[Freesurfer] Difference between V1_exvivo.label and v1.predict.label?

[Lee Subin Kristine]

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Dear FreeSurfers,

I am wondering what is the difference between V1 labels obtained from
V1_exvivo.label and v1.predict.label, and what is more exact?

When visualizing resutls from both labels, V1_exvivo.label occupies a larger 
portion than v1.predict label.

Thanks,
Kristine
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[Freesurfer] Longitudinal Registration

[Suzan Maleki]

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Hi FS experts,

I appreciate it if you help me with a question on your
longitudinal processing pipeline. If I use FreeSurfer to generate an
unbiased T1 image template from N time points (non-linear registration),
then how can I apply the within subject transformation matrix (Jacobian
matrix) to that subject's DTI maps.
Does FreeSurfer save the transformation matrix from N.Time-Points toward
Template image? and if so, in which folder directory it will be saved?
Also, given that FS uses vertices, should I first convert that
transformation matrix to voxel space  (eg. using surf2voxels ?) and then
multiply that into different time-points of one's DTI images.
Hope my questions are clear and looking forward to hearing from you:-)

Best
Suzan
-- 

*Suzan Maleki*

PhD Student


*Brain, Mind and Society Research Hub*

*Turner Institute for Brain and Mental Health*

School of Psychological Sciences

Monash University
770 Blackburn Road

Clayton VIC 3800 Australia


E: *suzan.mal...@monash.edu *
W: 
http://secure-web.cisco.com/11rJxuhHbcEcZqCYP3vJeG9D1pvF71PV1NgM7qYlH-yg7b7wbTp7stiDJEhMZtX_ueq824W2pn5A-097twlQNgjQm71geOqPiDw7vH2UhbHQk0xEXYH8z6SxTyr1HNLVBK0Q_W_2SmfU6v8Xtr5DSCZLJbI4eo2UpNR7887YlGQNGkYevdBxTfT5Qspj1yUN8T12Byiov-tnXzU_76nRiZI8wBmxqob23Ve814HgXR27gw0Km9aaAHzAYJY9uah3dky5YVVOz1aJpCbS-00f1Xw/http%3A%2F%2Fwww.brainmindsociety.com
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Re: [Freesurfer] Matlab version 2012b installation problem

[Georgia Kapizioni]

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Ok I understand. 

Thank you for your help.
Best,
Georgia

> On 9 Feb 2021, at 5:49 PM, Georgia Kapizioni  wrote:
> 
> Hello Andrew,
> 
> Thank you for your response!
> The output of the first command (meaning sudo cd $FREESURFER_HOME/bin && curl 
> https://secure-web.cisco.com/1Uw8kMcOACw-FvrURLDyTPgouP6SdSvLEnZNwjqUHGSLOq5daUPxIiN6uaLQN2M216zLZaao0O12iiaCeL1JpCvzxmrLsCSEy3QpkrRHIzmATgMeFzytHGjquyVagPunwSkUjGZdS2cnlY6OnBl5FUrKiVJGIGqeyr9BbJlXWfQhJnRqqyYVG5Ff0gQoIojew4VYNm_VucvUOD_5vNpiKbbzeqMS6QfbkQdz_fRjerOLPEkcqCN1d-az1eQK4W3vd/https%3A%2F%2Fraw.githubusercontent.com%2Ffreesurfer%2Ffreesurfer%2Fdev%2Fscripts%2Ffs_install_mcr
>  
> 
>  -o fs_install_mcr && chmod +x) was:
> 
>  % Total% Received % Xferd  Average Speed   TimeTime Time  Current
>  Dload  Upload   Total   SpentLeft  Speed
> 100  2010  100  20100 0   5275  0 --:--:-- --:--:-- --:--:--  5261
> usage:chmod [-fhv] [-R [-H | -L | -P]] [-a | +a | =a  [i][# [ n]]] 
> mode|entry file ...
>   chmod [-fhv] [-R [-H | -L | -P]] [-E | -C | -N | -i | -I] file …
> 
> However, when I type: ls -l $FREESURFER_HOME/bin/fs_install_mcr as you 
> suggested, it appears ls: /Applications/freesurfer/bin/fs_install_mcr: No 
> such file or directory
> When I type again fs_install_mcr while being in Freesurfer/bin path again 
> fs_install_mcr: command not found appears.
> Any idea what went wrong?
> 
> Thanks once again,
> Best,
> Georgia
> 
> 
> 
> 
>> On 9 Feb 2021, at 1:05 AM, Georgia Kapizioni > > wrote:
>> 
>> Dear Freesurfer experts, 
>> 
>> I am trying to install Matlab version 2012b but a message appears: command 
>> not found. 
>> 
>> Firstly, I ran: sudo cd $FREESURFER_HOME/bin && curl 
>> https://secure-web.cisco.com/1Uw8kMcOACw-FvrURLDyTPgouP6SdSvLEnZNwjqUHGSLOq5daUPxIiN6uaLQN2M216zLZaao0O12iiaCeL1JpCvzxmrLsCSEy3QpkrRHIzmATgMeFzytHGjquyVagPunwSkUjGZdS2cnlY6OnBl5FUrKiVJGIGqeyr9BbJlXWfQhJnRqqyYVG5Ff0gQoIojew4VYNm_VucvUOD_5vNpiKbbzeqMS6QfbkQdz_fRjerOLPEkcqCN1d-az1eQK4W3vd/https%3A%2F%2Fraw.githubusercontent.com%2Ffreesurfer%2Ffreesurfer%2Fdev%2Fscripts%2Ffs_install_mcr
>>  
>> 
>>  -o fs_install_mcr && chmod +x 
>> Then I typed: fs_install_mcr R2012b and I receive: command not found. 
>> My FS version is 6 and I have already install Matlab2016_b on my Mac. 
>> 
>> Could you please help me resolve this issue? 
>> Thank you in advance,
>> Georgia
>> 
> 

