Re: [Freesurfer] FreeSurfer LocalGI error

[Manoj Kumar]

Thank you very much, Dear Andrew! for your expert advise. I really
appreciated.
Its worked.

Best Regards
Manoj

On Tue, Jan 16, 2018 at 10:39 PM, Hoopes, Andrew 
wrote:

> Hi Manoj,
>
> This probably has to do with SIP being enabled, which blocks libraries
> stored in /usr. I would suggest disabling SIP and rerunning to see if
> that fixes things:
> http://osxdaily.com/2015/10/05/disable-rootless-system-
> integrity-protection-mac-os-x/
>
> best,
> Andrew
>
>
> On Jan 16, 2018, at 2:59 AM, Manoj Kumar  wrote:
>
> Hello Dear FreeSurfer Experts,
>
> I am trying to run "recon-all -s subject  -localGI" command on my Mac bash
> terminal. I am getting following error.
>
> I am using using Freesurfer V 6.0 and running on MacOS High Sierra
> (version 10.13)
>
> I also run the istallation update :"sudo -E fs_update" as per suggestion
> on the release note but still getting same error.
>
> Any help to resolve this issue would be greatly appreciated.
> Thank you so much for all your help and support.
>
> Best regards
> Manoj
>
> ***
> Manojs-iMac:cases manojkumar$ export SUBJECTS_DIR=/Users/
> manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf
> Manojs-iMac:cases manojkumar$ cd $SUBJECTS_DIR
> Manojs-iMac:surf manojkumar$ mris_compute_lgi --i lh.pial
> =
> rm -Rf /Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/
> surf/tmp-mris_compute_lgi-lh.pial
> =
> =
> mkdir -p /Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/
> surf/tmp-mris_compute_lgi-lh.pial
> =
> =
> mris_fill -c -r 1 lh.pial /Users/manojkumar/fs_dmd_
> process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.
> pial/lh.pial.filled.mgz
> =
> dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
>   Referenced from: /Applications/freesurfer/bin/.
> ./lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> dyld: Symbol not found: ___emutls_get_address
>   Referenced from: /Applications/freesurfer/bin/.
> ./lib/gcc/lib/libgomp.1.dylib
>   Expected in: /usr/lib/libSystem.B.dylib
>
> Abort
> ERROR: mris_fill -c -r 1 lh.pial /Users/manojkumar/fs_dmd_
> process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
> failed!
> Manojs-iMac:surf manojkumar$
> ___
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>
>
>
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>
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[Freesurfer] POST-DOCTORAL FELLOWSHIP IN NEUROIMAGING

[Xiaosong He]

*POST-DOCTORAL FELLOWSHIP*

*IN NEUROIMAGING *

*THOMAS JEFFERSON UNIVERSITY/ SIDNEY KIMMEL *

*MEDICAL** COLLEGE, PHILA., PA.*

The Department of Neurology at Thomas Jefferson University/Jefferson
Medical College has an opening for a Two-Year Postdoctoral Research
Fellowship in Neuroimaging focusing on both clinical brain mapping and
primary cognitive neuroscience investigations. The emphasis in our
neuroimaging program is on cognitive and behavioral network organization
and plasticity in neurologic disorders such as epilepsy. The lab is part of
the Jefferson Comprehensive Epilepsy Center, an internationally-known
epilepsy surgery program. Presurgical brain mapping studies are undertaken
(MRI volumetrics, task-fMRI, resting state functional connectivity,
diffusion imaging, neuropsychological assessment,
electrophysiology/electrocortical stimulation) as well as post-surgical
neuroimaging studies investigating clinical, cognitive, and behavioral
outcomes. The pre-surgical brain mapping studies are conducted on a regular
basis, utilized in image-guided surgery, and then made available for
research. Studies in brain recovery and the cognitive reorganization of
language and memory functions are emphasized, utilizing rich multi-modal
datasets for the investigation of both cognitive and pathologic (e.g.,
seizure) networks. Thomas Jefferson University provides a high-level
interdisciplinary research environment with grand rounds, seminars, case
conferences, and opportunities to collaborate with faculty across
departments such as neurosurgery and radiology. Successful applicants must
have a strong background in image processing and analysis using programs
such as MATLAB, SPM, and FSL with a strong interest in clinical
neuroimaging and cognitive neuroscience. Applicants must have a PHD or MD
in neuroscience,   biomedical engineering, statistics, neurology,
neuropsychology, radiology, or related field. Interested applicants should
send a CV and cover letter stating experience and interests, 2-3
peer-reviewed publications, and three letters of recommendation.
Anticipated start date is 7/1/18, but is flexible.  *Contact: Joseph I.
Tracy, Ph.D., ABPP(CN). Director, Cognitive Neuroscience and Brain Mapping
Laboratory, Thomas Jefferson Univ./Sidney Kimmel Medical Coll., Jefferson
Hospital for Neuroscience, 901 Walnut Street, Suite #447, Phila.,PA 19107,
phone:#215-955-4661, *e-mail: joseph.tr...@jefferson.edu.

