface?

bbregister --mov rReslice_Combined_roi_meanRD.nii --bold \ inflated -overlay 
--s  fsaverage \ --init-rr --lta register.lta

From: Fischl, Bruce
Sent: July 4, 2022 3:45 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to project SPM image

Well you can display it on inflated surfaces instead of white ones, which will 
remove most of the folds. Then you can smooth the surface overlay however you 
like (the colors on the surface) in freeview

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rachel Wagner
Sent: Monday, July 4, 2022 3:27 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image


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Thank you, noted!

I think I am on the right track, but I'd like to smooth the surface out 
(particularly the coloring and the sulci, which are quite deep) considerably - 
is there any way for me to do that?

From: Fischl, Bruce
Sent: July 3, 2022 7:44 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] How to project SPM image

I see, and what's wrong with the screen shot you have? (and "Bruce" is fine).

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Rachel Wagner
Sent: Sunday, July 3, 2022 7:41 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image


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Hi Dr. Fischl,

My apologies, I don't have much of a background in software generally!

For the SPM image, I used the AAL atlas to label lesioned brain regions and 
colored by frequency to generate the heatmap. Image dimensions: 1x1x1, Image 
Size [91 109 91], Pixel Dimensions [2 2 2], Bits Per Pixel: 32. I will map onto 
fsaverage!

I'm hoping to display it as a heatmap on an average surface, to look something 
like this: MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be | Decreased functional connectivity from 
Wernicke's area homologue in... | Download Scientific Diagram 
(researchgate.net)

This is a screenshot of what I currently have within FreeSurfer: MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be 
https://drive.google.com/file/d/150V0yIx6T1oSiCwiFmFiKU9rbNk1BfhD/view?usp=sharing

Thank you very much again for your help!
Rachel


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce 
mailto:bfis...@mgh.harvard.edu>>
Sent: Sunday, July 3, 2022 6:37:42 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] How to project SPM image


Can you give us more details? How did you create the 
rReslice_Combined_roi_meanRD.nii? What resolution is it? And how are you