[Freesurfer] Post-doctoral Position in Network Neuroscience at the University of Michigan

[Angstadt, Mike]

External Email - Use Caution


Post-doctoral Position in Network Neuroscience at the University of Michigan

A post-doctoral position is available in network neuroscience at the University 
of Michigan working with Chandra Sripada in Psychiatry, Liza Levina in 
Statistics, and Scott Peltier in Biomedical Engineering. The successful 
candidate will work on funded research projects that: 
1) develop new methods for quantifying individual differences and longitudinal 
change in brain networks (functional and structural imaging modalities); 
2) implement these methods in large datasets covering childhood (ABCD) and late 
adulthood (UKBiobank), with a focus on characterizing changes in neurocognition 
(executive functions, attention, learning and memory). 
 
Required Qualifications: a PhD in cognitive or computational neuroscience 
coupled with very strong quantitative skills; or a PhD in statistics, 
biostatistics, computer science, biomedical engineering, or another 
methodological discipline coupled with ability to work with brain and 
behavioral data. A strong background in the analysis and interpretation of 
neuroimaging data is a plus. Strong programming skills are a must; Matlab, R, 
and/or Python preferred. 
 
This is a 2-year position that has a possibility of being extended to a third. 
Start date is flexible, but September 2019 is preferred. If you are interested 
in this position, please send a CV and research statement to Chandra Sripada 
(srip...@umich.edu).


--
Mike Angstadt
Research Area Specialist Lead / PANLab Lab Manager
Department of Psychiatry / University of Michigan
(734) 936-8229

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Re: [Freesurfer] Colourful Brain

[Angstadt, Mike]

External Email - Use Caution

I've also done a brain print in color using Shapeways. There are probably a 
number of ways to do it, but what ended up working for me is up on my github at 
https://github.com/mangstad/freesurfer_to_3dprint

This uses freesurfer utilities to output the mesh to a more usable format, then 
creates per vertex color information from an annotation file and then runs a 
few modifications/fixes (reducing number of faces and some other stuff) and 
then outputs into an x3d file with color information.

A lot of trial an error was involved, and some things that should have worked 
didn't seem to for some reason, either errors on how I was handling the format 
or problems with getting Shapeways to recognize the format with color, etc.

-Mike

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Tim Schäfer 

Sent: Tuesday, April 2, 2019 10:37:21 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Colourful Brain

External Email - Use Caution

External Email - Use Caution

This depends on the 3D model formats that your 3D printer will accept, and of 
course what you want the colors to be (e.g., it could be different brain 
regions according to some atlas, or a colormap of some cortical measurement 
like the curvature at that point of the brain surface).

Maybe there is an easier way that somebody else on this list knows, but I have 
written an exporter that can write a FreeSurfer brain mesh and the respective 
morphometry data to a vertex-colored PLY (Stanford format) mesh file.

You could use it and then use standard modeling software like Blender to load 
that format and export it to a variety of other formats. Maybe you will have to 
reduce the mesh resolution in Blender before printing, or use a low-poly 
version from the start for 3D printing (?). You will know better than me. ;)

Afaik there already is an easy way to convert the Freesurfer mesh files to OBJ 
format, but I found no way to make it use vertex colors (which makes some 
sense, since OBJ seems to have no official support for that).

If you are interested in the exporter, just let me know. It's open source. You 
can see an example for a model with vertex colors that I exported to PLY and 
then loaded into Blender here: https://vimeo.com/325645975

In that video, the color is rather uninteresting (it's the surface area at each 
vertex), but you can see that it works.

Best,

Tim


--
Dr. Tim Schäfer
Postdoc Computational Neuroimaging
Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy
University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany

> On April 2, 2019 at 3:43 PM "May, Markus"  wrote:
>
>
> Hi,
> My university has a new FDM 3D printer which is able to print colours. They 
> want to print a brain in colour or maybe in multiple colours.
> Is there anybody who knows how I could get it?
>
> Best,
> Markus
> 
>
> With best regards,
> M.Eng. Markus May
>
> Ph.D. Student at
> Technische Hochschule Mittelhessen - University of Applied Sciences
>
>
> Wiesenstr. 14, 35390 Gießen, Germany
> Gebäude D10, Raum 0.16
> Telefon: 0049 641 309 2646
> Mail: markus@lse.thm.de
> Web: www.thm.de/imps
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Re: [Freesurfer] A note about the Freesurfer license file

[Angstadt, Mike]

Andrew,

Thank you for suggesting that. Turns out that's exactly what seems to have been 
the problem. Renamed the .license file and now things seem to be working. Not 
sure why there was even a .license file there, as I've been using license.txt 
as directed in the installation instructions and email with the license code, 
but oh well.

-Mike

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Hoopes, Andrew 
<ahoo...@mgh.harvard.edu>
Sent: Thursday, December 14, 2017 12:19:10 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] A note about the Freesurfer license file

Hi Mike,

Is it possible that freesurfer is reading the wrong license file? What are you 
naming the new license as? FS could be reading a hidden “.license” file in 
FREESURFER_HOME instead.