Thomas Jefferson University and Hospitals is an equal Opportunity Employer.
Jefferson values diversity and encourages applications from women, members
of minority groups, LGBTQ individuals, disabled individuals, and veterans.
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Re: [Freesurfer] Longitudinal Pipeline (fwd)

[Aaron Tanenbaum]

Oh wow. thank you very much. You just save me weeks worth of work.

On Tue, Jan 16, 2018 at 2:31 PM, Bruce Fischl 
wrote:

> FYI
>
> -- Forwarded message --
> Date: Tue, 16 Jan 2018 19:59:38 +
> From: Mark Jenkinson 
> To: Bruce Fischl 
> Cc: Freesurfer support list 
> Subject: Re: [Freesurfer] Longitudinal Pipeline
>
> Hi Aaron and Hi Bruce!
> There is code to convert ANTs format to FSL, so you can use that.
> It is part of this tool:
>   https://sourceforge.net/p/c3d/git/ci/master/tree/doc/c3d.md
>
> I've included a code snippet below to show how we've used this.
> Cheers,
> MJ
>
> ${antsFolder}/antsRegistrationSyN.sh -d 3 -f ${ref} -f ${ref2} -m ${src}
> -m ${src2} -o
> ${workdir}/${outname}_ -t 'b' -j 1
>
> ${c3dFolder}/c3d_affine_tool -ref ${ref} -src ${src} -itk
> ${workdir}/${outname}_0GenericAffine.mat
> -ras2fsl -o ${workdir}/${outname}_affine_fsl.mat
>
> ${c3dFolder}/c3d -mcs ${workdir}/${outname}_1Warp.nii.gz -oo
> ${workdir}/wx.nii.gz
> ${workdir}/wy.nii.gz ${workdir}/wz.nii.gz
> ${FSLDIR}/bin/fslmaths ${workdir}/wy -mul -1 ${workdir}/i_wy
> ${FSLDIR}/bin/fslmerge -t ${workdir}/${outname}_warp_fsl ${workdir}/wx
> ${workdir}/i_wy ${workdir}/wz
>
> ${FSLDIR}/bin/convertwarp --ref=${ref} --premat=${workdir}/${outname}
> _affine_fsl.mat
> --warp1=${workdir}/${outname}_warp_fsl --out=${workdir}/${outname}_wa
> rp_fsl
> ${FSLDIR}/bin/invwarp -w ${workdir}/${outname}_warp_fsl -o
> ${workdir}/${refBN}_to_${srcBN}_warp_fsl
> -r ${src}
>
>
>
>   On 15 Jan 2018, at 15:18, Bruce Fischl 
> wrote:
>
> Hi Aaron
>
> we compute the warp and save it in the mri/transforms/talairach.m3z, but
> don't apply it (so
> don't require an extra resampling). I know we have some tools around to
> convert to ANTS
> format, but I'm not sure about fnirt. I'll cc MJ who may know (hi MJ!)
>
> cheers
> Bruce
>
>
> On Mon, 15 Jan 2018, Aaron Tanenbaum wrote:
>
>   Is the warp saved anywhere and where can I find it? Also is the warp
> compatible
>   with FNIRT in any
>   way. I am interested in combining warps together to reduce the
> number of
>   re-sampling steps.
>   Thank you so much in advanced
>   On Mon, Jan 15, 2018 at 8:53 AM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
>in the last stage there is a nonlinear atlas alignment that is
> specific to
>each timepoint. We are working on building a nonlinear base,
> but it is not
>distributed yet.
>
>cheers
>Bruce
>  On Sun, 14 Jan 2018, Aaron
>Tanenbaum wrote:
>
>>
>> I am interested in knowing what type of alignment goes into
> the last stage
>   of the
>longitudinal
>> pipeline. Are each longitudinal time point non-linearly
> aligned to the base
>   image? If
>so can I find
>> the warp?
>>
>>
>   ___
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[Freesurfer] Research Assistant Positions in ECoG Lab in New York

