from:"Mira Michelle Raman"

[Freesurfer] Neuroimaging postdoctoral fellowship at Stanford University, USA

2023-02-27 Thread Mira Michelle Raman

External Email - Use Caution

Dear FreeSurfer community,

The Brain Imaging, Development, and Genetics (BRIDGE) lab, part of Stanford
University’s Division of Brain Sciences, is seeking two full-time Postdoctoral
Fellows in brain imaging and/or human genetic modeling. Ideal candidates will
have a solid neuroscience, neuroimaging, and/or human genetics background.

BRIDGE focuses on neuropsychiatric disorders, specifically those associated
with RASopathies, such as Noonan syndrome and neurofibromatosis 1 (NF1). In our
NIH-funded research, we employ three unique approaches: 1. Taking a
genetics-first approach, we study children with known genetic conditions who
exhibit attention problems, irritability, and deficits in social cognition. The
approach differs from traditional research, which begins with the child's
symptoms. 2. We apply in-depth phenotyping of the child's brain, genes, and
behavior using brain imaging, genetic testing, and behavioral assessment. 3. We
use large publicly available data sets (>10K children) focusing on child brain
and behavioral development. Our goal is, therefore, to uncover how genetic
variation and its associated downstream pathways affect children's
developmental disorders.

If interested, please see the official posting for additional details at
https://secure-web.cisco.com/1KzHM6M8eHNAqniwUwClGLco44e39zsXfqSw4bO6Ms6b1qUuvuo4MY973iIY7fnvySfyX8tVQzqJglrrCBZxiqaq6C4puOdoSBdUDsJOOZd8556hJJ2PfQeoOWRTUpZiRaioaERFk1H5LLCHBhLJLzgUYlBbEsNOBuRB9NGjiRnhesMqcepiIajAU-kPOXPom_5NnIDQ12qLxXyBBn4SbNXWiio_dFOK1NRpqV0k0oGBN_ck36BrGEF97oUCSjhOD5tDpNUniZXwh7EkOnjuxmfSBHrkFuMUqcAf57wGLm7Y0Kt5HTYrILM5hBChxyrc1AQlFZrrXj1GiJ8ogfjUaeg/https%3A%2F%2Fpostdocs.stanford.edu%2Fprospective%2Fopportunities%2Fopen-postdoctoral-position-faculty-mentor-tamar-green

Thank you,
Mira Raman, Research Data Analyst
BRIDGE, Stanford University

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Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during mris_smooth. dyld: lazy symbol binding

2017-03-01 Thread Mira Michelle Raman

HI,

 I had reported this issue a while ago and have been trying to track it down 
because it seems to be popping up in strange places on our El Capitan and 
Sierra machines.

So I initially encountered the error

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

  Referenced from: 
/Volumes/ToolsMac/freesurfer6.0/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address

  Referenced from: 
/Volumes/ToolsMac/freesurfer6.0/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib

when trying to run with  the -parallel flag for the same subject who finished 
fine through the traditional pipeline.

I have since encountered it when running mri_deface and mri_info. The good news 
about that is they are really quick to run, unlike having to run the whole 
pipeline.

Here is an example, and it is repeatable on my machine for multiple input 
images (so hopefully the developers can reproduce)

 I can do something as simple as

mri_info cert01.nii from the command line as it works as usual.  I then put the 
same command in a very simple script (I tried bash and tsch)

#! /bin/bash -f
#
mri_info cert01.nii

and it fails with

dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address

  Referenced from: 
/Volumes/ToolsMac/freesurfer6.0/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address

  Referenced from: 
/Volumes/ToolsMac/freesurfer6.0/bin/../lib/gcc/lib/libgomp.1.dylib

  Expected in: /usr/lib/libSystem.B.dylib

I then switch to Freesurfer 5.3 and run the same little script and it spits out 
the usual info.

Hopefully this can help in tracking down the problem, and creating a Sierra 
compatible  build, because we can't roll any of our newly ordered machines back 
to Yosemite anymore.

Sincerely,
Mira

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

Sent: Monday, February 20, 2017 9:11 PM
To: Freesurfer support list
Subject: Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra: during 
mris_smooth. dyld: lazy symbol binding

Hello Jared,

Would it be possible to tar up the subject directory and upload it to our 
server so I can take a look?

 https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
FtpFileExchange - Free Surfer 
Wiki
surfer.nmr.mgh.harvard.edu
top. Uploading Data. If you have been asked to send the FreeSurfer team a file, 
you can either send it via FTP or File Drop. Instructions for both are below.

