[Freesurfer] error mri_glmfit-sim with pvr

2015-03-21 Thread Dídac Vidal
Dear Freesurfer users,

I am trying to run mri_glmfit in simulation mode as the computed FWHM is
over 30

I run --> mri_glmfit-sim --glmdir GLMDIR
\--sim mc-z 1 1.3 mc-z.abs.13
\--sim-sign abs

However I get an dimension mismatch error

-->ERROR: dimension mismatch between X and contrast [...]X has
6 cols, C has 7 cols

Significantly the model included one per-vertex regressor (which is the
main reason why *mtx files have 7 cols)


Does anybody know how to solve this problem?
Should I create an extra column in the matrix?

Thank you very much in advance

-- 
Dídac Vidal Piñeiro
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Re: [Freesurfer] error mri_glmfit-sim with pvr

2015-03-23 Thread Dídac Vidal
Yes,

the mri_glmfit run correctly (also for a similar analysis where the
computed FWHM was under 30 mri_glmfit-sim run without problems)

the mri_glmfit command was:
*mri_glmfit --glmdir $path/resultsDIR --y
$path/lh.all_long.wm_orig_0.2.mgh-rate.fwhm15.fsaverage.mgh --fsgd
$path/gender_csf_stroop4th_rate.fsgd --C $path/Stroop_simple.mtx --C
$path/CTh_simple.mtx --surf fsaverage lh --pvr
$path/lh.all_long.thickness.mgh-rate.fwhm15.fsaverage.mgh*

I used the simulation because when I used cached data, I got this following
error:

*mri_glmfit-sim --glmdir $path/resultsDIR --cache 2.3 abs --2spaces*



*(...)fwhm = 35.068253ERROR: cannot find
$path/freesurfer/freesurfer.5.3.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/abs/th23/mc-z.csd*


I thought that the main the reason why it failed was that computed fwhm was
more than the maxium cached in freesurfer.

Thank you very much again.

2015-03-23 17:36 GMT+01:00 Douglas N Greve :

>
> did this run correctly with just mri_glmfit? What was your mri_glmfit
> command line? Why are you running a simulation instead of using cached
> data?
>
> doug
>
> On 03/21/2015 10:52 AM, Dídac Vidal wrote:
> > Dear Freesurfer users,
> >
> > I am trying to run mri_glmfit in simulation mode as the computed FWHM
> > is over 30
> >
> > I run --> mri_glmfit-sim --glmdir GLMDIR
> > \--sim mc-z 1 1.3 mc-z.abs.13
> > \--sim-sign abs
> >
> > However I get an dimension mismatch error
> >
> > -->ERROR: dimension mismatch between X and contrast [...]X
> > has 6 cols, C has 7 cols
> >
> > Significantly the model included one per-vertex regressor (which is
> > the main reason why *mtx files have 7 cols)
> >
> >
> > Does anybody know how to solve this problem?
> > Should I create an extra column in the matrix?
> >
> > Thank you very much in advance
> >
> > --
> > Dídac Vidal Piñeiro
> >
> >
> > ___
> > 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: 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/
>
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>
>
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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
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
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Re: [Freesurfer] error mri_glmfit-sim with pvr

2015-03-23 Thread Dídac Vidal
No;  it is not thickness; it is GM/WM intensity values;

thank you for the suggestion with mri_mcsim.

2015-03-23 18:22 GMT+01:00 Douglas N Greve :