[steph]

Dear all, 

 The ECoG Laboratory for Human Brain Mapping at the Feinstein Institute for 
Medical Research – Hofstra Northwell School of Medicine is looking for two 
research assistants. The successful candidates will help with the lab’s 
research into (1) improving the identification of functional and pathological 
brain regions in individuals suffering from epilepsy, (2) the neural mechanisms 
of cognition, and (3) characterization of macroscale human brain networks. The 
lab works exclusively with patients being evaluated for epilepsy surgery using 
methods such as electrocorticography (ECoG), MRI, fMRI, DTI, and direct 
electrical brain stimulation. The start date is as soon as possible.



The responsibilities of both research assistants include assisting with the 
collection and analysis of the aforementioned data, managing lab equipment, and 
helping to present lab findings at conferences and in journals.

One position will further focus on project management and administration, 
working with a research coordinator on IRB matters, and assistance with 
preparing progress reports and grant applications.

The second position is more computationally focused and will require more 
in-depth analysis of neural and behavioral data, database management, and the 
development of analysis scripts (depending on proficiency with coding and 
signal processing).

Both RAs will have their own scientific projects with dedicated time to work on 
them. Past research assistants in the lab have presented their work at clinical 
and basic research conferences, co-authored publications, and are working on 
first author publications. They have gone on to medical schools or PhD programs 
after spending 1-3 years in the lab.

These unique positions will expose the successful applicant to basic and 
clinical neuroscience as well as neurosurgery, neurology, and neuropsychology. 
The location of the institute allows living either in the suburban 
neighborhoods of Long Island, or in vibrant Brooklyn or Queens. Some employees 
also commute from Manhattan. It is a great opportunity for recent post-bacs 
interested in medical school or graduate school in neuroscience/biomedical 
engineering.


- Qualifications -

Minimum:
-B.A./B.S./B.E. in an appropriate discipline (e.g., neuroscience, psychology, 
biomedical engineering, computer science, physics)
-For the second RA position: Experience with at least one programming language 
(MATLAB, R, or Python) and statistical analyses
-1 year commitment

Desirable:
-Prior experience working with neuroimaging, EEG/MEG, or brain stimulation data
-Previous experience working with patients
-Previous work in a research laboratory that shows evidence of independent 
scholarship, problem solving, and motivation
-2 year commitment preferred

For more information about the position please send your CV along with your 
questions to Drs. Stephan Bickel (sbic...@northwell.edu 
) and Ashesh Mehta (amehta.northwell.edu 
). We are looking forward to hearing from you!

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Re: [Freesurfer] Longitudinal Pipeline (fwd)

[Bruce Fischl]

FYI

-- Forwarded message --
Date: Tue, 16 Jan 2018 19:59:38 +
From: Mark Jenkinson 
To: Bruce Fischl 
Cc: Freesurfer support list 
Subject: Re: [Freesurfer] Longitudinal Pipeline

Hi Aaron and Hi Bruce!
There is code to convert ANTs format to FSL, so you can use that.
It is part of this tool:
  https://sourceforge.net/p/c3d/git/ci/master/tree/doc/c3d.md

I've included a code snippet below to show how we've used this.
Cheers,
MJ

${antsFolder}/antsRegistrationSyN.sh -d 3 -f ${ref} -f ${ref2} -m ${src} -m 
${src2} -o
${workdir}/${outname}_ -t 'b' -j 1

${c3dFolder}/c3d_affine_tool -ref ${ref} -src ${src} -itk 
${workdir}/${outname}_0GenericAffine.mat
-ras2fsl -o ${workdir}/${outname}_affine_fsl.mat

