Hi Dan and Bruce,

Thanks for your getting back on the problem.
My concern is more about the dura being incorrectly labeled - It appears to me that the grey-CSF boundary has been incorrectly labeled as the GM-WM boundary across the entire image.
Any ideas what may have gone wrong?

Thanks,
Mayuresh



On Sat, Apr 2, 2011 at 3:28 AM, <freesurfer-request@nmr.mgh.harvard.edu> wrote:
Send Freesurfer mailing list submissions to
       freesurfer@nmr.mgh.harvard.edu

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Today's Topics:

  1. Re: incorrect GM/WM surfaces (Daniel G Wakeman)
  2. problems with loading a pial surface (Iris Steinmann)
  3. Re: incorrect GM/WM surfaces (Bruce Fischl)
  4. Re: problems with loading a pial surface (Bruce Fischl)
  5. preproc-sess OSX bug fix getrunlist (Juli Dolzhenko)
  6. MRI analyst position (Keith Schneider)
  7. Distance between two points along cortical (caoaize)


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

Message: 1
Date: Fri, 1 Apr 2011 05:53:20 +0100
From: Daniel G Wakeman <Daniel.Wakeman@mrc-cbu.cam.ac.uk>
Subject: Re: [Freesurfer] incorrect GM/WM surfaces
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <471C0967-FE19-409E-8174-31FBB56CDE1E@mrc-cbu.cam.ac.uk>
Content-Type: text/plain; charset="us-ascii"

Hi Mayuresh,

I assume you are talking about the area in the posterior midline, where the pial surface seems to go 'squiggly'. You also seem to have a problem with the right hemisphere (left visually: I hate radiology ;)), where some dura seems incorrectly labeled as pial surface (although the grey matter is very difficult to see on this sequence/ at this setting).

To fix these I recommend this wiki page:
http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits

Good Luck!
Dan

On 2011 Apr 1, at 05:08 , <freesurfer-request@nmr.mgh.harvard.edu> <freesurfer-request@nmr.mgh.harvard.edu> wrote:

> Send Freesurfer mailing list submissions to
>       freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
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> 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. incorrect GM/WM surfaces (Mayuresh K)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 1 Apr 2011 15:21:18 +1100
> From: Mayuresh K <mayureshk.82@gmail.com>
> Subject: [Freesurfer] incorrect GM/WM surfaces
> To: freesurfer@nmr.mgh.harvard.edu
> Message-ID:
>       <AANLkTi=BLTOKkZngtH5SxhsQvmFrUHakzG9u07Xzworn@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hello freesurfer experts,
>
> I have successfully finished running the recon-all analysis without any
> errors for a dataset scanned on the 1.5T GE scanner. The output GM/WM
> surfaces however look incorrect and I am not sure what may have gone wrong.
> See attached screenshot from tkmedit.
> Any suggestions how to fix this would be helpful.
>
> I have processed other datasets collected from the same scanner using the
> same sequence which seem to have correctly identified the pial and
> grey-white boundaries. I am using
> freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1.
>
> Thanks,
> Mayuresh
> -------------- next part --------------
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> -------------- next part --------------
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>
> ------------------------------
>
> _______________________________________________
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> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> End of Freesurfer Digest, Vol 86, Issue 1
> *****************************************
>
>
> 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.
>




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

Message: 2
Date: Fri, 01 Apr 2011 09:42:47 +0200
From: Iris Steinmann <Iris.Steinmann@uni-heidelberg.de>
Subject: [Freesurfer] problems with loading a pial surface
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <1301643767.2015.2.camel@steinmann>
Content-Type: text/plain; charset="UTF-8"

Hello Freesurfers

I still have the problem using a tcl script that should load the pial
surface on a patch in tksurfer. I tried to use the following three
commands:


1.  set gaLinkedVars(vertexset) 3
    SendLinkedVarGroup view
    redraw


2.  read_pial_vertex_coordinates
    redraw

3.  read_surface_vertex_set 3 lh.pial
    redraw


But none of them loaded the pial surface. I would be very thankful for
 a solution ore a hint.