-Zeke

On Feb 20, 2017, at 2:47 PM, Jared Saletin 
> wrote:

Dear Zeke,

Thanks for your reply. I can verify that recon-all completes without error on a 
single thread, but crashes on parallel.

I thought it may be hippocampus-subfield specific, but the same pattern 
remerges regardless of the subfield reconstruction.

Is there something in newer OS X that broke the libraries?

Thanks!
Jared

—

Jared M. Saletin, PhD

Assistant Professor of Psychiatry and Human Behavior
Alpert Medical School of Brown University

E.P. Bradley Sleep Research Lab
300 Duncan Drive
Providence, RI 02906

Email: jared_sale...@brown.edu
Phone: 401-421-9440
Fax: 401-453-3578

On Feb 17, 2017, at 12:00 PM, 
freesurfer-requ...@nmr.mgh.harvard.edu
 wrote:

Message: 30
Date: Fri, 17 Feb 2017 10:21:03 -0500
From: Z K >
Subject: Re: [Freesurfer] recon_all error on MacOS 10.12.13 Sierra:
during mris_smooth. dyld: lazy symbol binding
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: 
>
Content-Type: text/plain; charset=windows-1252; format=flowed

Hello Jared,

Curious... Can you try processing this particular subject with a single
thread and see what happens? If the problem persists let me know and I
will take a look at the subject.

-Zeke

On 02/17/2017 08:28 AM, Jared Saletin wrote:
Hi Freesurfer gurus:

I recently installed 6.0.0 on MacOS 10.12 and recon-all is exiting with
an error in mris_smooth. It looks like a library issue.

A prior post had the same issue and indicated uninstalling the whole
distribution and re-installing 6.0.0 fresh (as opposed to installing
over 5.3). I receive the same error however (pasted below).

Does anyone have any thoughts?

Thanks!
Jared

#@# Smooth1 rh Thu Feb 16 16:47:23 EST 2017
/Users/jared/Desktop/fMRITest/test/scripts
\n mris_smooth -nw -seed 1234 ../surf/rh.orig.nofix
../surf/rh.smoothwm.nofix \n
Waiting for PID 11130 of (11130 11133) to complete...

[Freesurfer] Version 6.0 - ?h.white.preaparc vs. ?h.white for determining the need to edit brainmask.mgz, wm.mgz, add control points, etc.

2017-02-15 Thread Mira Michelle Raman

Hi,

  My main question to the 6.0 experts is:


Is the lh.white.preaparc close enough to the lh.white to determine whether 
editing is needed (brainmask.mgz, wm.mgz,control points) or do we need to run 
the full pipeline and get ?h.white?


Here's the reasoning behind this question. In previous versions of Freesurfer 
we have run -autorecon1 -autorecon2, then checked surfaces, made edits if 
needed, and then only after we were satisfied with the surfaces we ran 
-autorecon3.  Primarily we have done this for 2 reason, first is to save 
processing time, on both the initial pass and running -autorecon2-cp or 
-autorecon2-wm. We also use this as a quality control method, in which ONLY 
subjects whose surfaces have been verified, have been through -autorecon3, 
those that haven't, don't have stats files, and thus can't get inadvertently 
included with finished data.


If ?h.white.preaparc doesn't topologically differ from the ?h.white could we 
use it for determining what edits to do?

if it does differ obviously we will have to run the whole pipeline.


Thank you in advance for your guidance.


Sincerely,

Mira

___

Mira Michelle Raman

Lead Scientific Programmer

The Center for Interdisciplinary Brain Sciences Research

Stanford University

401 Quarry Rd, Ste. 1356
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[Freesurfer] data not Surving FDR

2010-10-22 Thread Mira Michelle Raman

Hi,
  I have a dataset that seems to have some very nice group differences (please 
see the graph and qdec image), but they never seem to survive FDR.  I noticed 
when I run the Set Using FDR, it generates a very high threshold above 5; 
where as, with some of my other datasets FDR is set much lower (often in the 
2's and 3's). Can you please give me some insight into why the threshold is 
being set so high? Is it solely linked to the small sample size, or is there 
something additional we can do in the processing, so that regions with such 
large group differences will survive correction?