${c3dFolder}/c3d -mcs ${workdir}/${outname}_1Warp.nii.gz -oo 
${workdir}/wx.nii.gz
${workdir}/wy.nii.gz ${workdir}/wz.nii.gz
${FSLDIR}/bin/fslmaths ${workdir}/wy -mul -1 ${workdir}/i_wy
${FSLDIR}/bin/fslmerge -t ${workdir}/${outname}_warp_fsl ${workdir}/wx 
${workdir}/i_wy ${workdir}/wz

${FSLDIR}/bin/convertwarp --ref=${ref} 
--premat=${workdir}/${outname}_affine_fsl.mat
--warp1=${workdir}/${outname}_warp_fsl --out=${workdir}/${outname}_warp_fsl
${FSLDIR}/bin/invwarp -w ${workdir}/${outname}_warp_fsl -o 
${workdir}/${refBN}_to_${srcBN}_warp_fsl
-r ${src}


  On 15 Jan 2018, at 15:18, Bruce Fischl  wrote:

Hi Aaron

we compute the warp and save it in the mri/transforms/talairach.m3z, but don't 
apply it (so
don't require an extra resampling). I know we have some tools around to convert 
to ANTS
format, but I'm not sure about fnirt. I'll cc MJ who may know (hi MJ!)

cheers
Bruce


On Mon, 15 Jan 2018, Aaron Tanenbaum wrote:

  Is the warp saved anywhere and where can I find it? Also is the warp 
compatible
  with FNIRT in any
  way. I am interested in combining warps together to reduce the number of
  re-sampling steps.
  Thank you so much in advanced
  On Mon, Jan 15, 2018 at 8:53 AM, Bruce Fischl 
 wrote:
   in the last stage there is a nonlinear atlas alignment that is 
specific to
   each timepoint. We are working on building a nonlinear base, but it 
is not
   distributed yet.

   cheers
   Bruce
     On Sun, 14 Jan 2018, Aaron
   Tanenbaum wrote:

   >
   > I am interested in knowing what type of alignment goes into the 
last stage
  of the
   longitudinal
   > pipeline. Are each longitudinal time point non-linearly aligned to 
the base
  image? If
   so can I find
   > the warp?
   >
   >
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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.


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Re: [Freesurfer] recon-all exited with error

[Bruce Fischl]

you can put it on our ftp site:

https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange
On Tue, 16 Jan 
2018, Trisanna Sprung-Much 
wrote:

> Hi Bruce
> Thanks for the speedy reply. Should I attach it here or is there a place I 
> can upload it to?
> 
> best
> Trisanna
> 
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
> On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl  
> wrote:
>   hmmm, I've never seen label2label core dump before. Can you tar, gzip 
> and
>   upload the entire subject dir?
>   On Tue, 16 Jan 2018, Trisanna Sprung-Much
>   wrote:
>
>   > Hi there
>   >
>   > I ran Freesurfer 6.0 on a subject last night and it took about 12 
> hours (seemed to get
>   to the very end) and then exited with
>   > errors. I can open my surfaces so I think it ended roughly with the 
> atlas labelling. I
>   attach the recon-all log file here.
>   >
>   > best wishes
>   >
>   > Trisanna
>   > --
>   > Ph.D. CandidateMcGill University
>   > Integrated Program in Neuroscience
>   > Psychology
>   >
>   >
>   >
>   >
>   ___
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> 
>
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> 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
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> in error
>   but does not contain patient information, please contact the sender and 
> properly
>   dispose of the e-mail.
> 
> 
> 
>
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Re: [Freesurfer] FreeSurfer LocalGI error

[Hoopes, Andrew]

Hi Manoj,

This probably has to do with SIP being enabled, which blocks libraries stored 
in /usr. I would suggest disabling SIP and rerunning to see if that fixes 
things:
http://osxdaily.com/2015/10/05/disable-rootless-system-integrity-protection-mac-os-x/

best,
Andrew


On Jan 16, 2018, at 2:59 AM, Manoj Kumar 
> wrote:

Hello Dear FreeSurfer Experts,

I am trying to run "recon-all -s subject  -localGI" command on my Mac bash 
terminal. I am getting following error.

