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. V6 beta freeview - stopped loading remaining files when one
      is missing (Antonin Skoch)
   2. freeview V6beta - reposition surface option (Antonin Skoch)
   3. Re: mri_convert error message (Bruce Fischl)
   4. Re: V6 beta freeview - stopped loading remaining files when
      one is missing (Ruopeng Wang)
   5. Re: 6.0.0 release (Tobias Granberg)
   6. Problem with freeview (Jennifer Szeto)
   7. Re: minor edits to aseg lead to exist with errors in about
      25% of my scans (Lucette Cysique)
   8. Re: minor edits to aseg lead to exist with errors in about
      25% of my scans (Bruce Fischl)
   9. Re: Problem with freeview (Ruopeng Wang)
10. Re: Problem with freeview (Jennifer Szeto)
11. Postdoctoral Fellow in Machine Learning in Neuroimaging
      (Thomas Yeo)
12. Postdoctoral fellow in mental disorder subtypes (Thomas Yeo)
13. Fwd: REMINDER: OHBM 2017 Call For Council Nominations
      (Douglas N Greve)

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

Message: 1
Date: Wed, 4 Jan 2017 21:38:53 +0100
From: Antonin Skoch <ansk@ikem.cz>
Subject: [Freesurfer] V6 beta freeview - stopped loading remaining
        files when one is missing
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <1798454155-32478@posta.medicon.cz>
Content-Type: text/plain; charset="utf-8"

Dear experts,

with V6 beta version of freeview I encountered, that when some input file specified in command line is missing, the loading of remaining files is stopped. This was not the case with 5.3 version. I found this feature handy. Do you think that it would be good to implement this behavior also for V6 version of freeview?

Regards,

Antonin Skoch

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170104/b3a23719/attachment-0001.html

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

Message: 2
Date: Wed, 4 Jan 2017 21:50:49 +0100
From: Antonin Skoch <ansk@ikem.cz>
Subject: [Freesurfer] freeview V6beta - reposition surface option
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <1798681432-5170@posta.medicon.cz>
Content-Type: text/plain; charset="utf-8"

Dear experts,

I have several questions regarding "reposition surface" tool in freeview (V6beta):

1.
Are here any documentation how to use "reposition surface" tool? I would especially velcome the explanation of significance of "sigma", "size" and "gradient direction" parameter. I tried to play with the parameters by trial and error, but I could not get satisfactory results.

2.
It seems to me that the selection of the active volume (i.e. the volume according to that the surface is repositioned) does not reflect the currently highlighted volume. It seems to always use the volume on top of the list of the volumes, but I am not sure given the unpredictive behaviour of this tool I got so far.

3.
It would be maybe handy to include special flag to recon-all to rerun remaining recon-all pipeline after the reposition of the surface in freeview have been used. What do you think?

4.
Do you think there is a chance to implement recon-all to preserve part of the surface which has been repositioned by this tool in case of recon-all rerun (similarly like it is done with other edits)?

Regards,

Antonin Skoch

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170104/167e137f/attachment-0001.html

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

Message: 3
Date: Wed, 4 Jan 2017 16:18:42 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] mri_convert error message
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <alpine.LRH.2.20.1701041617550.28877@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=US-ASCII; format=flowed

Hi Robert

disk space and permissions are really the only two things I can think of.
Can you try writing it somewhere else? Or using .mgz as output (or .nii
without the .gz)?

cheers
Bruce

On Wed, 4 Jan 2017, Wujek, Robert
wrote:

> I'm trying to convert a group of .dcm files to .nii.gz, but I've been getting the following output with an error at the end...
>
> mri_convert IM-0020-0001.dcm example.nii.gz
>
> $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $
>
> reading from IM-0020-0001.dcm...
>
> Starting DICOMRead2()
>
> dcmfile = /Users/Desktop/example/IM-0020-0001.dcm
>
> dcmdir = /Users/Desktop/example
>
> Ref Series No = 23
>
> Found 482 files, checking for dicoms
>
> Found 480 dicom files in series.
>
> First Sorting
>
> Computing Slice Direction
>
> Vs: 0 0 3
>
> Vs: 0 0 1
>
> Second Sorting
>
> Counting frames
>
> nframes = 6
>
> nslices = 80
>
> ndcmfiles = 480
>
> PE Dir = ROW (dicom read)
>
> TransferSyntaxUID: --1.2.840.10008.1.2.1--
>
> jpegUID:           --1.2.840.10008.1.2.4--
>
> Loading pixel data
>
> TR=7584.00, TE=11.10, TI=1500.00, flip angle=111.00
>
> i_ras = (-1, 0, 0)
>
> j_ras = (0, -1, 0)
>
> k_ras = (-0, -0, 1)
>
> writing to example.nii.gz...
>
> niiWrite(): error opening file example.nii.gz
>
> ERROR: failure writing example.nii.gz?
>
> I'm wondering how I should interpret this error. I have disk space, and proper permissions. I also have experience using mri_convert with other projects, so generally speaking, I am capable with this script. I would appreciate any suggestions. Thank you.
>
> -Robert Wujek?
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>

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

Message: 4
Date: Wed, 4 Jan 2017 17:16:16 -0500
From: Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] V6 beta freeview - stopped loading remaining
        files when one is missing
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5a40d567-94b0-5218-9dc2-3c93ee198b61@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"

I will add a "-continue" option for this. It may not make it to the
final V6 release. But you can always download our nightly dev build of
freeview anytime.

Best,
Ruopeng

On 01/04/2017 03:38 PM, Antonin Skoch wrote:
> Dear experts,
>
> with V6 beta version of freeview I encountered, that when some input
> file specified in command line is missing, the loading of remaining
> files is stopped. This was not the case with 5.3 version. I found this
> feature handy. Do you think that it would be good to implement this
> behavior also for V6 version of freeview?
>
> Regards,
>
> Antonin Skoch
>
>
>
> _______________________________________________
> 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/20170104/0942bee8/attachment-0001.html

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

Message: 5
Date: Wed, 4 Jan 2017 22:26:57 +0000
From: Tobias Granberg <tobias.granberg@ki.se>
Subject: Re: [Freesurfer] 6.0.0 release
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <4444515FD469E3449E34E2CDA544959C010340FC93@KIMSX04.user.ki.se>
Content-Type: text/plain; charset="iso-8859-1"

Great! Thanks for the quick response.

Best wishes,
Tobias
_________________________________________
Tobias Granberg, MD, PhD

Karolinska Institutet | Department of Clinical Science, Intervention and Technology
Karolinska University Hospital | Department of Radiology
141 86 Stockholm, Sweden
Cellular: +46 700 60 60 87

________________________________________
Fr?n: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] för Douglas N Greve [greve@nmr.mgh.harvard.edu]
Skickat: den 4 januari 2017 18:23
Till: freesurfer@nmr.mgh.harvard.edu
?mne: Re: [Freesurfer] 6.0.0 release

Hi Tobias, we have a release candidate that we are testing now. If all
goes well, then our release date will be Jan 17 (of 2017:).

doug

On 01/04/2017 05:56 AM, Tobias Granberg wrote:
> Dear Bruce, Doug and the rest of the team,
>
> I hope you have had a pleasant start of the new year!
>
> We have noticed that there is now a 6.0.0 RC but that the modification
> date changes while the file name persists. We are planning on running
> some processing, but it seems to be better to hold off until the
> stable release. Any time perspective for the release? Will the Linux
> version be finished before the OSX version?
>
> Thanks a lot!
>
> Best wishes,
> Tobias
> _________________________________________
> Tobias Granberg, MD, PhD
>
> Karolinska Institutet | Department of Clinical Science, Intervention
> and Technology
> Karolinska University Hospital | Department of Radiology
> 141 86 Stockholm, Sweden
> Cellular: +46 700 60 60 87
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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