Thank you,
Mira

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[Freesurfer] QDEC 5.0 with data from 4.x recon-all data

2010-09-30 Thread Mira Michelle Raman

Hi,
  I was wondering if it were possible/advisable to use data processed and 
cached using earlier versions of FreeSurfe with the new 5.0 QDEC, since it has 
enhanced capabilities.

Sincerely,
Mira

Mira Michelle Raman
Scientific Programmer
Center for Interdisciplinary Brain Sciences Research
Stanford University
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[Freesurfer] preserving control points and wm edits

2010-08-16 Thread Mira Michelle Raman

Hi,
  I want to re-run subjects in 5.0 that have been 
edited in 4.5(wm.mgz, brainmask.mgz, control points). 
 
What command should I use to preserve these edits?

-Mira
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Re: [Freesurfer] Any suggestions for imaging parameters on a GE 3T with 8 channel head coil

2010-07-19 Thread Mira Michelle Raman

Hello, 
  Thank you both very much, I will definitely try these parameters next time I 
get development 
time on the scanner, and re-investigate the ADNI T1 sequence. Last time we 
tried it, 
I think the scans were on the order of 9 minutes, which just won't work with 
these 
particular participants. 
  We definitely do have the 8-channel geometry issues Bruce mentioned and that 
was the main 
reason for my post, I had assumed that all the GE's with the 8-channel had the 
same problem 
we have been seeing, and we would love to be able to use FreeSurer without 
having to drop 
100's or 1000's of control points for each subject, even after shortening the 
distance in 
N3 to 50. 

Thank you both again,
Sincerely,
Mira  

- Original Message -
From: Bruce Fischl fis...@nmr.mgh.harvard.edu
To: antonio cerasa a.cer...@isn.cnr.it
Cc: Mira Michelle Raman mra...@stanford.edu, freesurfer@nmr.mgh.harvard.edu
Sent: Monday, July 19, 2010 5:05:42 AM
Subject: Re: [Freesurfer] Any suggestions for imaging parameters on a GE 3T 
with 8 channel head coil

that's an awfully short TR. Not sure how good the SNR is for the 8 
channel, but that might be noisy. We also try to shorten the TE if we 
can, although you might not be able to. There is an ADNI mprage the 
exists on the GE platforms, although I'm not sure you're allowed to run 
it. It's a reasonable sequence. Your results will also depend on the 
geometry of the 8 coil elements. Some 8 channels we've seen have a very 
large signal falloff near the top of the head that make them difficult to 
analyze.

cheers
Bruce


On Mon, 19 Jul 2010, antonio cerasa wrote:

 Dear Sira
 Using the same scanner we developed this sequence for Freesurfer analysis
 BRAVO: TR=9.2 ms; TE = 3.7 ms; flip angle 12°; FOV = 25.6 cm; preparation
 time= 650 ms; slice thickness= 1 mm; Bandwith= 25.
 Running time: 5 min, 32 sec.

 --
 Antonio Cerasa, PhD
 Neuroimaging Research Unit,
 National Research Council, Catanzaro, 88100 Italy.

 - Original Message -
 From: Mira Michelle Raman mra...@stanford.edu
 To: freesurfer@nmr.mgh.harvard.edu
 Sent: Friday, July 16, 2010 7:27 PM
 Subject: [Freesurfer] Any suggestions for imaging parameters on a GE 3T with
 8 channel head coil


 Hi Freesurfers,
  We would like to optimize the 'Freesurferability' of images for a new
 project involving fidgety young children.  Ideally, the structural scan
 time will be under 5 minutes.  We have a GE Signa 3T MR750, with an
 8-channel head coil. Preliminary experiments have found two short
 structural scan options, but both require some intervention after
 autorecon2 in the Freesurfer pipeline.

 Does anyone have a suggestion for a sequence that

 a) runs in under 5 minutes
 b) freesurfs with minimal intervention

 and c) that they would be kind enough to share.

 Thank you in advance,
 Mira
 
 Mira Michelle Raman
 Scientific Programmer
 Center for Interdisciplinary Brain Sciences Research
 Stanford University
 401 Quarry Rd.
 Stanford, CA 94305
 (650)498-4620

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[Freesurfer] Any suggestions for imaging parameters on a GE 3T with 8 channel head coil

2010-07-16 Thread Mira Michelle Raman

Hi Freesurfers,
  We would like to optimize the 'Freesurferability' of images for a new project 
involving fidgety young children.  Ideally, the structural scan time will be 
under 5 minutes.  We have a GE Signa 3T MR750, with an 8-channel head coil. 
Preliminary experiments have found two short structural scan options, but both 
require some intervention after autorecon2 in the Freesurfer pipeline.

