Send Freesurfer mailing list submissions to
    freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit
    https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
    freesurfer-request@nmr.mgh.harvard.edu

You can reach the person managing the list at
    freesurfer-owner@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."

Today's Topics:

   1. Data Analyst Position - Child Mind Institute (New York)
      (Suk Jun Hong)
   2. Re: Did not find any volume info. Warning: MatrixInverse
      failed (Ruopeng Wang)
   3. Using the new Thalamus tool (Erik O'Hanlon)
   4. Parcellations (e.g.,    labels for Brodmann Areas) for
      Connectome Workbench? (Dinicola, Lauren)

----------------------------------------------------------------------

Message: 1
Date: Thu, 6 Sep 2018 14:52:13 +0000
From: Suk Jun Hong <SukJun.Hong@childmind.org>
Subject: [Freesurfer] Data Analyst Position - Child Mind Institute
    (New York)
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <AD459B82-DE8C-4200-8C08-95A81D6A66FC@childmind.org>
Content-Type: text/plain; charset="utf-8"

        External Email - Use Caution

The Child Mind Institute is seeking a Data Analyst to support a collaborative study with Dr. Amy Roy at Fordham University. The Data Analyst?s role is to assist with the analysis of functional MRI data, as well as reporting results. In particular, the work includes: 1) preprocessing of a large fMRI dataset and implementing quality assurance protocols, 2) maintaining the database and imaging processing pipeline; 3) supporting post-doctoral researchers by implementing novel analytic methods; and 4) training graduate and undergraduate students in how to preprocess and analyze resting state and task-based functional MRI data.

Reporting to Dr. Suk Jun Hong and the Director of the Center for the Developing Brain, this is a full-time position, primarily located at the CMI headquarters (101 E 56th St, New York, NY 10022).

Responsibilities:
Implementation, execution, and maintenance of fMRI imaging analysis pipelines
Conduct neuroanatomical profile analyses as well as analyses of resting-state functional MRI data using novel software packages and neuroinformatic platforms
Develop graphs, reports, and presentations of project results
Training undergraduate and graduate students in data analysis theory and implementation
Perform basic statistical analyses for projects and reports

Qualifications:
Master?s degree in neuroscience, computer science, mathematics, statistics or related areas is preferred
Extensive neuroimaging experience in fMRI analysis and proficiency with one or more packages (e.g. FreeSurfer, AFNI, FSL, Workbench or SPM)
Programming experience in one or more languages (e.g., Python, Matlab, R or similar platforms is required)
Significant prior neuroimaging experience with more imaging and/or simulation modalities (e.g., DTI, EEG, MEG, TMS etc.) is a plus, but not required
A passion for the applying computational methods to understand clinical conditions.

If you are interested in the positions, please apply to
https://workforcenow.adp.com/mascsr/default/mdf/recruitment/recruitment.html?cid=1b50a554-ed4a-4219-a358-aa3cbeea1e70&jobId=259986&lang=en_US&source=CC3&ccId=19000101_000001

Thank you!

--------------------------
Suk-Jun Hong, PhD
Postdoc, Center for the Developing Brain
Child Mind Institute
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180906/c8892422/attachment-0001.html

------------------------------

Message: 2
Date: Thu, 6 Sep 2018 11:29:32 -0400
From: Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Did not find any volume info. Warning:
    MatrixInverse failed
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <57736545-c834-b94f-8fe1-289f6a6d00dd@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

Were they loaded with the same command? Can you check freeview's build
time to make sure they are the same build? You can check it from menu
Help->About.

Ruopeng

On 09/06/2018 09:15 AM, Sofia Rodriguez Penuela wrote:

????????External Email - Use Caution

Hello team!

We are trying to load the same set of images with Freeview on two
different computers. One of the computers, load the images correctly
(see attached image 1). On the other computer the surfaces are shown
misaligned (see attached image 2). When we try to load surfaces after
loading a volume the Command Console shows the following error:*"Did
not find any volume info. Warning: MatrixInverse failed".*This happens
with all subjects in this computer.