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: 6
Date: Wed, 4 Jan 2017 23:49:52 +0000
From: Jennifer Szeto <jennifer_szeto@hotmail.com>
Subject: [Freesurfer] Problem with freeview
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <HK2PR02MB1506A12A0A450FA800BD8793F0610@HK2PR02MB1506.apcprd02.prod.outlook.com>

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

Hi Freesurfer Experts,

I have installed Freesurfer5.3 and it seems to be working fine. However when i tried to load up the GLM analysis (after doing mris_preproc and mri_glmfit) results on freeview, i got the following message:

"OpenGL warning: No pincher, please call crStateSetCurrentPointers () in your SPU Did not find any volume geometry information in the surface"

Just wondering if anyone knows the solution to this?

Thanks for your help!

Jen
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170104/a5080f76/attachment-0001.html

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

Message: 7
Date: Thu, 5 Jan 2017 01:13:19 +0000
From: Lucette Cysique <lcysique@unsw.edu.au>
Subject: Re: [Freesurfer] minor edits to aseg lead to exist with
        errors in about 25% of my scans
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Cc: "Madeleine Nichols $Redirection$" <mcmaddie@gmail.com>
Message-ID:
        <ME1PR01MB068965C9774CE98CFD4A07D288600@ME1PR01MB0689.ausprd01.prod.outlook.com>

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

Please could someone consider my email question sent dec 14th?
Email below
Thanks

Lucette A. Cysique, Ph.D.

NHMRC Clinical Career Development Fellow / UNSW Medicine 2013-2017
NeuroHIV and Quantitative Neuropsychology Group Leader @ NeuRA
Senior Lecturer SoMs, UNSW Medicine
Affiliated senior researcher at the St. Vincent's Hospital Sydney, Applied Medical Research Centre, Peter Duncan Neuroscience Unit

Postal Address:
Neuroscience Research Australia
PO Box 1165 (Street Address: 139 Barker Street)
Randwick NSW 2031
Australia

Office Ph: +61 2 9399 1880
Mobile Ph: (+61) (0)431 576 710 (text preferred)

Emails:
lcysique@unsw.edu.au (primary)
Lucette.Cysique@svha.org.au (St. Vincent's Hospital Sydney, related project)
lcysique@ucsd.edu (HIV Neurobehavioral Research Center/UCSD related project)
Twitter: @Lucette_C
http://www.neura.edu.au/research/themes/cysique-group
________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Lucette Cysique
Sent: Monday, December 19, 2016 12:37:13 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Madeleine Nichols (Redirection)
Subject: Re: [Freesurfer] minor edits to aseg lead to exist with errors in about 25% of my scans

sending this again as I have had no responses

Thanks

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Lucette Cysique
Sent: Wednesday, December 14, 2016 12:52:11 PM
To: freesurfer@nmr.mgh.harvard.edu
Cc: Madeleine Nichols (Redirection)
Subject: [Freesurfer] minor edits to aseg lead to exist with errors in about 25% of my scans

Dear FS Wiki

I run my scan in FS without any problem

example:

#@#%# recon-all-run-time-hours 8.342

recon-all -s 877 finished without error

then I do some edits to the aseg in freeview

edits include: relabelling correctly lateral ventricles voxels mostly in the posterior horn of the lateral ventricles; white matter hyperintensities around those voxels which are erroneously considered as cortex also more often in the posterior horn of the lateral ventricles; and correcting erroneous allocation of choroid plexus also typically in the posterior horn of the lateral ventricles

Once done, I re-run using

recon-all -s $i -autorecon2-noaseg

example:

/mridata/workingdata/HIV/subjects/877

/usr/local/FREESURFER/freesurfer5.3.0/bin/recon-all

-s 877 -autorecon2-noaseg

in 25% of cases, I get the following error message and the process exists

example:

#--------------------------------------------

#@# Intensity Normalization2 Wed Dec 14 12:33:54 AEDT 2016

/mridata/workingdata/HIV/subjects/011/mri

mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz

mri_normalize: aseg volume aseg.mgz must be conformed

using segmentation for initial intensity normalization

using MR volume brainmask.mgz to mask input volume...

reading from norm.mgz...

