[Freesurfer] Brain anatomy research, tenure track position @ University of Trento, Italy

[Jovicich, Jorge]

   External Email - Use Caution

Great opportunity for human brain anatomy research at the new center for 
Medical Sciences, University of Trento, Italy.


Tenure track academic position ("ricercatore tipo-B)".

Italian fluency needed.

More 
info:https://secure-web.cisco.com/1vzhVWZ9-OWOrVIhfuHnXfJBfI5lmi5S_h7-IuTPOg2dkMqGpHQJtyTmOW-suTsxsR-_Uqcs847ECTV3pwqDFC-HpnI_qVou1uMXSs5VkTRKZFbGxhZ6BD44GASG7n18r8iarwwKzfXfUYD5iTvkcrCt5uss4TlMEzpvF6SI7fnxOVSThLFvXyVhpJcq-NCE6EOAqNvgvInGTfFpDF0RJ4EYTiVzIePPXf5Vktst2FMh4ULVs02NKaTHeE8hTc8cs2Xfpw-a5oQ3tpwhHlI3R8OD4lRWnbdWJ-uOmZVMCNSC_XjU7E8GnQmxX8_k_bhb30tUBXGJMXOeilxpXz2V9pg/https%3A%2F%2Flnkd.in%2FdJZMEeiz

Best,

    Jorge

--
Jorge Jovicich, Ph.D.

Center for Mind/Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email:jorge.jovic...@unitn.it
MRI Methods 
Group:http://secure-web.cisco.com/11uWcxONRxELcw7jCN4wNZjQzxMmcXhCU-lfnRwLE9TtgLh7cjnS_97s7uT8wEp_zp1d8LC-x8OcqUukwZQbwu3Nm5ZohuSbU9HJBS6TabQ2ijbcVFX8Q0n5I8whWsaMzAR9AvjxkzV6Z1zMaiC7IgQiY6qSdiF5-YgLnRdKzB0WuUIhsom-lB8nPxBz6eko76ZvyU63DamwdJCqfdF8k2ntpnw5Gvhk3rHPbF1eHwzzCNd6TwEt0vDBT2bMsgMBVWtMgtffBvvR28M2DHeNDc8rfCK7LYOpqd48LjlTaZMn-2sE68_ApywXu3jQn7TOQVGEtflZo_I5iFXzeFNpc4g/http%3A%2F%2Fr.unitn.it%2Fen%2Fcimec%2Fmri
CIMEC:http://secure-web.cisco.com/1lgKoHi8Hch5pXnEZ8OgMecbLjDE_PhoBBDbeUFFtyRvZIv0FfNo1yMmfdrmBhmj8GTkufBFWPl17eVmCHa5lRtZUdhpkwHj2lDBR2qNTlrLq92itD6drF3CZ_voUb24PQqCPQ-73xmNIA2f4u49sy8I0-OE69buVgP92nTg6sMEL95X5DTOK_y2kOV-oVmlTgUx7SSu69v1zNtBzrAMmQbCK5FDPBBnIFAE8PJabzhgHwtOZ2Qwt8sjTgPbQMNlUoBNkKRkb8G9aFD6xvlTPHa-1xVk0HR4ckR9a1mPRbHWvIF53DTlWPOp_qRD1kf0-Jtc4VjGBeVkVySQPVTa12A/http%3A%2F%2Fwww.cimec.unitn.it%2F
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[Freesurfer] Postdoc position - Functional connectomics in glioma - CIMeC - University of Trento

[Jovicich, Jorge]

   External Email - Use Caution


Apologies for the multiple posting

A postdoctoral position in *functional brain connectomics in glioma* 
will be available towards the end of 2021 to work with Dr. Silvio 
Sarubbo (Neurosurgery Unit, "S. Chiara" Hospital, Trento, Italy) and 
Prof. Jorge Jovicich  (Center for Mind/Brain Sciences, University of 
Trento, Italy).