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Re: [Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Iglesias Gonzalez, Juan E.]

Dear Franziska,
Can you please send the automated segmentations as well?
Cheers,
/Eugenio

 
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com 
 
 

On 3/11/21, 09:45, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
Gronow, Franziska"  wrote:

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Here are the norm.mgz files of two subjects as .zip file:

https://secure-web.cisco.com/1APo2l-OLKuGnU9Z0d-bUlzi3og8pCdkJHpflzBF05TNzIdjkIjTOvtomItfqHsdtu1RXIan9sqawThsD1AInX2PV_jNS-9gp_FPgvgzSNu5cvTJ3FuX_AJhQoY7ADXl3WDZ7EypfhlOS6dgCV2hdRIEtwFUpEFgZxu8x62DXJzDHVEYp5Edr22tcIE79zGpIu-qXANDWaexYIMUXA9XJvYhyCYYfcsyIlXrXQk9MkoF3_ONddEpAyG3iOnx4ErXzREE-nIZebs_59EE0Bp7Kgg/https%3A%2F%2Fcloudstore.zih.tu-dresden.de%2Findex.php%2Fs%2Fz53CsHgjz7rC2zj

Thanks for your help!

Best regards, Franziska


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[Freesurfer] Thalamic nuclei segmentation - PuM nucleus mis-segmentation?

[Gronow, Franziska]

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Here are the norm.mgz files of two subjects as .zip file:
https://secure-web.cisco.com/1APo2l-OLKuGnU9Z0d-bUlzi3og8pCdkJHpflzBF05TNzIdjkIjTOvtomItfqHsdtu1RXIan9sqawThsD1AInX2PV_jNS-9gp_FPgvgzSNu5cvTJ3FuX_AJhQoY7ADXl3WDZ7EypfhlOS6dgCV2hdRIEtwFUpEFgZxu8x62DXJzDHVEYp5Edr22tcIE79zGpIu-qXANDWaexYIMUXA9XJvYhyCYYfcsyIlXrXQk9MkoF3_ONddEpAyG3iOnx4ErXzREE-nIZebs_59EE0Bp7Kgg/https%3A%2F%2Fcloudstore.zih.tu-dresden.de%2Findex.php%2Fs%2Fz53CsHgjz7rC2zj

Thanks for your help!

Best regards, Franziska


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[Freesurfer] Postdoctoral Research Assistant on the neuroscience of visual processing and decision making

[Etienne B. Roesch]

** Postdoc opportunity ** for neuroscientists and/or neuro-enthusiast engineers


We are seeking to appoint a highly motivated, adventurous, interdisciplinary 
neuroscientist to help us understand how humans prioritise information in 
support of the decisions they make. We focus on visual perception, attention 
and individual differences, and will be using psychometrics assessments and 
psychophysics measurements as well as concurrent EEG-fMRI recording. Full time, 
fixed term for up to 24 months, with possibility of extension.