Reading aseg aseg.mgz

Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s 011 exited with ERRORS at Wed Dec 14 12:33:56 AEDT 2016

in the other no problem

example:

#@#%# recon-all-run-time-hours 1.116

recon-all -s 877 finished without error at Thu Dec 1 14:42:27 AEDT 2016

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20170105/54de506f/attachment-0001.html

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

Message: 8
Date: Wed, 4 Jan 2017 20:17:46 -0500 (EST)
From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] minor edits to aseg lead to exist with
        errors in about 25% of my scans
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Cc: "Madeleine Nichols $Redirection$" <mcmaddie@gmail.com>
Message-ID:
        <alpine.LRH.2.20.1701042016110.28877@door.nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="iso-8859-1"

Hi Lucette

how do you do the editing? Looks like it was in some other package, which
probably accounts for the error. You should be able to fix it by
cding into the mri dir and running:

mri_convert -rt nearest -rl orig.mgz aseg.your_edits.mgz aseg.mgz

cheers
Bruce

On
Thu, 5 Jan 2017, Lucette Cysique wrote:

> Please could someone consider my email question sent dec 14th?
> Email below
> Thanks
>
>
> Lucette A. Cysique, Ph.D.
>
> NHMRC Clinical Career Development Fellow / UNSW Medicine 2013-2017
> NeuroHIV and Quantitative Neuropsychology Group Leader @ NeuRA
> Senior Lecturer SoMs, UNSW Medicine
> Affiliated senior researcher at the St. Vincent's Hospital Sydney, Applied
> Medical Research Centre, Peter Duncan Neuroscience Unit
>
> Postal Address:
> Neuroscience Research Australia
> PO Box 1165 (Street Address: 139 Barker Street)
> Randwick NSW 2031
> Australia
>
> Office Ph: +61 2 9399 1880
> Mobile Ph: (+61)? (0)431 576 710 (text preferred)
>
> Emails:
> lcysique@unsw.edu.au (primary)
> Lucette.Cysique@svha.org.au (St. Vincent's Hospital Sydney, related project)
> lcysique@ucsd.edu (HIV Neurobehavioral Research Center/UCSD related project)
> Twitter: @Lucette_C
> http://www.neura.edu.au/research/themes/cysique-group
>
> ____________________________________________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Lucette Cysique
> Sent: Monday, December 19, 2016 12:37:13 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Cc: Madeleine Nichols (Redirection)
> Subject: Re: [Freesurfer] minor edits to aseg lead to exist with errors in
> about 25% of my scans ?
>
> sending this again as I have had no responses
>
> Thanks
>
> ____________________________________________________________________________
> From: freesurfer-bounces@nmr.mgh.harvard.edu
> <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Lucette Cysique
> Sent: Wednesday, December 14, 2016 12:52:11 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Cc: Madeleine Nichols (Redirection)
> Subject: [Freesurfer] minor edits to aseg lead to exist with errors in about
> 25% of my scans ?
>
> Dear FS Wiki
>
>
> I run my scan in FS without any problem
>
> example:
>
> #@#%# recon-all-run-time-hours 8.342
>
> recon-all -s 877 finished without error
>
>
> then I do some edits to the aseg in freeview
>
> edits include: relabelling correctly lateral ventricles voxels mostly?in the
> posterior horn of the lateral ventricles; white matter hyperintensities
> around those voxels?which are erroneously considered as?cortex also
> more?often?in the posterior horn of the lateral ventricles; and?correcting
> erroneous allocation of choroid plexus also typically in the posterior horn
> of the lateral ventricles
>
>
> Once done, I re-run using
>
> recon-all -s $i -autorecon2-noaseg
>
>
> example:?
>
> /mridata/workingdata/HIV/subjects/877
>
> /usr/local/FREESURFER/freesurfer5.3.0/bin/recon-all
>
> -s 877 -autorecon2-noaseg
>
>
> in 25% of cases, I get the following error message and the process exists
>
> example:
>
> #--------------------------------------------
>
> #@# Intensity Normalization2 Wed Dec 14 12:33:54 AEDT 2016
>
> /mridata/workingdata/HIV/subjects/011/mri
>
>
> ?mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz?
>
>
> mri_normalize: aseg volume aseg.mgz must be conformed
>
> using segmentation for initial intensity normalization
>
> using MR volume brainmask.mgz to mask input volume...
>
> reading from norm.mgz...
>
> Reading aseg aseg.mgz
>
> Linux katana.neura.edu.au 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17
> 01:55:02 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
>
>
> recon-all -s 011 exited with ERRORS at Wed Dec 14 12:33:56 AEDT 2016
>
>
>
>
> in the other no problem
>
> example:
>
> #@#%# recon-all-run-time-hours 1.116
>
> recon-all -s 877 finished without error at Thu Dec ?1 14:42:27 AEDT 2016
>
>
>
>