>
> Yes, 35 is more than I've precomputed. But another question is whey it
> is 35 when it looks like you've smoothed it by only 15. What is the
> nature of this data? Is it thickness?
>
> If this is something you really need/want to do, I'm recommending that
> people start using mri_mcsim instead of running the simulation from
> mri_glmfit-sim
> http://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
>
>
> On 03/23/2015 01:14 PM, Dídac Vidal wrote:
> > Yes,
> >
> > the mri_glmfit run correctly (also for a similar analysis where the
> > computed FWHM was under 30 mri_glmfit-sim run without problems)
> >
> > the mri_glmfit command was:
> > /mri_glmfit --glmdir $path/resultsDIR --y
> > $path/lh.all_long.wm_orig_0.2.mgh-rate.fwhm15.fsaverage.mgh --fsgd
> > $path/gender_csf_stroop4th_rate.fsgd --C $path/Stroop_simple.mtx --C
> > $path/CTh_simple.mtx --surf fsaverage lh --pvr
> > $path/lh.all_long.thickness.mgh-rate.fwhm15.fsaverage.mgh/
> >
> > I used the simulation because when I used cached data, I got this
> > following error:
> > /mri_glmfit-sim --glmdir $path/resultsDIR --cache 2.3 abs --2s
> > paces/
> >
> > /(...)
> > fwhm = 35.068253
> > ERROR: cannot find
> >
> $path/freesurfer/freesurfer.5.3.0/average/mult-comp-cor/fsaverage/lh/cortex/fwhm35/abs/th23/mc-z.csd/
> >
> >
> > I thought that the main the reason why it failed was that computed
> > fwhm was more than the maxium cached in freesurfer.
> >
> > Thank you very much again.
> >
> > 2015-03-23 17:36 GMT+01:00 Douglas N Greve  > <mailto:gr...@nmr.mgh.harvard.edu>>:
> >
> >
> > did this run correctly with just mri_glmfit? What was your mri_glmfit
> > command line? Why are you running a simulation instead of using
> > cached data?
> >
> > doug
> >
> > On 03/21/2015 10:52 AM, Dídac Vidal wrote:
> > > Dear Freesurfer users,
> > >
> > > I am trying to run mri_glmfit in simulation mode as the computed
> > FWHM
> > > is over 30
> > >
> > > I run --> mri_glmfit-sim --glmdir GLMDIR
> > > \--sim mc-z 1 1.3 mc-z.abs.13
> > > \--sim-sign abs
> > >
> > > However I get an dimension mismatch error
> > >
> > > -->ERROR: dimension mismatch between X and contrast
> > [...]X
> > > has 6 cols, C has 7 cols
> > >
> > > Significantly the model included one per-vertex regressor (which is
> > > the main reason why *mtx files have 7 cols)
> > >
> > >
> > > Does anybody know how to solve this problem?
> > > Should I create an extra column in the matrix?
> > >
> > > Thank you very much in advance
> > >
> > > --
> > > Dídac Vidal Piñeiro
> > >
> > >
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu>
> > Phone Number: 617-724-2358 
> > Fax: 617-726-7422 
> >
> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> > <http://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  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, pleas

[Freesurfer] Optimal registration

2013-12-17 Thread Dídac Vidal
Hi,

I'd like to ask whether there exist any (implemented/objective) measure to
identify a correct surface reconstruction beyond the visual inspection in
order to identify gross defect or wm/gm boundary.


Thanks in advance.


-- 
Dídac Vidal Piñeiro

Dept. Psychiatry and Clinical Psychobiology
Faculty of Medicine
University of barcelona
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[Freesurfer] Plot Histograms

2014-05-01 Thread Dídac Vidal
Hi!

I would like to plot an histogram with values from sig.mgh across all
cortical mantle
(as represented in qdec or in tksurfer-overlay options).
Which function would allow me to obtain/create histograms from *mgh files?

I also would like to obtain a similar histogram, but restricted to a
cortical label.
How I could do that?



Thanks in advance



-- 
Dídac Vidal Piñeiro

Dept. Psychiatry and Clinical Psychobiology
Faculty of Medicine
University of barcelona
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[Freesurfer] mri_glmfit dev

2015-10-07 Thread Dídac Vidal
Hi Freesurfers!

I am using development version of mri_glmfit (as I want to take advantadge
of --frame-mask option).

As control analysis I performed an identical (simple) analysis both in
mri_glmfit and its dev version.
Suprisingly, while F.nii.gz were identical for the given contrast
sig.nii.gz map differed betweem both versions.
If possible (and If I am not doing anything wrong), I'd like to know the
reason why they differ and also which one I should stick with.

