Re: [Freesurfer] mris_flatten Version 6 vs. 7

[Fischl, Bruce R.,PHD]

Yes, well, that is totally my fault! Doug is much better about adding help text 
than I am ☹
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Nasr, Shahin,Ph.D.
Sent: Friday, April 7, 2023 5:18 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7

Hi Bruce,
 In both versions, I use this command:

mris_flatten rh.occip.patch.3d rh.occip.patch.flat

They are applied to the same patch.

Also may be I missed it but when I used help (mris_flatten --help) I didn't see 
any of these flags.

Regards,

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Fischl, Bruce R.,PHD 
mailto:bfis...@mgh.harvard.edu>>
Sent: Friday, April 7, 2023 5:11:49 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7


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Hi Shahin



What is your command line? mris_flatten does some random sampling of distances 
since the whole N^2 distance matrix is too big. You can remove the randomness 
by either specifying -norand or using a specific seed like -seed 1234.



That said, you second image looks like a failure of the flattening. This 
usually means the distances aren’t sampled out far enough/densely enough. The 
defaults are super old (7 neighbor ring, 12 distances/ring). You could try 
something like -distances 20 20 and see if that fixes things (and -norand if 
you want)



Cheers

Bruce



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Nasr, Shahin,Ph.D.
Sent: Friday, April 7, 2023 3:15 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] mris_flatten Version 6 vs. 7



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Hi Surfers,

 This is the second time that I have brought this issue up.  When applied 
to the same 3D patch, the command mris_flatten generates two completely 
different outcomes when runs under stable 6 vs. 711 (see the attached files). I 
checked the documentation if there is any flags by which I can control the 
process. But I couldn't find anything relevant.  Any idea what has happened?



Regards



Shahin Nasr, Ph. D.

Assistant Professor in Radiology

Harvard Medical School

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Re: [Freesurfer] mris_flatten Version 6 vs. 7

[Nasr, Shahin,Ph.D.]

Hi Bruce,
 In both versions, I use this command:

mris_flatten rh.occip.patch.3d rh.occip.patch.flat

They are applied to the same patch.

Also may be I missed it but when I used help (mris_flatten --help) I didn't see 
any of these flags.

Regards,

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Fischl, Bruce R.,PHD 

Sent: Friday, April 7, 2023 5:11:49 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] mris_flatten Version 6 vs. 7


External Email - Use Caution

Hi Shahin



What is your command line? mris_flatten does some random sampling of distances 
since the whole N^2 distance matrix is too big. You can remove the randomness 
by either specifying -norand or using a specific seed like -seed 1234.



That said, you second image looks like a failure of the flattening. This 
usually means the distances aren’t sampled out far enough/densely enough. The 
defaults are super old (7 neighbor ring, 12 distances/ring). You could try 
something like -distances 20 20 and see if that fixes things (and -norand if 
you want)



Cheers

Bruce



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Nasr, Shahin,Ph.D.
Sent: Friday, April 7, 2023 3:15 PM
To: Freesurfer support list 
Subject: [Freesurfer] mris_flatten Version 6 vs. 7



External Email - Use Caution

Hi Surfers,

 This is the second time that I have brought this issue up.  When applied 
to the same 3D patch, the command mris_flatten generates two completely 
different outcomes when runs under stable 6 vs. 711 (see the attached files). I 
checked the documentation if there is any flags by which I can control the 
process. But I couldn't find anything relevant.  Any idea what has happened?



Regards



Shahin Nasr, Ph. D.

Assistant Professor in Radiology

Harvard Medical School

MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://mesovision.martinos.org/
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Re: [Freesurfer] mris_flatten Version 6 vs. 7

[Fischl, Bruce R.,PHD]

External Email - Use Caution

Hi Shahin

What is your command line? mris_flatten does some random sampling of distances 
since the whole N^2 distance matrix is too big. You can remove the randomness 
by either specifying -norand or using a specific seed like -seed 1234.