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

Message: 9
Date: Wed, 4 Jan 2017 20:19:37 -0500
From: Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Problem with freeview
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <9E7D3C9C-0362-498A-AC84-E065B804A56D@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"

I?m not sure about the first part of the message, but "Did not find any volume geometry information in the surface? can be ignored. It is just a warning. Did the program still run? If so, you can ignore these warnings.

Best,
Ruopeng

> On Jan 4, 2017, at 6:49 PM, Jennifer Szeto <jennifer_szeto@hotmail.com> wrote:
>
> Hi Freesurfer Experts,
>
> I have installed Freesurfer5.3 and it seems to be working fine. However when i tried to load up the GLM analysis (after doing mris_preproc and mri_glmfit) results on freeview, i got the following message:
>
> "OpenGL warning: No pincher, please call crStateSetCurrentPointers () in your SPU Did not find any volume geometry information in the surface"
>
> Just wondering if anyone knows the solution to this?
>
> Thanks for your help!
>
> Jen
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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/20170104/b0560b7b/attachment-0001.html

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

Message: 10
Date: Thu, 5 Jan 2017 01:30:17 +0000
From: Jennifer Szeto <jennifer_szeto@hotmail.com>
Subject: Re: [Freesurfer] Problem with freeview
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
        <HK2PR02MB150647FE24FBB62E72CD783AF0600@HK2PR02MB1506.apcprd02.prod.outlook.com>

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

Thank you Ruopeng,

I manage to have Freeview loaded up but not the results from the GLM_FIT analyses...

Jen

________________________________
From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Ruopeng Wang <rpwang@nmr.mgh.harvard.edu>
Sent: 05 January 2017 01:19
To: Freesurfer support list
Subject: Re: [Freesurfer] Problem with freeview

I'm not sure about the first part of the message, but "Did not find any volume geometry information in the surface" can be ignored. It is just a warning. Did the program still run? If so, you can ignore these warnings.

Best,
Ruopeng

On Jan 4, 2017, at 6:49 PM, Jennifer Szeto <jennifer_szeto@hotmail.com<mailto:jennifer_szeto@hotmail.com>> wrote:

Hi Freesurfer Experts,

I have installed Freesurfer5.3 and it seems to be working fine. However when i tried to load up the GLM analysis (after doing mris_preproc and mri_glmfit) results on freeview, i got the following message:

"OpenGL warning: No pincher, please call crStateSetCurrentPointers () in your SPU Did not find any volume geometry information in the surface"

Just wondering if anyone knows the solution to this?

Thanks for your help!