Thank you in advance




-- 
Dídac Vidal Piñeiro
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Re: [Freesurfer] mri_glmfit dev

2015-10-07 Thread Dídac Vidal
s/psyklab/freesurfer/current/subjects/fsaverage/surf/lh.whiteNumber
of vertices 163842Number of faces327680Total area
65416.984375AvgVtxArea   0.399269AvgVtxDist
0.721953StdVtxDist   0.195470$Id: mri_glmfit.c,v 1.241 2015/08/12
21:03:09 greve Exp $cwd
/net/tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-fam
<http://tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-fam>cmdline
/net/tsd-evs.tsd.usit.no/p23/data/colossus/psyklab/freesurfer/dev/mri_glmfit
<http://tsd-evs.tsd.usit.no/p23/data/colossus/psyklab/freesurfer/dev/mri_glmfit>
--y cespct.nii.gz --fsgd
/tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex.fsgd
--C
/tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex_con/Int.mtx
--C
/tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex_con/Age.mtx
--surface fsaverage lh --glmdir glm_dev --mask
/tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/mask.nii.gz
--nii.gz sysname  Linuxhostname compute-2-32.localmachine  x86_64user
p23-didacvpFixVertexAreaFlag = 1UseMaskWithSmoothing
1OneSampleGroupMean 0y
/net/tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-fam/cespct.nii.gz
<http://tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-fam/cespct.nii.gz>logyflag
0usedti  0FSGD
/tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex.fsgdmask
/tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/mask.nii.gzmaskinv
0glmdir glm_devIllCondOK 0ReScaleX 1DoFFx 0Creating output directory
glm_devLoading y from
/net/tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-fam/cespct.nii.gz
<http://tsd-evs.tsd.usit.no/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/All_GLM/all_subjects/STUDY.sm8.lh/recoll-v-fam/cespct.nii.gz>
... done reading.INFO: gd2mtx_method is dodsSaving design matrix to
glm_dev/Xg.datComputing normalized matrixNormalized matrix condition is
1.19608Matrix condition is 1684.09Pruning voxels by thr: 1.175494e-38Found
147820 voxels in maskSaving mask to glm_dev/mask.nii.gzReshaping
mriglm->mask...search space = 73502.831427DOF = 137Starting fit and testFit
completed in 0.194133 minutesComputing spatial AR1 on surfaceResidual:
ar1mn=0.995427, ar1std=0.005476, gstd=5.977751, fwhm=14.076528Writing
results  Intmaxvox sig=13.6436  F=70.0366  at  index 137153 0 0
seed=1445192785  Agemaxvox sig=3.60222  F=12.1485  at  index 66347 0
0seed=1445192785mri_glmfit donegdfReadHeader: reading
/tsd/p23/data/colossus/projects/MemConstruct_fMRI/fmri_task/MC_Aging_didac/lists/fsgd/AgeN_sex.fsgdINFO:
DeMeanFlag keyword not found, DeMeaning will NOT be done.Continuous
Variable Means (all subjects)0 Age -0.172747 20.02381 Sex 5.96046e-09
0.489898Class Means of each Continuous Variable1 Main  -0.1727   0.
INFO: gd2mtx_method is dodsReading source surface
/tsd/p23/data/colossus/psyklab/freesurfer/current/subjects/fsaverage/surf/rh.whiteNumber
of vertices 163842Number of faces327680Total area
65020.765625AvgVtxArea   0.396850AvgVtxDist
0.717994StdVtxDist   0.193566*




2015-10-07 20:59 GMT+02:00 Douglas Greve :

> when you say "both versions" what do you mean? Just two different calls to
> the dev version of mri_glmfit? Or one call to the 5.3 and one call to the
> dev? What are your command lines? What is the terminal output?
>
>
> On 10/7/15 10:54 AM, Dídac Vidal wrote:
>
> Hi Freesurfers!
>
> I am using development version of mri_glmfit (as I want to take advantadge
> of --frame-mask option).
>
> As control analysis I performed an identical (simple) analysis both in
> mri_glmfit and its dev version.
> Suprisingly, while F.nii.gz were identical for the given contrast
> sig.nii.gz map differed betweem both versions.
> If possible (and If I am not doing anything wrong), I'd like to know the
> reason why they differ and also which one I should stick with.
>
> Thank you in advance
>
>
>
>
> --
> Dídac Vidal Piñeiro
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/fre