For more information: 
https://secure-web.cisco.com/1xoZqsnhBBxXbYFohlAErnlMyWXQJ_4A3AOb4aNgirjKRCwPsqrM0mYLWvj1jcT0NITMy6ONq2L9Nly_zcZLKo8Fh1ad51diDQx1dR4a1JcLyApmM3JyLMEypZz7ZhCs989YKnPTpbS_X-HMjfVqm6KR3ytXQ1kyX8YqUUlvKt273GtmIKhzSqRgu9rAAd0cV8yRk0oBR2Ouwm6VyaY0RrT8XS1NSiyfi6-9Q_MMdjAGkA8EbesGJ2M0l8EvyCzkAfDSKRXaLHa2mWNx7ChubmQ/https%3A%2F%2Fr.unitn.it%2Fen%2Fcimec%2Fmri%2Fopportunities.

Thanks,

    Jorge

--
Jorge Jovicich, Ph.D.

Center for Mind/Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: 
http://secure-web.cisco.com/1oo6NimY-2hpj-cpDfN0FxxBTMfombqbvNDmT6tUAfmtd5tu3siC8WQfBpUnc8cmJr29A7De8YyTPkVe_wn77imJ7XU6DYL1jUv_ZRp4tCw8TBk9tI3Yqt6Ah-Udig0t7G0gY1fYKKohlmdItS0hMQA4Fo11goinf3riXopdbJUjChHCXONd1EQf00zYABKxI9sTEweQMndCefE2nUwaPI0DajOHT7FdZriFpm27Ep03wY__r6xaYeaiSx2ffmKkTOPG0zvpfv4viz2DAs5OGzQ/http%3A%2F%2Fr.unitn.it%2Fen%2Fcimec%2Fmri
CIMEC: 
http://secure-web.cisco.com/17e8diJzu-3lHswjNzmQwRotmhQxVMDrJ4i5jl7UqtGE_H5a0Fo4TjZWT7MRhqZimAgdvxWalMTeLXL6B4SuQZkJ3HFJFhAp6si_39oMIv8XDJ5ic7ilIMpajlG6_Jsfxib8kBNKVNHiJ2kbwKsQJ6vCcZJymFBodGf7V5sI6oFv5B6erEcf8Pv4zBKRTS38exfk0jiBjDlJy5mVWG429413qR-PnMjUZi80KiP3V9ey_7IGXn6jbjiEaaz9bJ3_RCHm8LuOBvk1BrrI1weKNTg/http%3A%2F%2Fwww.cimec.unitn.it%2F

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[Freesurfer] Brain connectivity postdoctoral position @ CIMeC University of Trento, Italy

[Jovicich, Jorge]

External Email - Use Caution

POSTDOCTORAL RESEARCH FELLOW (call open till December 6, 2019)

- Development, testing and validation of MRI microstructural and 
functional connectivity methods to advance human neuroscience.
- Center for Mind/Brain Sciences (CIMeC), University of Trento, Italy.
- More details in the link below. Feel free to contact me for further 
information.

Call Outline: https://r.unitn.it/en/cimec/mri/opportunities
Application: http://bit.ly/CIMEC-MRI-Postdoc-Call-2019a

Best,

     Jorge

-- 
Jorge Jovicich, Ph.D.

Center for Mind/Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: http://r.unitn.it/en/cimec/mri
CIMEC: http://www.cimec.unitn.it/


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[Freesurfer] Postdotoral call, human brain microstructure with MRI, Italy

[Jovicich, Jorge]

External Email - Use Caution

A 2-year postdoctoral call is available at the MRI Group of the Center 
for Mind/Brain Sciences  (CIMeC) at the University of Trento, Italy. The 
focus of this position will involve the development, testing and 
validation of MRI techniques that allow quantification of function and 
tissue microstructure properties.

The successful candidate will be part of an international 
multidisciplinary team developing and applying MRI techniques to study 
brain structure and function supporting normal higher cognitive function 
as well as the study of cognitive dysfunction in various neurological 
and neuropsychiatric conditions (including pre-surgical planning, 
plasticity in deaf and blind, novel markers sensitive
to the progression of neurodegenerative diseases).