I am using using Freesurfer V 6.0 and running on MacOS High Sierra (version 
10.13)

I also run the istallation update :"sudo -E fs_update" as per suggestion on the 
release note but still getting same error.

Any help to resolve this issue would be greatly appreciated.
Thank you so much for all your help and support.

Best regards
Manoj

***
Manojs-iMac:cases manojkumar$ export 
SUBJECTS_DIR=/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf
Manojs-iMac:cases manojkumar$ cd $SUBJECTS_DIR
Manojs-iMac:surf manojkumar$ mris_compute_lgi --i lh.pial
=
rm -Rf 
/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial
=
=
mkdir -p 
/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial
=
=
mris_fill -c -r 1 lh.pial 
/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
=
dyld: lazy symbol binding failed: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: ___emutls_get_address
  Referenced from: /Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib
  Expected in: /usr/lib/libSystem.B.dylib

Abort
ERROR: mris_fill -c -r 1 lh.pial 
/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
 failed!
Manojs-iMac:surf manojkumar$
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Re: [Freesurfer] Cortical White matter/corpus callisum

[Del Re, Elisabetta]

Alan,

thank you.

Of course, but my question was different:

Is the volume of the corpus callosum included in the calculation of the volume 
of the 'cerebral white matter'? Or does the volume of the cerebral white matter 
not include the volume of the corpus?

My understanding is that the volume of the corpus is included in the 
calculation of the volume of the cerebral white matter.

Can you confirm?

Thank you,

Elisabetta





From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Alan Francis 

Sent: Tuesday, January 16, 2018 11:42 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] Cortical White matter/corpus callisum

Hello Elisabetta -

The Corpus callosal volumes are included in the ASEG output and not in the WM 
files. They are titled CC_Anterior, CC_Midbody etc.

Best,

Alan

On Mon, Jan 15, 2018 at 2:11 PM, Del Re, Elisabetta 
> 
wrote:
Dear experts,
Is the corpus callosum volume included in the 'cortical White matter' volume?

Thank you,
Best,
Elisabetta

Get Outlook for 
iOS

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Alan N. Francis PhD
Instructor - Imaging Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu
afran...@mclean.harvard.edu

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Re: [Freesurfer] recon-all exited with error

[Trisanna Sprung-Much]

Hi Bruce

Thanks for the speedy reply. Should I attach it here or is there a place I
can upload it to?

best
Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Tue, Jan 16, 2018 at 11:44 AM, Bruce Fischl 
wrote:

> hmmm, I've never seen label2label core dump before. Can you tar, gzip and
> upload the entire subject dir?
> On Tue, 16 Jan 2018, Trisanna Sprung-Much
> wrote:
>
> > Hi there
> >
> > I ran Freesurfer 6.0 on a subject last night and it took about 12 hours
> (seemed to get to the very end) and then exited with
> > errors. I can open my surfaces so I think it ended roughly with the
> atlas labelling. I attach the recon-all log file here.
> >
> > best wishes
> >
> > Trisanna
> > --
> > Ph.D. CandidateMcGill University
> > Integrated Program in Neuroscience
> > Psychology
> >
> >
> >
> >
> ___
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>
>
> 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
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Re: [Freesurfer] recon-all exited with error

[Bruce Fischl]

hmmm, I've never seen label2label core dump before. Can you tar, gzip and 
upload the entire subject dir?
On Tue, 16 Jan 2018, Trisanna Sprung-Much 
wrote:

> Hi there
> 
> I ran Freesurfer 6.0 on a subject last night and it took about 12 hours 
> (seemed to get to the very end) and then exited with
> errors. I can open my surfaces so I think it ended roughly with the atlas 
> labelling. I attach the recon-all log file here.
> 
> best wishes
> 
> Trisanna
> --
> Ph.D. CandidateMcGill University
> Integrated Program in Neuroscience
> Psychology
> 
> 
> 
>
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Re: [Freesurfer] Cortical White matter/corpus callisum

[Alan Francis]

Hello Elisabetta -

The Corpus callosal volumes are included in the ASEG output and not in the
WM files. They are titled CC_Anterior, CC_Midbody etc.

