[Freesurfer] Research engineer – Neuroimaging in Alzheimer’s disease and dementia (ICM, Paris, France)
Research engineer – Neuroimaging in Alzheimer’s disease and dementia (ICM, Paris, France) Recruitment date: as soon as possible Type of contract: Limited duration (18 months) Gross salary: 33.000 Euros / year Status / category: Engineer Context: The Brain & Spine Institute (ICM) is a research centre of international dimensions located within the Pitié-Salpêtrière hospital in Paris. Its mission is to develop new strategies to improve the management of neurological diseases. The ICM is localized in the largest European hospital, in a top-level French university (University Pierre and Marie Curie). Its research activity takes place in a unique environment associating core technological facilities, space for industrial partners and a centre for clinical investigations. This position is offered within the IHU A-ICM project, a Foundation of Scientific Cooperation that federates the scientific and medical expertise of four partners from the public sector (Public Hospitals of Paris (AP-HP), National Center for Scientific Research (CNRS), National Institute of Health and Medical Research (INSERM) and Pierre and Marie Curie University-Paris6 (UPMC). Mission and main activities Main mission: Develop brain image analysis projects for the teams of the IHU working on Alzheimer’s disease and related dementias (fronto-temporal dementia, dementia with Lewy bodies, primary progressive aphasias…) Functional links: The recruited engineer will work within the brain image analysis team Cogimage (O. Colliot) of the ICM. He/she will be in close connection with IM2A (Pr B. Dubois), CENIR (Pr S. Lehéricy), the Functional Imaging Laboratory (H. Benali) and the other teams of the IHU working on Alzheimer’s disease and dementia. Activities: Analysis of MRI data (volumetry, morphometry, tractography, resting-state, classifiers) of the projects coordinated by the teams of the IHU working on Alzheimer’s disease and dementia Scientific monitoring and litterature updates on brain image analysis methods applied to dementia Development of new image analysis tools and automatic classifiers for the identification of biomarkers Assistance to the design and set-up of new studies (choice of protocols and imaging markers) Evaluation of the different available methods and choice of the most appropriate ones Management of the interface between researchers in image and signal processing, clinical and neuroscience teams of the IHU and the neuroimaging platform CENIR Profile of the candidate PhD in neuroimaging An experience in development of brain image analysis methods or/and their application to neuroimaging studies in patients Qualities Knowledge of one or several brain image analysis packages (SPM, Freesurfer, BrainVISA or FSL) Knowledge of statistical methods and tools. Knowledge of one or several programming languages (Matlab, Python or C/C++) Mastering oral and written scientific English Autonomy, having initiative, ability to work at the interface between multidisciplinary teams For more information, please contact: Olivier Colliot - olivier.coll...@upmc.fr ___ 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.
Re: [Freesurfer] fs-fast preprocessing resting state
Hi there
I am running a program to generate a patient group specific template from
T1 brains. I need to know which of the Free Surfer outputs will be best for
creating a patient brain template. The T1 images need to be cleaned for
skull, meninges and neck. My guess is brain.finalsurfs.mgz.
thanks!
Javeria.
On Mon, Nov 5, 2012 at 9:44 PM, Douglas Greve wrote:
>
> Hi Chris, it should have been done with preproc-sess. What was your
> preproc-sess command line? At some point, I had it set up so that it
> would go to the bold directory by default unless you used "-fsd rest".
> Newer versions require you to specify the FSD specifically.
>
> doug
>
>
> On 11/5/12 9:38 PM, Chris McNorgan wrote:
> > Hello,
> >
> >I'm getting started with freesurfer. I've played around with some of
> > the tutorial data for fs-fast
> > (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1) and was
> > able to follow along and successfully carry out the preprocessing
> > exercises (which sufficed for my purposes), which also included running
> > register-sess on the "rest" tutorial data for sess01.
> >
> > I've run into a few gotchas with some resting state data, and wanted to
> > know if there are any problems specific to processing resting state data
> > that can be easily avoided?
> >
> > For example, here's the file structure:
> > Project root:
> > /home/chris/resting
> >
> > Anatomical data root ($SUBJECTS_DIR):
> > /home/chris/resting/anat
> >
> > Functional data root ($FUNCTIONALS_DIR):
> > /home/chris/resting/func
> >
> > Subject 1 anatomical directory:
> > $SUBJECTS_DIR/sub00156
> > (already run through recon-all)
> >
> > Subject 1 functional directory:
> > $FUNCTIONALS_DIR/sub00156
> > contains:
> >subjectname ("sub00156")
> > and a nii file in a nested subdirectory:
> > $FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz
> > Where f.nii.gz is some resting state data (hence no paradigm files)
> >
> > For my inaugural attempt, I've run anatomical data for a participant
> > through recon-all, and was having problems registering
> > $FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz to the surface map in
> > $SUBJECTS_DIR/sub00156. After some trial and error and wandering through
> > this mailing list, I found I had to first run mktemplate-sess and then
> > register-sess (the fs-fast tutorial lead me to believe everything was
> > automatically handled by preproc-sess). Are these deviations a
> > foreseeable consequence of working with resting state data? Is there
> > some documentation of important considerations for working with resting
> > state data?