best,
Andrew

> On Dec 7, 2017, at 4:35 PM, Angstadt, Mike <mangs...@med.umich.edu> wrote:
>
> I am getting this same glibc message with Freesurfer 6. Unfortunately I have 
> tried twice now to re-register and updated the license file to the new file 
> that gets emailed to me, but I am still getting the same error. Any ideas 
> what else I can try to troubleshoot this issue?
>
> -Mike
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Z K 
> <zkauf...@nmr.mgh.harvard.edu>
> Sent: Friday, February 3, 2017 1:23:04 PM
> To: Freesurfer support list
> Subject: [Freesurfer] A note about the Freesurfer license file
>
> Hello All,
>
> Users on newer linux distributions who upgrade from Freesurfer version
> 5.3 to version 6.0 may get the following error message:
>
> --
> GNU libc version: 2.17
> ERROR: Systems running GNU glibc version greater than 2.15
>   require a newly formatted license file (it's free). Please
>   download a new one from the following page:
>   http://surfer.nmr.mgh.harvard.edu/registration.html
> --
>
> This is a known issue, and as the message says, it is resolved by
> downloading a newly formatted license file from our registration page:
>
>   http://surfer.nmr.mgh.harvard.edu/registration.html
>
> Simply overwrite the old license file with the newly formatted one.
> Sorry for any inconvenience this may have caused.
>
> -The Freesurfer team
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>
>
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> at
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> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>
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> Electronic Mail is not secure, may not be read every day, and should not be 
> used for urgent or sensitive issues
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>
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Re: [Freesurfer] A note about the Freesurfer license file

[Angstadt, Mike]

I am getting this same glibc message with Freesurfer 6. Unfortunately I have 
tried twice now to re-register and updated the license file to the new file 
that gets emailed to me, but I am still getting the same error. Any ideas what 
else I can try to troubleshoot this issue?

-Mike

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Z K 

Sent: Friday, February 3, 2017 1:23:04 PM
To: Freesurfer support list
Subject: [Freesurfer] A note about the Freesurfer license file

Hello All,

Users on newer linux distributions who upgrade from Freesurfer version
5.3 to version 6.0 may get the following error message:

--
GNU libc version: 2.17
ERROR: Systems running GNU glibc version greater than 2.15
   require a newly formatted license file (it's free). Please
   download a new one from the following page:
   http://surfer.nmr.mgh.harvard.edu/registration.html
--

This is a known issue, and as the message says, it is resolved by
downloading a newly formatted license file from our registration page:

   http://surfer.nmr.mgh.harvard.edu/registration.html

Simply overwrite the old license file with the newly formatted one.
Sorry for any inconvenience this may have caused.

-The Freesurfer team
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dispose of the e-mail.

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Re: [Freesurfer] Structural resolution and longitudinal processing

[Angstadt, Mike]

Martin,

The problem is not due to a different acquired resolution, but different 
reconstruction scripts being used at the scanner, so the underlying DICOM data 
is actually the same dimensions throughout the study. 

This means that some subjects have a bit of squishing in the x/y dimensions. 
And since it's a non-uniform effect in x/y only, that means the degree of 
effect depends on the participant's head's orientation in the scanner.

When you say that if it was different processing after scanning it could be 
fixed, are you suggesting there's something we could do to fix it while still 
maintaining our original cross-sectional processing and edits, or are you just 
suggesting that it could be fixed by correcting the dimensions and then 
re-running cross-sectional processing.  We were hoping to avoid the latter as 
it's several hundred scans, but I suspect that's ultimately what will need to 
happen.

-Mike


From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Martin Reuter
Sent: Monday, April 04, 2016 4:35 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] Structural resolution and longitudinal processing

Hi Mike,

you can't change this retrospectively. It means that different protocols were 
used when scanning (or different processing after scanning, before passing it 
to freesurfer-in that case it could be fixed). It would be good to try to 
understand what exactly changed between acquisitions (is this on the same 
scanner/headcoil)? If it is the same scanner and no parameters that affect the 
image intensity changed, I would not worry too much about this small difference 
in voxel size.
You may also want to check if this happens in all subjects, or only some. And 
if in some, are they all in one of your groups or distributed across groups, to 
avoid potential bias. 

Best, Martin
On 04/04/2016 12:07 PM, Angstadt, Mike wrote:
We have a large number of scans that have been processed through the standard 
cross-sectional stream. Subjects have a number of repeated scans, so we now 
want to take advantage of the longitudinal stream.
 
When first beginning to run subjects through longitudinal template creation, we 
noticed a warning message in some cases in the log:
***
WARNING: Image geometries differ across time, maybe due to aquisition changes?
 This can potentially bias a longitudinal study! Will continue in 10s.
***
 
Looking into it, there does indeed appear to have been a change in the 
reconstruction stream that led to images at different times during the study to 
have slightly different voxel dimensions, changing from 1x1x1.2 to 
1.01x1.01x1.2mm voxels.
 
Our question is if there is some way to fix this prior to starting the 
longitudinal stream but without having to redo the original cross-sectional 
processing and editing that has been completed?
 
 
--
  Mike Angstadt
  Research Computer Specialist / PANLab Lab Manager
  Department of Psychiatry / University of Michigan
  (734) 936-8229
 
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-- 
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web  : http://reuter.mit.edu 
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[Freesurfer] Structural resolution and longitudinal processing

[Angstadt, Mike]

We have a large number of scans that have been processed through the standard 
cross-sectional stream. Subjects have a number of repeated scans, so we now 
want to take advantage of the longitudinal stream.

When first beginning to run subjects through longitudinal template creation, we 
noticed a warning message in some cases in the log:
***
WARNING: Image geometries differ across time, maybe due to aquisition changes?
 This can potentially bias a longitudinal study! Will continue in 10s.
***

Looking into it, there does indeed appear to have been a change in the 
reconstruction stream that led to images at different times during the study to 
have slightly different voxel dimensions, changing from 1x1x1.2 to 
1.01x1.01x1.2mm voxels.

Our question is if there is some way to fix this prior to starting the 
longitudinal stream but without having to redo the original cross-sectional 
processing and editing that has been completed?


--
  Mike Angstadt
  Research Computer Specialist / PANLab Lab Manager
  Department of Psychiatry / University of Michigan
  (734) 936-8229

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The information in this e-mail is intended only for the person to whom it is
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contains patient information, please contact the Partners Compliance HelpLine at
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