Best,

Alan

On Mon, Jan 15, 2018 at 2:11 PM, Del Re, Elisabetta <
elisabetta_de...@hms.harvard.edu> wrote:

> Dear experts,
> Is the corpus callosum volume included in the 'cortical White matter'
> volume?
>
> Thank you,
> Best,
> Elisabetta
>
> Get Outlook for iOS 
>

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*Alan N. Francis PhD*
Instructor - Imaging Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
al...@bwh.harvard.edu 
afran...@mclean.harvard.edu


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[Freesurfer] PhD and postdoctoral positions - Investigating sensory aspects of human communication

[Katharina von Kriegstein]

Several researcher positions (Postdocs and PhD students) are available at the 
Human Communication Research Group, led by Katharina von Kriegstein. The group 
is currently based at the Max Planck Institute for Human Cognitive and Brain 
Sciences in Leipzig (MPI CBS; 
http://www.cbs.mpg.de/independent-research-groups/human-communication ) and 
will transfer to the Psychology Faculty of the TU Dresden in 2018.

The positions are funded by the ERC consolidator grant SENSOCOM. The aim of the 
SENSOCOM project is to investigate the role of auditory and visual subcortical 
sensory structures in analysing human communication signals and to specify how 
their dysfunction contributes to human communication disorders such as 
developmental dyslexia and autism spectrum disorders. For examples of our work 
on these topics see von Kriegstein et al., 2008 Current Biology, Diaz et al., 
2012 PNAS; Müller-Axt et al., 2017 Current Biology. The projects include 
experiments using cognitive neuroscience methods to understand the basic 
mechanisms of cortico-subcortical interactions as well as development of 
training programmes that are aimed at creating behavioural intervention 
programmes for communication deficits (for a brief description see 
http://cordis.europa.eu/project/rcn/199655_en.html ).

The positions will be based at the TU Dresden. Research will be performed at 
the Neuroimaging Centre at the TU Dresden ( http://www.nic-tud.de ) and MPI CBS 
in Leipzig. The centres offer cutting-edge infrastructure with 3-Tesla MRI, 
7-Tesla MRI, a Connectom scanner, MRI compatible eye-tracking, several EEG 
systems, 306-channel MEG, neurostimulation units including neuronavigaton, TMS 
and tDCS devices. Besides an excellent infrastructure, the centres offer an 
international and friendly environment with researchers from diverse 
backgrounds. All experimental facilities are supported by experienced physics 
and IT staff. For analyses with high computational demands, there is access to 
high-performance computing clusters.

Candidates should have a strong interest in perceptual aspects of human 
communication and experience with experimental methods of cognitive 
neuroscience, such as psychophysics, functional or structural MRI, TMS, 
diffusion-weighted imaging, brainstem recordings or EEG/MEG. Experience with 
clinical populations (e.g. developmental dyslexia) would be an asset but is not 
essential. PhD student candidates must have a Master’s degree (or equivalent) 
in neuroscience, clinical linguistics, psychology, cognitive science, biology, 
or a related field. Postdoc candidates must have a PhD in similar fields and 
should be able to demonstrate a consistently outstanding academic record, 
including publications.

The position starting date is flexible. Initially for two (postdocs) or three 
(PhD) years, the positions offer the possibility of an extension. Remuneration 
depends on experience and is based on regulations of the Max Planck Society 
payscale. MPI CBS is an equal opportunities employer, committed to the 
advancement of individuals without regard to ethnicity, religion, gender, or 
disability. PhD students will have the opportunity to participate in the TU 
Dresden graduate academy (https://tu-dresden.de/ga?set_language=en). TU Dresden 
is one of eleven German Universities of Excellence and offers an 
interdisciplinary scientific environment.

To apply, please submit a CV, contact information of two references, a brief 
personal statement describing your qualifications and future research 
interests, copies of up to two of your publications. Please submit your 
application via our online system at http://www.cbs.mpg.de/vacancies (using 
subject heading “ERC 01/18”). The deadline for application submission is 15st 
February 2018. Contact for informal enquiries regarding the post: Prof. Dr. 
Katharina von Kriegstein (katharina.von_kriegst...@tu-dresden.de).