> >
> > Thanks for any help,
> >
> > Chris
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
>
> ___
> 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.
>
>
--
Javeria Ali Hashmi , PhD.
Research Fellow
Athinoula A. Martinos Center for Biomedical Imaging
Department of Psychiatry
Massachusetts General Hospital
Harvard Medical School
120 Second Ave., Suite 103
Charlestown, MA 02129, USA
Email: jhash...@nmr.mgh.harvard.edu
___
Freesurfer mailing list
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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.
Re: [Freesurfer] fs-fast preprocessing resting state
yes, that is probably best
cheers
Bruce
On Tue, 6 Nov 2012, Javeria Ali Hashmi wrote:
Hi there
I am running a program to generate a patient group specific template from T1
brains. I need to know which of the Free Surfer outputs will be best for
creating a patient brain template. The T1 images need to be cleaned for
skull, meninges and neck. My guess is brain.finalsurfs.mgz.
thanks!
Javeria.
On Mon, Nov 5, 2012 at 9:44 PM, Douglas Greve
wrote:
Hi Chris, it should have been done with preproc-sess. What was
your
preproc-sess command line? At some point, I had it set up so
that it
would go to the bold directory by default unless you used "-fsd
rest".
Newer versions require you to specify the FSD specifically.
doug
On 11/5/12 9:38 PM, Chris McNorgan wrote:
> Hello,
>
> I'm getting started with freesurfer. I've played around
with some of
> the tutorial data for fs-fast
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1)
and was
> able to follow along and successfully carry out the
preprocessing
> exercises (which sufficed for my purposes), which also
included running
> register-sess on the "rest" tutorial data for sess01.
>
> I've run into a few gotchas with some resting state data, and
wanted to
> know if there are any problems specific to processing resting
state data
> that can be easily avoided?
>
> For example, here's the file structure:
> Project root:
> /home/chris/resting
>
> Anatomical data root ($SUBJECTS_DIR):
> /home/chris/resting/anat
>
> Functional data root ($FUNCTIONALS_DIR):
> /home/chris/resting/func
>
> Subject 1 anatomical directory:
> $SUBJECTS_DIR/sub00156
> (already run through recon-all)
>
> Subject 1 functional directory:
> $FUNCTIONALS_DIR/sub00156
> contains:
> subjectname ("sub00156")
> and a nii file in a nested subdirectory:
> $FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz
> Where f.nii.gz is some resting state data (hence no paradigm
files)
>
> For my inaugural attempt, I've run anatomical data for a
participant
> through recon-all, and was having problems registering
> $FUNCTIONALS_DIR/sub00156/rest/001/f.nii.gz to the surface map
in
> $SUBJECTS_DIR/sub00156. After some trial and error and
wandering through
> this mailing list, I found I had to first run mktemplate-sess
and then
> register-sess (the fs-fast tutorial lead me to believe
everything was
> automatically handled by preproc-sess). Are these deviations a
> foreseeable consequence of working with resting state data? Is
there
> some documentation of important considerations for working
with resting
> state data?
>
> Thanks for any help,
>
> Chris
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
___
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.
--
Javeria Ali Hashmi , PhD.
Research Fellow
Athinoula A. Martinos Center for Biomedical Imaging
Department of Psychiatry
Massachusetts General Hospital
Harvard Medical School
120 Second Ave., Suite 103
Charlestown, MA 02129, USA
Email: jhash...@nmr.mgh.harvard.edu
___
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.
Re: [Freesurfer] fs-fast preprocessing resting state
Hi Doug, Thanks for your help. To be sure of my preproc-sess line, I just ran preproc-sess on my other participant: preproc-sess -s sub00294 -fsd rest -per-run -surface self lhrh -mni305 -fwhm 0 Here's the error output from where it goes south: Tue Nov 6 16:32:30 CST 2012 mc-sess completed SUCCESSFULLY sub00294 To Surface - rawfunc2surf-sess -fwhm 0 -s sub00294 -d /home/chris/resting/func -fsd rest -self -update instem fmcpr outstem fmcpr.sm0.self.hemi -- 1/1 sub00294 1/1 sub00294 001 lh - Tue Nov 6 16:32:30 CST 2012 ERROR: cannot find /home/chris/resting/func/sub00294/rest/001/register.dof6.dat Try running register-sess with -per-run sub00294 To MNI305 - rawfunc2tal-sess -fwhm 0 -s sub00294 -d /home/chris/resting/func -fsd rest -update -subcort-mask -- 1/1 sub00294 1/1 sub00294 001 Tue Nov 6 16:32:30 CST 2012 ERROR: cannot find /home/chris/resting/func/sub00294/rest/001/register.dof6.dat Try running register-sess with -per-run Started at Tue Nov 6 16:32:25 CST 2012 Ended at Tue Nov 6 16:32:30 CST 2012 preproc-sess done Date: Mon, 05 Nov 2012 21:44:23 -0500 From: Douglas Greve Subject: Re: [Freesurfer] fs-fast preprocessing resting state To:freesurfer@nmr.mgh.harvard.edu Message-ID:<50987987.7010...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Chris, it should have been done with preproc-sess. What was your preproc-sess command line? At some point, I had it set up so that it would go to the bold directory by default unless you used "-fsd rest". Newer versions require you to specify the FSD specifically. doug ___ 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.