Does anyone have a suggestion for a sequence that

a) runs in under 5 minutes
b) freesurfs with minimal intervention

and c) that they would be kind enough to share.

Thank you in advance,
Mira

Mira Michelle Raman
Scientific Programmer
Center for Interdisciplinary Brain Sciences Research
Stanford University
401 Quarry Rd.
Stanford, CA 94305
(650)498-4620

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[Freesurfer] are paired compairisons possible using QDEC

2010-06-11 Thread Mira Michelle Raman

Hi,
 I have a group of siblings (one disorder, one unaffected). 
Is it possible for me to set up the group analysis 
in a way so that siblings are compared to their sibling, 
something analogous to a paired t-test, and if so do you 
have a tutorial or example to which you could direct me.

Thank you,
Mira

Mira Michelle Raman
Scientific Programmer
Center for Interdisciplinary Brain Sciences Research
Stanford University
401 Quarry Rd.
Stanford, CA 94305
(650)498-4620

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[Freesurfer] ETA on next version of FS?

2010-02-12 Thread Mira Michelle Raman

Hi,
  We are about to start processing data from several projects using FreeSurfer, 
and I wanted to find out if the next version is coming out in the near future.  
   I know Nick had asked if anyone wanted Tiger builds about a month ago, which 
has me thinking a new version is on the horizon, and if so will it work with 
Snow Leopard?

Thanks,
Mira

Mira Michelle Raman
Center for Interdisciplinary Brain Sciences Research
Stanford University

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Re: [Freesurfer] white/pial surface in lateral ventricle

2009-08-17 Thread Mira Michelle Raman

Hi Doug,
  That's a good thought, but we ran it through straight from the DICOM's both 
times 4.3 and 4.5 (obviously with different freesurfer subject IDs).  So this 
couldn't be the problem, if it even is a problem.
-Mira 

- Original Message -
From: Douglas N Greve gr...@nmr.mgh.harvard.edu
To: Bruce Fischl fis...@nmr.mgh.harvard.edu
Cc: Mira Michelle Raman mra...@stanford.edu, freesurfer@nmr.mgh.harvard.edu
Sent: Monday, August 17, 2009 10:40:25 AM GMT -08:00 US/Canada Pacific
Subject: Re: [Freesurfer] white/pial surface in lateral ventricle

I've seen this in cases where the wm.mgz was created with an older 
version of freesurfer and then the subjects was re-run with a newer 
version. You might try deleting (or renaming!) the wm.mgz and re-running

recon-all -s 000502083470__0002 -autorecon2-cp

to see if the problem goes away.

doug

Bruce Fischl wrote:
 Hi Mira,

 usually the aseg will fill in the ventricle and choroid. What version are 
 you using? What is the label of the stuff in the ventricle that wasn't 
 filled?

 cheers,
 Bruce
 On Mon, 17 Aug 2009, Mira Michelle Raman wrote:

 Hi,
  I was looking at some of my data and noticed that the white and pial 
 surfaces occasionally invade the lateral ventricle (see attached picture).  
 I went over to the bert sample dataset and noticed the same thing (coronal 
 slice 87).  Is this something I should be correcting or is it something that 
 is ignored during the registration and labeling process?  If I don't care 
 about the choroid plexus volume, should I fill the white matter mask 
 throughout the ventricle?

 Thank you in advance,
 Mira

 Mira Michelle Raman
 Scientific Programmer
 Center for Interdisciplinary Brain Sciences Research
 Stanford University
 401 Quarry Rd.
 Stanford, CA 940305
 http://cibsr.stanford.edu

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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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[Freesurfer] restarting after edits to brainmask.mgz and wm.mgz

2009-07-07 Thread Mira Michelle Raman

Hi,
  I was just wondering if I should use -autorecon2-wm or -autorecon2-pial after 
making adjustments to both the brainmask.mgz and wm.mgz when restarting 
freesurfer.
-Mira

Mira Michelle Raman
Scientific Programmer
Center for Interdisciplinary Brain Sciences Research
Stanford University
401 Quarry Rd.
Stanford, CA 940305
(650)498-4538
http://cibsr.stanford.edu
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