---

Prof. Dr. Katharina von Kriegstein

Max Planck Institute for Human Cognitive and Brain Sciences
Stephanstr. 1A, 04103 Leipzig, Germany

Technische Universität Dresden
Bamberger Str. 7, 01187 Dresden, Germany

Phone +49 (0) 341-9940-2476

http://www.cbs.mpg.de/independent-research-groups/human-communication
https://twitter.com/kvonkriegstein

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Re: [Freesurfer] Question about compare left and right hemi of longitudinal data

[Martin Reuter]

Hi Lanbo,

what is the exact command you use for this? The problem is that the 
script or your command does not pass the right flags to recon all. 
Whenever recon-all is supposed to work on a longitudinal directory it 
needs to know the base and the long so the recon all command needs to show


-long subj_02_1 s02_base

as part of its arguments. So either adjust your command line, or if the 
recon-all call is performed from within another script, we need to 
change that script (add a -long flag so that the script performs the 
correct recon-all call in those cases when working on a longitudinal 
time point).


Once you have the left right difference (define on one of the 
hemispheres), you can treat it similar as a thickness map and run it 
through the Matlab LME code. 
https://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels



Best, Martin


Am 27.12.2017 um 16:11 schrieb lanbo Wang:

Thanks for replying me. But I still have two questions.
Firstly, when I try xhemi on pre-possessed longitudinal data, it 
showed error like this:

Performing left-right swap of labels
TR=2300.00, TE=2.98, TI=900.00, flip angle=9.00
i_ras = (-1, 3.72529e-08, 3.35276e-08)
j_ras = (-2.6077e-08, -3.72529e-09, -1)
k_ras = (-1.78814e-07, 1, 6.98492e-10)
writing to 
/HD4/symptom_test//subj_02_1.long.s02_base/xhemi/mri/aparc+aseg.mgz...

Wed Dec 20 17:46:35 EST 2017
recon-all -sb subj_02_1.long.s02_base/xhemi -talairach

ERROR: Are you trying to run or re-run a longitudinal time point?
   If so, please specify the following parameters:

   \' -long   \'

   where  is the time point id (SAME as cross sectional
   ID) and  is the ID created in the -base run.
   The directory .long. will be created
   automatically or used for output, if it already exists.

Secondly, how I can get the change rate after construct left -right 
registration.


Thanks,
Lanbo

On Fri, Dec 22, 2017 at 5:40 AM, Martin Reuter 
> wrote:


Hi Lanbo,

you could look at longitudinal changes of the left-right
difference in volume per ROI. Or do you mean on the cortical
thickness map (I have never done that, but probably works
similarly, construct left -right registration, compute difference,
then run the LME on that).

Best, Martin


Am 17.12.2017 um 17:54 schrieb lanbo Wang:

Hi, all experts.
I want to compare changes rate between left and right hemisphere
of longitudinal data, How should I do that, how to combine xhemi
with two stage or LME?

Best,
Lanbo


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[Freesurfer] FreeSurfer LocalGI error

[Manoj Kumar]

Hello Dear FreeSurfer Experts,


I am trying to run "recon-all -s subject  -localGI" command on my Mac bash
terminal. I am getting following error.


I am using using Freesurfer V 6.0 and running on MacOS High Sierra (version
10.13)


I also run the istallation update :"sudo -E fs_update" as per suggestion on
the release note but still getting same error.


Any help to resolve this issue would be greatly appreciated.

Thank you so much for all your help and support.


Best regards

Manoj


***

Manojs-iMac:cases manojkumar$ export
SUBJECTS_DIR=/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf

Manojs-iMac:cases manojkumar$ cd $SUBJECTS_DIR

Manojs-iMac:surf manojkumar$ mris_compute_lgi --i lh.pial

=

rm -Rf
/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial

=

=

mkdir -p
/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial

=

=

mris_fill -c -r 1 lh.pial
/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz

=

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

  Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

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


dyld: Symbol not found: ___emutls_get_address

  Referenced from:
/Applications/freesurfer/bin/../lib/gcc/lib/libgomp.1.dylib

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


Abort

ERROR: mris_fill -c -r 1 lh.pial
/Users/manojkumar/fs_dmd_process/cases/HRUDAY/bert/surf/tmp-mris_compute_lgi-lh.pial/lh.pial.filled.mgz
failed!

Manojs-iMac:surf manojkumar$
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