Re: [Freesurfer] fs-fast preprocessing resting state
Can you send me the full terminal output? On 11/06/2012 05:39 PM, Chris McNorgan wrote: > Hi Doug, > > Thanks for your help. To be sure of my preproc-sess line, I just ran > preproc-sess on my other participant: > > preproc-sess -s sub00294 -fsd rest -per-run -surface self lhrh -mni305 -fwhm 0 > > Here's the error output from where it goes south: > > > Tue Nov 6 16:32:30 CST 2012 > mc-sess completed SUCCESSFULLY > sub00294 To Surface - > rawfunc2surf-sess -fwhm 0 -s sub00294 -d /home/chris/resting/func -fsd rest > -self -update > instem fmcpr > outstem fmcpr.sm0.self.hemi > -- > 1/1 sub00294 > 1/1 sub00294 001 lh - > Tue Nov 6 16:32:30 CST 2012 > ERROR: cannot find > /home/chris/resting/func/sub00294/rest/001/register.dof6.dat > Try running register-sess with -per-run > sub00294 To MNI305 - > rawfunc2tal-sess -fwhm 0 -s sub00294 -d /home/chris/resting/func -fsd rest > -update -subcort-mask > -- > 1/1 sub00294 > 1/1 sub00294 001 > Tue Nov 6 16:32:30 CST 2012 > ERROR: cannot find > /home/chris/resting/func/sub00294/rest/001/register.dof6.dat > Try running register-sess with -per-run > > Started at Tue Nov 6 16:32:25 CST 2012 > Ended at Tue Nov 6 16:32:30 CST 2012 > preproc-sess done > > > Date: Mon, 05 Nov 2012 21:44:23 -0500 > From: Douglas Greve > Subject: Re: [Freesurfer] fs-fast preprocessing resting state > To:freesurfer@nmr.mgh.harvard.edu > Message-ID:<50987987.7010...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > Hi Chris, it should have been done with preproc-sess. What was your > preproc-sess command line? At some point, I had it set up so that it > would go to the bold directory by default unless you used "-fsd rest". > Newer versions require you to specify the FSD specifically. > > doug > > ___ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
Re: [Freesurfer] qcache error
Do you have write permissions to the output dir? I noticed a perm error in the log. The recon-all.log file has the permission: -rw-rw-r-- 1 guest phd doug On 11/06/2012 03:53 PM, Berg, S.F. van den wrote: > Hi Doug and Bruce > > There is enough disc space. A text file is attached, this file is created > with the "recon-all -s 0050 -qcache |& tee mylog.txt" command. I try the > "recon-all -s 0050 -qcache" command. The command start to run but finished > with errors. > > Have you got any idea of the problem in this case? Also the recon-all.log > file is attached (subject 0050). > > Thanks, > > Stan > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: 05 November 2012 19:37 > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] qcache error > > Do run out of disk space? Also, please send terminal output in a text > file rather than as a snapshot. You can do this with > > recon-all ... |& tee mylog.txt > > doug > > On 11/05/2012 10:21 AM, Berg, S.F. van den wrote: >> Dear Freesurfer experts, >> >> I have got a problem with the qcache function. I have already runned >> 150 subjects with the recon-all command. Before i can work with the >> statistical program qdec i have to smooth the subjects. I want to >> smooth them with the command: recon-all -s -qcache. The >> command start to run but finished with errors. A overview of the >> terminal output is attached to this email in JPEG format. What is the >> problem in this case? >> >> further information about freesurfer version: >> >> recon-all -version: Id: recon-all, v 1.373 2011/03/15 00:43:47 mreuter >> Exp $ >> >> We run FreeSurfer-Linux-centos5_x86_64-dev-201110315 under Debian >> Squeeze. >> >> Thanks a lot, >> >> Stan van den Berg >> >> >> >> ___ >> 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 > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > ___ > 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. > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