[Freesurfer] Postdoctoral position, University of Oslo (UiO)

2018-10-30 Thread Dídac Vidal
External Email - Use Caution

I am delighted to advertise the following postdoctoral position on behalf
of Prof Anders M Fjell:



At the Center for Lifespan Changes in Brain and Cognition, University of
Oslo, Norway, we have an available postdoc position for an excellent
candidate, on the "The Missing Link of Episodic Memory Decline in Aging".
The aim is to systematically test how within-person variability in several
different variables affect encoding, consolidation, and retrieval of
memories using experimental data, functional and structural neuroimaging.

The position is for a period of 3 years. The application deadline is:
10.12.2018  Please see more info here:
https://www.jobbnorge.no/en/available-jobs/job/159506/postdoctoral-fellowship-the-missing-link-of-episodic-memory-decline-in-aging-2nd-announcement






P.S. Interested candidates are welcome to contact Anders M Fjell
a.m.fj...@psykologi.uio.no if they have questions.

All the best, Dídac


-- 
Dídac Vidal Piñeiro
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[Freesurfer] Job positions available. Science Programmer and Head Engineer in neuroimaging lab (LCBC, University of Oslo, Norway).

2018-12-19 Thread Dídac Vidal
External Email - Use Caution

I am delighted to advertise the following positions on behalf of Prof
Anders M Fjell:



At the Center for Lifespan Changes in Brain and Cognition, University of
Oslo, Norway, we have available two new positions for excellent candidates.
The main aim of LCBC research is to explain, predict and promote cognitive
function from birth to old age, in health and disease.



1) We offer a full-time permanent Scientific Programmer position (
https://www.jobbnorge.no/en/available-jobs/job/161563/scientific-programmer).
 The candidate needs to have a master’s degree or similar in a relevant
field, such as informatics, bioinformatics, computer science, etc. The
candidate will have the opportunity to work collaboratively in an active
group and analyze cognitive measures, imaging of brain activity and
structure (MRI), genetics, molecular biology, and registry information
across large data sets.



2) We offer a position in neuroinformatics/ brain imaging position on the
Lifebrain project as Head engineer/lab engineer (
https://www.jobbnorge.no/en/available-jobs/job/160891/position-in-neuroinformatics-brain-imaging-on-the-lifebrain-project).
The position is suited for a person with strong programming competence and
interest in signal and image processing and requires a master’s degree in a
relevant field. Imaging of the human brain by MRI and PET is central to
LCBC research and included in all projects. Main tasks include data
preprocessing and higher-level analyses; development and maintenance of the
neuroimaging database and the processing pipeline; implementation and
testing of new processing procedures. The appointment is for 1 year while
the possibility of extension is pending on further external funding.



The application deadlines are 04.01.2018.



P.S. Interested candidates are welcome to contact Anders M Fjell
a.m.fj...@psykologi.uio.no if they have questions.

All the best,

Dídac


-- 
Dídac Vidal Piñeiro
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[Freesurfer] Extraction Longitudinal Stats

2012-04-11 Thread Dídac Vidal
Hi everybody,
I have a question about FS longitudinal post-processing. Currently I
obtained some corrected results comparing a Control vs. an Experimental
group (pre-post).
What i would like to know is if there's a thinning in the control group or
a increase in the thickness of the experimental group.
I tought in create a label and extract the individual values of both
timepoints and then do a t test in order to see if the mean differs to 0.
How I can do that?; There is an easier way to do it?
Thanks in advance

-- 
Dídac Vidal Piñeiro

Dept. Psychiatry and Clinical Psychobiology
Faculty of Medicine
University of barcelona
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[Freesurfer] Postdoctoral Position, University of Oslo

2019-07-10 Thread Dídac Vidal
External Email - Use Caution

I am delighted to advertise the following postdoctoral research fellowship
on behalf of Prof Anders M Fjell:

At the Center for Lifespan Changes in Brain and Cognition, University of
Oslo, Norway, we have an available postdoc position for an excellent
candidate with strong skills in functional neuroimaging and linked to the
project “The Missing Link of Episodic Memory Decline in Aging: The Role of
Inefficient Systems Consolidation”. The position is for a period of 3 years.