That said, you second image looks like a failure of the flattening. This 
usually means the distances aren't sampled out far enough/densely enough. The 
defaults are super old (7 neighbor ring, 12 distances/ring). You could try 
something like -distances 20 20 and see if that fixes things (and -norand if 
you want)

Cheers
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Nasr, Shahin,Ph.D.
Sent: Friday, April 7, 2023 3:15 PM
To: Freesurfer support list 
Subject: [Freesurfer] mris_flatten Version 6 vs. 7


External Email - Use Caution
Hi Surfers,
 This is the second time that I have brought this issue up.  When applied 
to the same 3D patch, the command mris_flatten generates two completely 
different outcomes when runs under stable 6 vs. 711 (see the attached files). I 
checked the documentation if there is any flags by which I can control the 
process. But I couldn't find anything relevant.  Any idea what has happened?

Regards

Shahin Nasr, Ph. D.
Assistant Professor in Radiology
Harvard Medical School
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
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[Freesurfer] T1 with contrast

[Carlos Alcocer]

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Can you use T1 with contrast in freesurfer or does it have to be
non-contrast images?

Tks,

Carlos
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[Freesurfer] Fwd: Research scientist positions at OSUMC!

[Douglas N. Greve]

Forwarding on an interesting job working Jessica Turner!


 Forwarded Message 
Subject:Research scientist positions at OSUMC!
Date:   Fri, 7 Apr 2023 13:42:55 +
From:   Turner, Jessica 
To: Douglas N. Greve 



External Email - Use Caution

https://osu.wd1.myworkdayjobs.com/OSUCareers/job/Medical-Center-Campus/Senior-Researcher_R74255-1 



_Job Description_

The Senior Researcher designs and conducts independent complex 
experimental research in a foundational (basic) biological/health 
science research laboratory with a psychiatric neuroimaging and genetics 
research program, in the Department of Psychiatry and Behavioral Health. 
 Expected responsibilities include developing and investigating 
neuroimaging models of symptoms and response to various treatments 
across diagnostic groups; applying current analysis techniques to the 
analysis of behavioral, neurophysiological, and genetic data in 
combinations; interpreting and evaluating research data; working with 
collaborative multi-site teams in the analysis of large-scale data 
collections; preparing manuscripts, articles, reports and abstracts for 
publication in peer-reviewed journals; attending and presenting results 
at national and international scientific conferences, seminars, and 
workshops; collaboratively developing and contributing to grant 
proposals to obtain extramural funding to support research; developing 
and implementing new research projects; directing and training other 
research staff, participating in laboratory meetings and project 
meetings.  Some mentoring of other research personnel may be available.


_Minimum Education Required _

Doctorate (Academic) in psychology, biology, engineering, computer 
science, or a relevant field.


_Required Qualifications _

The candidate will be analyzing data as part of their research work and 
must be capable of independently using some neuroimaging analysis 
pipelines (for example, fmriprep, SPM, FSL), ideally for structural, 
resting state, task-based analyses (the more imaging modalities the 
candidate has worked with, the better).  The ability to work in a Linux 
environment is a must. Experience with multivariate analyses of 
functional MRI data or combined analysis of imaging and other datatypes 
such as EEG, EMA, PET, genetics is a strength. An interest in the 
integration of genetic data with neuroimaging and behavioral data within 
clinical populations is ideal.  Clinical experience is not required but 
would be a strength. The candidate will also be writing in support of 
the research program, and must be capable of developing first author 
papers on neuroimaging results (as demonstrated by previous publications).


Many thanks!

Jess

Jessica A. Turner, Ph.D.

/Professor, Department of Psychiatry and Behavioral Health/

/Wexner Medical Center/

/The Ohio State University/

/jessica.tur...@osumc.edu/

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[Freesurfer] VM Password

[Janssen, J.A.M. (Julia)]

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Dear Freesurfer developers,

I am attempting to set up virtual box with the Ubuntu image provided in the 
installation guide. I would like to request the password to unzip 
'FS_7_2_0_ubuntu_18_04_06.ova.7z' - I hope this is the right place to ask. If 
anyone knows it, would they kindly contact me?

Thank you in advance!
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