This role falls in the remit of CHAI, a new £2.4M research project funded by 
the UK EPSRC and led by the Internet of Things and Security Centre (ISEC) at 
the University of Greenwich, in collaboration with University College London 
(UCL), the University of Bristol and Queen Mary University of London, as well 
as industrial partners. As a follow up to the €1.5M EU project “Cocoon: Emotion 
psychology meets Cyber Security” (2016-2020) led by us, which measured and 
established how users of connected Internet-of-Things devices react to cyber 
security risks, “CHAI: Cyber Hygiene in AI-enabled domestic life” (2021-2024) 
examines the particular threats posed by Artificial Intelligence. CHAI 
addresses the challenge of figuring out how to best help users protect 
themselves against the security risks they will face in a world supported by AI 
(see: 
http://secure-web.cisco.com/1CuL6BnF558JaAbIWP-jb9e7cD4U7zHl1-pWk2LQxyAupLd-yppflj7TFgfH63UUrz5zeN3dJCXB-TEpIuSbxJs0iAzLrX8YZqeYiXVQjtskhrOuW8cCy_ZunoTRJw9t2QqrF3w_4iZm6kWOKcx-wX_lHf1QOrg_YPkfKY2e7OnnYM79Tk63PT4nLTChjJWzPlWOEHWzJQs19NXtnBYw-ZnCDVaTn5Fyne6aYR7RurbmWDMX5xMkeg_-HSj14HsIwN891H0ZbbdmRiMwhnaqxNw/http%3A%2F%2Fbit.ly%2Fchai-introduction-video).

The role advertised relates to the fundamental research on human decision 
making that will inform the technical and pedagogical developments of our 
partners in the project. The remit is intentionally flexible to allow emerging 
opportunities for collaborations and includes funding for networking and 
training.

You will have:
- excellent computer and statistical skills, including a programming language 
(Python)
- experience analysing neuroimaging data, including EEG and/or fMRI
- the motivation to pursue research at the interface between academia and 
industry

This work will be carried out in the Centre for Integrative Neuroscience & 
Neurodynamics (CINN), in the School of Psychology and Clinical Language 
Sciences, at the University of Reading. CINN is a research platform currently 
gathering over 100 research staff and students. It is host to a 
research-dedicated 3T PRISMA Siemens MR scanner, MR compatible EEG (Brain 
Products) and TMS (MagVenture) equipments, eye-tracking and versatile computing 
clusters (incl. cloud management and GPUs), all of which available to the 
project.

Other research projects in the lab currently include the development of a novel 
Bayesian framework for the analysis of data in psychology and neuroscience, 
neuroimaging of visual perception and attention, as well as projects with 
industrial partners on topics as varied as machine learning and brain-computer 
interfaces for a wide range of sectors.

CINN and the School of Psychology are a tight-knit community, committed to open 
research and reproducibility, at the forefront of what is done in the UK in 
many ways. The post holder will have the opportunity to participate in many 
initiatives, and propose new ones, including training events on 
reproducibility, and best practices in neuroimaging, data analysis and coding, 
including Software Carpentry workshops.

The University of Reading was the first University in the UK to publicly commit 
to open research. It is one of the first institutional members of the UK 
Reproducibility Network, and a member of the data and software Carpentries. The 
University is signatory to the Leiden Manifesto for Research Metrics 
(http://secure-web.cisco.com/1aBHEAMNXjJYh_EJEn0MRa5fBIIXw7ol-w2THK9rK4UhZahwBbpeDT24jPHl_0eJ93G4dM8thXZ_qTq46Ia4sIbPBIh-gUBWGHLsT2svakDmRYtVQNzPkWQ3ntqB_ixQZ7zxIPxF5M0vm28HsXRh_89bShmCByllnNKbTqBkBJxbH3KLIHHWF8w5i4WUB05tsiLoPGtgXpxQcnGblxaiW1-kkr4ORmmEpUCmIh-Q654A9kGAb9wqD6rFHOEL8daUji3dydLUGnBVw5LuUugr_Gw/http%3A%2F%2Fleidenmanifesto.org),
 is  committed to having a diverse and inclusive workforce, supports the gender 
equality Athena SWAN Charter and the Race Equality Charter, and is a Diversity 
Champion for Stonewall, the leading LGBT+ rights organisation in the UK. 
Applications for job-share, part-time and flexible working arrangements are 
welcomed and will be considered in line with the project’s needs.