Jen
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu<mailto: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/20170105/a1444758/attachment-0001.html

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

Message: 11
Date: Thu, 5 Jan 2017 10:49:12 +0800
From: Thomas Yeo <ythomas@csail.mit.edu>
Subject: [Freesurfer] Postdoctoral Fellow in Machine Learning in
        Neuroimaging
To: "FSL - FMRIB's Software Library" <fsl@jiscmail.ac.uk>,      freesurfer
        <freesurfer@nmr.mgh.harvard.edu>, SPM@jiscmail.ac.uk
Message-ID:
        <CANZVnTZDuadLL1WN0MdKfj_Q+iujdsmhX1eMuwXax=T=TMJXDQ@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Dear All,

I am looking to hire a postdoc to develop machine learning algorithms
for large-scale publicly available MRI and behavioral data. Experience
with probabilistic machine learning (aka graphical models) or deep
learning is a plus.

The ultimate goal is automatic scientific discovery (see recent paper
from our lab: http://www.pnas.org/content/113/42/E6535). Topics are
flexible, e.g., multi-modal fusion, individual-subject brain
parcellation, individual subject behavior prediction, dynamic
functional connectivity, meta-analysis, neural mass modeling,
multi-scale neuroscience, graph theory, mental disorder subtypes, etc.

Other details below.

Regards,
Thomas

Requirements: Ph.D. in computer science, electrical engineering,
statistics, computational neuroscience or related fields. The
successful applicant will work with an interdisciplinary team of
computer scientists and neuroscientists, and must be willing to learn
some neuroscience.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world (http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (ythomas@csail.mit.edu) with your CV.

Deadline: Whenever the position is filled.

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

Message: 12
Date: Thu, 5 Jan 2017 10:57:58 +0800
From: Thomas Yeo <ythomas@csail.mit.edu>
Subject: [Freesurfer] Postdoctoral fellow in mental disorder subtypes
To: "FSL - FMRIB's Software Library" <fsl@jiscmail.ac.uk>,      freesurfer
        <freesurfer@nmr.mgh.harvard.edu>, SPM@jiscmail.ac.uk
Message-ID:
        <CANZVnTbzd-MNfW10L5YNFyK6PNrDcPOEGKi19ZNk1VnsOa97rw@mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Dear All,

I am looking for a neuroscience/psychology postdoc to apply machine
learning algorithms (possibly developed in our lab) to discover and
understand mental disorder subtypes from existing large-scale public
databases.

See recent example from our lab
(http://www.pnas.org/content/113/42/E6535). Experience with
psychiatric disorders (especially ASD and ADHD) is a plus, but not
required.

Other details below.

Regards,
Thomas

Requirements: Ph.D. in neuroscience, psychology or related fields. The
successful applicant will work with an interdisciplinary team of
computer scientists and neuroscientists. Programming experience is
required. He or she does NOT need to code a new algorithm, but must be
able to apply existing code (or modify existing code) for his or her
project.

Research Webpage: https://sites.google.com/site/yeoyeo02/home

Compensation: Competitive and commensurate with experience

Attraction: Perform ground-breaking research at the National
University of Singapore (NUS), while enjoying the beautiful sceneries
and cultures of South-East Asia. NUS is a research-intensive
university consistently ranked among the top 30 universities in the
world (http://en.wikipedia.org/wiki/National_University_of_Singapore#University_rankings).

Contact: Email BT Thomas Yeo (ythomas@csail.mit.edu) with your CV.

Deadline: Whenever the position is filled.

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

Message: 13
Date: Thu, 5 Jan 2017 11:17:21 -0500
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Fwd: REMINDER: OHBM 2017 Call For Council
        Nominations
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <74630c58-b826-77d5-ef09-f973876cef93@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=utf-8; format=flowed

-------- Forwarded Message --------
Subject:         REMINDER: OHBM 2017 Call For Council Nominations
Date:    Thu, 05 Jan 2017 05:31:34 -0600
From:    info@humanbrainmapping.org
Reply-To:        info@humanbrainmapping.org
To:      greve@nmr.mgh.harvard.edu

Dear OHBM Member:

The OHBM Nominating Committee is pleased to invite current OHBM members
to nominate individuals to serve on the OHBM Executive Council. Open
positions include Chair-Elect, Secretary-Elect, Treasurer-Elect, Program
Chair-Elect and Education Chair-Elect.