    Iris



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

Message: 3
Date: Fri, 1 Apr 2011 08:27:58 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] incorrect GM/WM surfaces
To: Daniel G Wakeman <Daniel.Wakeman@mrc-cbu.cam.ac.uk>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
       <Pine.LNX.4.62.1104010827050.28555@gate.nmr.mgh.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

Hi Mayuresh

the "squiggly" stuff isn't necessarily a problem. You need to look at it in
a different view, but it can be a region in which the surface is nearly
paralell to the viewing plane to that it crosses back and forth a ton of
times in a small patch.

cheers
Bruce


 On Fri, 1 Apr 2011, Daniel G Wakeman wrote:

> Hi Mayuresh,
>
> I assume you are talking about the area in the posterior midline, where the pial surface seems to go 'squiggly'. You also seem to have a problem with the right hemisphere (left visually: I hate radiology ;)), where some dura seems incorrectly labeled as pial surface (although the grey matter is very difficult to see on this sequence/ at this setting).
>
> To fix these I recommend this wiki page:
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/PialEdits
>
> Good Luck!
> Dan
>
> On 2011 Apr 1, at 05:08 , <freesurfer-request@nmr.mgh.harvard.edu> <freesurfer-request@nmr.mgh.harvard.edu> wrote:
>
>> 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. incorrect GM/WM surfaces (Mayuresh K)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Fri, 1 Apr 2011 15:21:18 +1100
>> From: Mayuresh K <mayureshk.82@gmail.com>
>> Subject: [Freesurfer] incorrect GM/WM surfaces
>> To: freesurfer@nmr.mgh.harvard.edu
>> Message-ID:
>>      <AANLkTi=BLTOKkZngtH5SxhsQvmFrUHakzG9u07Xzworn@mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hello freesurfer experts,
>>
>> I have successfully finished running the recon-all analysis without any
>> errors for a dataset scanned on the 1.5T GE scanner. The output GM/WM
>> surfaces however look incorrect and I am not sure what may have gone wrong.
>> See attached screenshot from tkmedit.
>> Any suggestions how to fix this would be helpful.
>>
>> I have processed other datasets collected from the same scanner using the
>> same sequence which seem to have correctly identified the pial and
>> grey-white boundaries. I am using
>> freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.1.
>>
>> Thanks,
>> Mayuresh
>> -------------- next part --------------
>> An HTML attachment was scrubbed...
>> URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110401/f494b1a2/attachment.html
>> -------------- next part --------------
>> A non-text attachment was scrubbed...
>> Name: tkmedit ** brainmask.mgz ** (T1.mgz).png
>> Type: image/png
>> Size: 81386 bytes
>> Desc: not available
>> Url : http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20110401/f494b1a2/attachment.png
>>
>> ------------------------------
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> End of Freesurfer Digest, Vol 86, Issue 1
>> *****************************************
>>
>>
>> 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.
>>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>


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

Message: 4
Date: Fri, 1 Apr 2011 08:51:34 -0400 (EDT)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] problems with loading a pial surface
To: Iris Steinmann <Iris.Steinmann@uni-heidelberg.de>
Cc: freesurfer@nmr.mgh.harvard.edu
Message-ID:
       <Pine.LNX.4.62.1104010837040.28555@gate.nmr.mgh.harvard.edu>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed

Hi Iris,

updating. I would try:


set_current_vertex_set 3
UpdateLinkedVarGroup view
UpdateAndRedraw


if this doesn't work, tell us, and if you don't get a response in the next
day or so, can you repost in a week? We are flat out trying to prepare for
our upcoming course and also get 5.1 out the door. The tcl scripting is
confusing and could use serious

cheers,
Bruce

p.s. I am a bit confused about what you are trying to do though. Why do you
want only a patch of the pial surface? And not flattened I assume as I
don't even know what that would mean (it wouldn't be the pial surface
anymore).

On Fri, 1 Apr 2011, Iris Steinmann wrote:

> Hello Freesurfers
>
> I still have the problem using a tcl script that should load the pial
> surface on a patch in tksurfer. I tried to use the following three
> commands:
>
>
> 1.  set gaLinkedVars(vertexset) 3
>     SendLinkedVarGroup view
>     redraw
>
>
> 2.  read_pial_vertex_coordinates
>     redraw
>
> 3.  read_surface_vertex_set 3 lh.pial
>     redraw
>
>
> But none of them loaded the pial surface. I would be very thankful for
> a solution ore a hint.
>
>     Iris
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>


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

Message: 5
Date: Fri, 1 Apr 2011 12:00:17 -0400 (EDT)
From: "Juli Dolzhenko" <juli@nmr.mgh.harvard.edu>
Subject: [Freesurfer] preproc-sess OSX bug fix getrunlist
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
       <44911.68.162.255.42.1301673617.squirrel@mail.nmr.mgh.harvard.edu>
Content-Type: text/plain;charset=iso-8859-1

Hello,

I am running into an issue with running preproc-sess on OSX as outlined here:
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg15896.html

I saw Doug posted a bug fix that should solve this problem, however, I am
unable to access it from:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/getrunlist

Is there a way I can download this new version of getrunlist?

