[Freesurfer] postdoc position

[Bruce Fischl]

FYI
---

The Neuroradiology Section at the University of California, San Francisco
(UCSF) is seeking an exceptional postdoctoral candidate in multimodal
imaging of neuropsychiatric and neurodegenerative disorders. 

Combining neuroimaging, genetics, and computational methods, our group is
interested in elucidating mechanisms underlying neuropsychiatric and
neurodegenerative conditions ranging from obsessive compulsive disorder to
dementia. Our emphasis is on using multimodal imaging (including structural
and functional MRI, MR spectroscopy, EEG/MEG) and imaging genetics to
develop genetic and imaging biomarkers that can be leveraged to both
diagnose neuropsychiatric disease and to provide a rational framework for
targeting and monitoring therapy - including emerging neuro-modulatory
technologies - in individual patients.

We seek a postdoctoral candidate with advanced training in neurosciences or
biomedical engineering, a strong background in human imaging, and a desire
to pursue translational research using a multi-disciplinary approach. The
ideal candidate should have considerable experience with data analysis,
simulation, and visualization using  packages such as Matlab, R, or Python,
as well as facility with MRI image analysis tools such as Freesurfer, FSL,
and SPM. Applicants should have a Ph.D. or M.D. degree with less than five
years of postdoctoral experience. Highly motivated individuals with a record
of productive research are encouraged to apply. The position is
available starting August 1, 2016.

UC San Francisco seeks candidates whose experience, teaching, research, or
community service has prepared them to contribute to our commitment to
diversity and excellence. The University of California is an Equal
Opportunity/Affirmative Action Employer. All qualified applicants will
receive consideration for employment without regard to race, color,
religion, sex, sexual orientation, gender identity, national origin,
disability, age or protected veteran status.

Salary is commensurate with qualifications and experience. Interested
applicants should send curriculum vitae/NIH biosketch, Cover Letter, and
three references to: Dr. Leo Sugrue (leo.sug...@ucsf.edu) and Dr. Rahul
Desikan (rahuldesi...@gmail.com).


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Re: [Freesurfer] Coordinates in TRACULA group analysis

[Anastasia Yendiki]

Hi Anri - Instead of hard-coding some ROIs in the white matter that the 
tract is forced to go through, TRACULA uses information like "what is the 
probability that this tract goes lateral/anterior/etc to XXX", where XXX 
any of the labels in the aparc+aseg. TRACULA computes these prior 
probabilities from a set of training subjects, where the tracts have been 
labeled manually. So it knows how likely a tract is to go through a 
certain aparc+aseg label, or to he left, right, anterior, etc of a certain 
aparc+aseg label. This is computed separately at each position along the 
tract. It's computed from the training subjects, and then used when 
reconstructing the tract in the new subject that you run TRACULA on.


Hope this helps,
a.y

On Sun, 31 Jul 2016, Anri WATANABE wrote:


Thanks, AnastasiaI know that TRACULA use probabilistic tractography but if ROIs 
are not
set how determine the origin and the end of a certain tract? I think that the 
first we
have to determine the origin and the end of the tract, the second it constructs 
possible
pathway not with the deterministic way (only 1 direction / 1 voxel) but with the
probabilistic way (considering which direction should be next to). Is this 
comprehension
wrong?
Thank you.

Anri


**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里
**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine
**

2016-07-31 13:22 GMT+09:00 Anastasia Yendiki :

  Hi Anri - TRACULA does not use deterministic ROIs. It uses a probabilistic
  model of how likely each tract is to go through or next to each of the 
labels
  of the freesurfer subcortical segmentation and cortical parcellation, as a
  function of position along the trajectory of the tract.

  Best,
  a.y

  On Sun, 31 Jul 2016, Anri WATANABE wrote:

Hi Anastasia,
Thank you! It seems work well!!
I have another question. Are ROIs for automatic tractography in
TRACULA the same ROIs
presented in Wakana et al. 2007?

Anri




**
京都府立医科大学附属病院
精神科・心療内科
渡辺 杏里

**
Anri WATANABE, M.D.
Department of Psychiatry,
University Hospital, Kyoto Prefectural University of Medicine

**

2016-07-27 13:17 GMT+09:00 Anastasia Yendiki
:

      Hi Anri - The problem is in this line:

                   set cmd = ($cmd --ref $cvstempdir/$cvstemp)

      It should be changed to this:

                   set cmd = ($cmd --ref
$cvstempdir/$cvstemp/mri/norm.mgz)

      For this to take effect, you need to run "which trac-all"
and make the change in
      the trac-all file that the which commands shows you.

      Hope this helps,

      a.y

      On Fri, 15 Jul 2016, Anri WATANABE wrote:

            Hi, AnastasiaThis is trac-all.local-copy from 1
subject. Thank you!

            Anri

           

**
            京都府立医科大学附属病院
            精神科・心療内科
            渡辺 杏里
           

**
            Anri WATANABE, M.D.
            Department of Psychiatry,
            University Hospital, Kyoto Prefectural University of
Medicine
           

**

            2016-07-13 6:16 GMT+09:00 Anastasia Yendiki
            :

                  Hi Anri - This may be a bug that was fixed at
some point. Can
                  you send me the scripts/trac-all.local-copy from
one of your
                  subjects? Thanks!

                  a.y

                  On Mon, 11 Jul 2016, Anri WATANABE wrote:

                        Hi Anastasia,There is an error in .log
files of left
                        corticospinal tract in cvs template and I
attached
                        one
                        of file. In addition