Freesurfer (v6.0) and Freeview are updated correctly. In both
computers there are Ubuntu 16.04.

Why Freeview didn?t find any volume info in this computer? Can you
help us to solve this problem?

Thank you.

--
Sof?a Rodr?guez Pe?uela, T?cnico de Laboratorio.
Laboratorio de Neurociencia Funcional
Departamento de Fisiolog?a, Anatom?a y Biolog?a Celular.
Universidad Pablo de Olavide
Ctra. de Utrera, Km.1
41013 - Sevilla
- Espa?a -
Movil: 627273085
Email: srodpen@upo.es <mailto:srodpen@upo.es>
http://www.upo.es/neuroaging/es/

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180906/8a78ef6c/attachment-0001.html

------------------------------

Message: 3
Date: Thu, 6 Sep 2018 15:44:57 +0000
From: "Erik O'Hanlon" <erikohanlon@rcsi.ie>
Subject: [Freesurfer] Using the new Thalamus tool
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
    <AM0PR07MB42099A3FD257DFA6FF51F59EA3010@AM0PR07MB4209.eurprd07.prod.outlook.com>

Content-Type: text/plain; charset="iso-8859-1"

        External Email - Use Caution

Hi FS Experts

I've run my data through the brainstem, hippocampus and amygdala following the usual Recon_all and using the developmental version downloaded and stalled around Jan2018. I'd like to use the new thalamus tool and am wondering if I need to do a full install of the latest DEV version to do so. As I am still working on certain aspects of the analyses I've run so far, I don't want to overwrite my main FS installation mid analysis. Is it possible to download the toolbox and add it to my current dev version or is it best just to do another install with teh complete new Dev version? Is it possible to run the Thalamus analysis as an addtional component without having to rerun the recon_all again?

Thanks and regards

Erik

Erik O'Hanlon
Postdoctoral researcher

[cid:rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png]

RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont D9 Ireland
T: 8093740
E: erikohanlon@rcsi.ie W: www.rcsi.com<http://www.rcsi.com/>

Transforming Healthcare Education, Research and Service: RCSI Strategic Plan 2018-2022<http://www.rcsi.ie/strategy2018>

[cid:both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png]

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180906/1a7fc43a/attachment-0001.html
-------------- next part --------------
A non-text attachment was scrubbed...
Name: rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png
Type: image/png
Size: 8772 bytes
Desc: rcsi-crest-signature_f581c185-1d03-45c8-a786-23d8ece3d391.png
Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180906/1a7fc43a/attachment-0002.png
-------------- next part --------------
A non-text attachment was scrubbed...
Name: both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png
Type: image/png
Size: 16296 bytes
Desc: both3_b9da8717-e91f-4ea7-8729-dc2c4d0a7a5f.png
Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180906/1a7fc43a/attachment-0003.png

------------------------------

Message: 4
Date: Thu, 6 Sep 2018 11:54:31 -0400
From: "Dinicola, Lauren" <lmd600@g.harvard.edu>
Subject: [Freesurfer] Parcellations (e.g.,    labels for Brodmann Areas)
    for Connectome Workbench?
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
    <CAOF8=m1nAt30HVshEsFUrqtGJUu5QkoNgv2AxGp7Ozqgmzn0qA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi all,

I have been searching for the Freesurfer label or annot files for fsaverage
in the formats compatible with Connectome Workbench and have not yet found
them. Are these available?
If not, is there a way to convert all the BA labels to then convert them to
borders for viewing on fsaverage? I tried mris_convert -annot but was
unsuccessful opening the output files.

Thank you very much for any help.

Lauren
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20180906/57c2f5ab/attachment-0001.html

------------------------------

_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

End of Freesurfer Digest, Vol 175, Issue 7
******************************************

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.