Deadline: 19/4
Interviews (online): Early may

Informal inquiries to Etienne Roesch, e.b.roe...@reading.ac.uk

More information at: 

Re: [Freesurfer] Matlab version 2012b installation problem

[Hoopes, Andrew]

The 'matlab runtime' (MCR) installed by fs_install_mcr lets you run compiled 
matlab binaries, but it’s different from having matlab actually installed on 
your system. MCR is used to run the sub-structure segmentation tools, but 
mris_compute_lgi is a command that runs matlab scripts directly, so it’s 
required that you have matlab installed on your computer to use it.

best
Andrew

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

Date: Wednesday, March 10, 2021 at 6:35 AM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Matlab version 2012b installation problem

External Email - Use Caution
Hello Andrew,

Thank you once again for your help and apologies for writing one more time, but 
it seems that Freesurfer cannot detect/recognise Matlab. When I tried to ran 
local gyrification index for one participant, I got the following error:

recon-all -s HD01 -localGI
Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
INFO: SUBJECTS_DIR is /Users/georgina/Downloads/HDf
Actual FREESURFER_HOME /Applications/freesurfer
-rw-rw-r--  1 georgina  staff  1188013 Mar 10 13:20 
/Users/georgina/Downloads/HDf/HD01/scripts/recon-all.log
Darwin Georgias-MacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 
31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64
/Users/georgina/Downloads/HDf/HD01/surf
#
#@# Local Gyrification Index lh Wed Mar 10 13:24:00 EET 2021
\n mris_compute_lgi --i lh.pial \n
ERROR: Matlab is required to run mris_compute_lgi!
Darwin Georgias-MacBook-Pro.local 19.6.0 Darwin Kernel Version 19.6.0: Mon Aug 
31 22:12:52 PDT 2020; root:xnu-6153.141.2~1/RELEASE_X86_64 x86_64

recon-all -s HD01 exited with ERRORS at Wed Mar 10 13:24:00 EET 2021


Attached please also find the recon-all.error.

When I go to Freesurfer directory and type: ls -l 
$FREESURFER_HOME/bin/fs_install_mcr
The output is: -rw-r--r--  1 root  wheel  2010 Mar  6 12:03 
/Applications/freesurfer/bin/fs_install_mcr

Do you have any idea about what went wrong?
Thank you once more time.
Best,
Georgia



On 1 Mar 2021, at 5:57 PM, Georgia Kapizioni 
mailto:geo.kapizi...@gmail.com>> wrote:

Hello Andrew,

Thank you so much for your response.

Here is the output when running the command you suggested:

Georgias-MacBook-Pro:~ georgina$ curl MailScanner has detected a possible fraud 
attempt from "secure-web.cisco.com" claiming to be 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
 -o fs_install_mcr
  % Total% Received % Xferd  Average Speed   TimeTime Time  Current
 Dload  Upload   Total   SpentLeft  Speed
100  2010  100  20100 0   8170  0 --:--:-- --:--:-- --:--:--  8137
(base) Georgias-MacBook-Pro:~ georgina$ ls fs_install_mcr
fs_install_mcr




I assume, it didn’t download it, right?

Georgia





On 26 Feb 2021, at 8:03 PM, Georgia Kapizioni 
mailto:geo.kapizi...@gmail.com>> wrote:

Hello Andrew,

Please accept my apologies for such a detailed response, I had a health issue, 
and I was just able to test what you suggested.

When I use the wget command, again I have an error: -bash: wget: command not 
found

Any ideas on how to overcome this issue?



Thank you once again,
Best,
Georgia



On 9 Feb 2021, at 5:49 PM, Georgia Kapizioni 
mailto:geo.kapizi...@gmail.com>> wrote:

Hello Andrew,

Thank you for your response!
The output of the first command (meaning sudo cd $FREESURFER_HOME/bin && curl 
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" 
claiming to be 
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/fs_install_mcr
 -o fs_install_mcr && chmod +x) was:

 % Total% Received % Xferd  Average Speed   TimeTime Time  Current
 Dload  Upload   Total   SpentLeft  Speed
100  2010  100  20100 0   5275  0 --:--:-- --:--:-- --:--:--  5261
usage: chmod [-fhv] [-R [-H | -L | -P]] [-a | +a | =a  [i][# [ n]]] mode|entry 
file ...
chmod [-fhv] [-R [-H | -L | -P]] [-E |