The researcher will be able to work on uni- and multivariate analyses of
high-quality task-related fMRI data acquired at our Siemens Prisma 3T MRI
scanner using state-of-the-art sequences (multi-band/multi-echo EPI).
Topics currently under investigation in our lab cover cognitive functions
during episodic memory operations, as well as mechanisms subserving spatial
navigation and spatial working memory.

The application deadline is: 18.08.2019 Please see more info here:
https://www.jobbnorge.no/en/available-jobs/job/172827/postdoctoral-research-fellowship-in-functional-neuroimaging

P.S. Interested candidates are welcome to contact Anders M Fjell
a.m.fj...@psykologi.uio.no
All the best,
Dídac


-- 
Dídac Vidal Piñeiro
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[Freesurfer] PhD position

2019-11-19 Thread Dídac Vidal
External Email - Use Caution

At the Center for Lifespan Changes in Brain and Cognition, University of
Oslo, Norway, we have an available PhD fellowship for a candidate highly
interested in (functional) neuroimaging analysis and cognitive neuroscience
research. The PhD researcher will focus on investigating the functional
mechanisms supporting lifespan changes in cognition. Cognitive functions of
interest are episodic memory operations, spatial navigation, and spatial
working memory. The Ph.D. fellow will work on large, longitudinal
multimodal data, including task fMRI and state-of-the-art sequences.



The fellowship is for a period of three or four years.

The application deadline is: 10.12.2019

Please see more info here:
https://www.jobbnorge.no/en/available-jobs/job/178345/phd-fellowship-in-functional-neuroimaging




P.S. Interested candidates are welcome to contact Didac Vidal-Pineiro (
d.v.pine...@psykologi.uio.no) or Anders M Fjell (ander...@psykologi.uio.no)



 All the best,

Dídac


-- 
Dídac Vidal Piñeiro
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[Freesurfer] PhD position

2021-12-10 Thread Dídac Vidal
External Email - Use Caution

At the Center for Lifespan Changes in Brain and Cognition, University of
Oslo, Norway, we have an available PhD fellowship for a candidate highly
interested in applying longitudinal, multimodal models on neuroimaging data
and its relation to genetics and cognition to understand the brain
foundations for episodic memory preservation and loss in older age



The application deadline is: 16.01.2022

Please see more info here:
https://secure-web.cisco.com/1wnEXnVTSaJxvqRbBY18QbYibaL9-BHWSM5gMKGsdW_VLEHg65ZqBeTrBVwgeRihCpg9nN6Ipl_a197YvYueq93SHqmDBYqSroGEJil7tQeRA8reCaKPH9TXhdPA9RvoJhoJkbORW-JZlVfRRQ2TM43dhDW1uOYODATehyYLKb1j3TDOcyI0OhxHYqAXMj4i7RlVvR5yQpQWnoaf5NrGesyPe3iLVT-A_6RkRDeS-JUEPtEo6zJEIcUARRJeQzOumVPuWeLr36dnB6dNDopHU-pKbg88ElEnZXMqXqOaGxffQzo9Bq0i-ykvkZ8zkTOuM0DLv61vn2toDZ-lxDuVaJw/https%3A%2F%2Fwww.jobbnorge.no%2Fen%2Favailable-jobs%2Fjob%2F216380%2Fphd-fellowship-in-neuroimaging




P.S. Interested candidates are welcome to contact Didac Vidal-Pineiro (
d.v.pine...@psykologi.uio.no)



All the best,

Dídac

-- 
Dídac Vidal Piñeiro
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