We are seeking individuals with proven scientific leadership expertise,
strategic thinking and planning skills, strong problem solving skills,
results oriented, visionary, strong ethics, have a global perspective
and are available to participate and commit time.   A knowledge of OHBM
activities and consistent attendance at the Annual Meeting is desired.
The Council is committed to supporting a diverse membership and strongly
encourages nominations from women, minorities, and members of other
underrepresented groups. The OHBM Nominating Committee will continue to
work diligently to develop a slate of candidates for election on the
Executive Council, but *we need your participation now in identifying
leadership candidates.*

The term of service begins in June 2017, and each term is for three years.

*Remember *to make your nominations by completing the *Call for
Nominations*
<https://www.humanbrainmapping.org/i4a/forms/index.cfm?id=97> form no
later than *Wednesday, January 11^th at* *11:59 PM US CST*.
Self-nominations are welcome and encouraged.

The OHBM By-Laws
<http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3292>,
Article 5 provides the framework and process for the election of new
Council members.

*OHBM Nominating Committee:*
Tor Wager, Secretary
Christian Grefkes, Secretary-Elect
Tonya White, Past Secretary
Alan Evans, Chair
Bernard Mazoyer, Chair-Elect
Karl Zilles, Past Chair

You must, when making your nominations, specify a position you want the
person to fill (Chair Elect, Treasurer Elect, Secretary Elect, Program
Chair Elect, Education Chair-Elect). Please check with this person
before you make the nomination to be sure they would be interested in
serving.

Once the final slate is prepared and distributed, members will be able
to see a brief bio on each candidate and vote online via the OHBM
website. The results of these elections will be announced during the
Town Hall Meeting, Wednesday, June 29, 2017, during the OHBM Annual
Meeting in Vancouver, Canada. All candidates identified on the ballot
will be informed of the results prior to the Annual Meeting.

Councilors are not eligible for re-election for any council position for
three years after serving one term. Individuals who are currently
ineligible as nominees due to service on Council within the past 3 years
are listed below. Current 2016-2017 OHBM Council.
<http://www.humanbrainmapping.org/i4a/pages/index.cfm?pageid=3313>

*Not Eligible Until 2019/2020*

* Karen Berman, 2015-2016 Chair
* Jeannette Mumford, 2015-2016 Treasurer
* Doug Greve, 2015-2016 Secretary
* Jack Van Horn, 2015-2016 Program Chair
* Niko Kriegeskorte, 2015-2016 Education Chair

*Not Eligible Until 2018/2019*

* Steve Smith, 2014-2015 Chair
* Jia-Hong Gao, 2014-2015 Treasurer
* Simon Eickhoff, 2014-2015 Secretary
* Pedro Valdes Sosa, 2014-2015 Program Chair

We look forward to your involvement in the identification and election
of your association?s leadership.   Please contact the OHBM Executive
Office at info@humanbrainmapping.org <mailto:info@humanbrainmapping.org>
with any questions.

Sincerely,

JoAnn Taie
Executive Director
Organization for Human Brain Mapping (OHBM)

*Organization for Human Brain Mapping*
5841 Cedar Lake Road, Suite 204
Minneapolis, MN 55416 USA
Phone: 1 952-646-2029
Fax: 1 952-545-6073
www.humanbrainmapping.org <http://www.humanbrainmapping.org>
info@humanbrainmapping.org <mailto:info@humanbrainmapping.org>

To opt out of OHBM emails, contact the OHBM Executive Office at
info@humanbrainmapping.org
<mailto:info@humanbrainmapping.org?subject=Opt%20Out%20of%20Emails>.

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

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

End of Freesurfer Digest, Vol 155, Issue 8
******************************************