Thanks so much,
Juli



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

Message: 6
Date: Fri, 1 Apr 2011 12:26:03 -0400
From: Keith Schneider <keiths@yorku.ca>
Subject: [Freesurfer] MRI analyst position
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <EAFD6B8F-3D65-4EF3-AF30-7D3938EBAE02@yorku.ca>
Content-Type: text/plain; charset=windows-1252

YORK UNIVERSITY

Job Type: Contract
Location: Toronto, ON, CANADA;
Industry: Education
Company URL: http://www.yorku.ca
Date Posted:  March 31, 2011

JOB TITLE: MRI Analyst, Neuroimaging Laboratory

TYPE OF POSITION: Contract ? 1 year contract with a possibility of renewal

SALARY: $60,000 - $75,000 per annum plus benefits

HOURS:  35 hours per week, with flexible work times

CLOSING DATE FOR POSITION:  April 14, 2011

JOB PURPOSE:
Reporting to the Director of the Neuroimaging Laboratory, the MRI Analyst will serve as the primary support person for the computational and analytical needs of the Neuroimaging Laboratory.

The Neuroimaging Laboratory at York University with a research-dedicated Siemens Trio MRI scanner is part of York?s world-class Centre for Vision Research.  Located at the Sherman Health Science Research Centre, the MRI Analyst is a key component of this new unit.

FUNCTIONS/DUTIES:
1.     Consult with users of the Neuroimaging Laboratory to help them design and program experimental paradigms and assist in analyzing their MRI data
2.     Develop new data analysis tools and write scripts to efficiently implement existing tools
3.     Manage the MRI data server
4.     Manage the Analysis Lab computer network
5.     Assist with programming for the Neuroimaging Laboratory website
6.     Provide IT support
7.     Assist users of the Neuroimaging Laboratory with the design and fabrication of new stimulus equipment

EDUCATIONAL REQUIREMENTS:
University undergraduate degree in science or engineering required, Master's degree preferred.

EXPERIENCE REQUIREMENTS:
Experience with the analysis of MRI data desirable.   Experience with parallel processing on CPU clusters and/or GPUs is desirable.   Experience with system administration and network management is desirable.

SKILLS (Specialized knowledge):
Superior interpersonal skills and the ability to deal courteously and effectively with a wide range of people; excellent oral and written communication skills; demonstrated ability in exercising good judgment and initiative; excellent troubleshooting and problem-solving skills; ability to prioritize and work with deadlines; good organizational skills; ability to administer Mac and Linux computers; ability to utilize neuroimaging programs and statistical packages; computer programming (C, Matlab, shell scripts and/or other languages); ability to assess computer/network security, identify security risks and implement appropriate solutions.

Application Process Details

Your complete application package must include a cover letter, r?sum?, and the names of at least two           referees.

By submitting an application package, you agree that your referees may be contacted prior to any interview offer to gauge your suitability for the position.

Please ensure that ?MRI Analyst? is quoted in e-mail subject lines and all hard copy applications.

Only those selected for an interview will be contacted. Priority consideration is given to Canadian citizens and permanent residents in Canada. York University is committed to Employment Equity and encourages applications from all qualified candidates.

Applications should be submitted to:

MRI Analyst Hiring Committee
The Office of the Vice-President, Research & Innovation
Fifth Floor, York Research Tower
York University
4700 Keele Street
Toronto, Ontario, Canada, M3J 1P3
Fax ? 416-650-8197
Email ? rsrchjbs@yorku.ca


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

Message: 7
Date: Sat, 2 Apr 2011 00:28:31 +0800
From: caoaize <caoaize@hotmail.com>
Subject: [Freesurfer] Distance between two points along cortical
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <SNT103-W613DC3E0168318D3F2B966B5BE0@phx.gbl>
Content-Type: text/plain; charset="gb2312"



Hello FS Experts,

Suppose we have two points on the cortical surface (pial for example), we want to know the distance between these two point along cortical surface (not direct distance). Does FS report this kind of distance? Any suggestion will be very appreciated.

Aize
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------------------------------

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