Facilities: The CIMeC MRI neuroimaging lab uses a Siemens Prisma 3T 
scanner designed for research and clinical studies. The position will 
allow for training opportunities in pulse sequence development, brain 
anatomy, and translational clinical research.
The fellow is expected to be able to work independently as well as part 
of a multidisciplinary team with supervisory responsibilities of 
graduate student research. The fellow will support research MRI users, 
will have opportunities to develop new ideas and advance their own 
research interests in an international academic environment. Beyond 
work, there are outstanding opportunities for enjoying outdoors activities.

Requirements: Minimum qualifications are a doctoral degree in cognitive 
neurosciences, physics, engineering, computer sciences or related area, 
strong scientific publication record, and demonstrated expertise in MRI 
methods development and applications. The ideal candidates should be 
proficient in programming, such as C++, Matlab. Experience in pulse 
sequence design, particularly on Siemens platform, and/or image 
reconstruction will be a plus. Additional requirements include high 
self-motivation, ability of solving research problems independently, and 
excellent communication skills.

Contact:  Jorge Jovicich, Ph.D, MSc, Associate Professor 
(jorge.jovic...@unitn.it)
      Attending ISMRM, contact me for an informal meeting if 
interested

Postdoc call: http://bit.ly/CIMEC-MRI-Postdoc-Call-2019

-- 
Jorge Jovicich, Ph.D.

MR Lab Head
Center for Mind/Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: http://r.unitn.it/en/cimec/mri
CIMEC: http://www.cimec.unitn.it/


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[Freesurfer] Italian Summer School: Interdisciplinary Research on Brain Network Dynamics

[Jovicich, Jorge]

External Email - Use Caution

Dear all,

we are organizing an international summer school on interdisciplinary 
research oriented to the study of brain network dynamics (June 24-28, 
2019). More information: https://event.unitn.it/brandyschool2019/

Feel free to disseminate to relevant groups.

Regards,

     Jorge

-- 
Jorge Jovicich, Ph.D.

MR Lab Head
Center for Mind/Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: http://r.unitn.it/en/cimec/mri
CIMEC: http://www.cimec.unitn.it/


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[Freesurfer] Postdoctoral position open to work on brain MRI function & microstructure (Italy)

[Jovicich, Jorge]

External Email - Use Caution

[Apologies for cross-posting]

The MRI Group of the Center for Mind/Brain Sciences, University of 
Trento, Italy  (https://r.unitn.it/en/cimec/mri/) has an open 
postdoctoral position to develop/apply MRI acquisition and analyses 
methods to characterize structural and dynamic functional  connectivity 
(deadline October 30, 2018).

More information about our group, the call and application links can be 
found here:
https://r.unitn.it/en/cimec/mri/opportunities

Feel free to distribute this announcement to potentially interested people.

Best,

     Jorge Jovicich

-- 
Jorge Jovicich, Ph.D.

MR Lab Head
Center for Mind/Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: http://r.unitn.it/en/cimec/mri
CIMEC: http://www.cimec.unitn.it/


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[Freesurfer] Brain microstructure MRI postdoc (Italy)

[Jovicich, Jorge]

Hello,

We will soon advertise a 2-year postdoctoral fellowship at the MRI Group 
 of the Center for Mind/Brain Sciences 
(CIMeC ), University of Trento 
, Italy. The focus of this position will 
involve the development, testing and validation of MRI techniques that 
allow quantification of tissue microstructure properties. The successful 
candidate will be part of an international multidisciplinary team 
developing and applying MRI techniques to study brain structure and 
function supporting normal higher cognitive function as well as the 
study of cognitive dysfunction in various neurological and 
neuropsychiatric conditions (including pre-surgical planning, plasticity 
in deaf and blind, novel markers sensitive to the progression of 
neurodegenerative diseases).

Facilities: The CIMeC MRI neuroimaging lab will house a Siemens Prisma 
3T scanner (tentatively May 2018) designed for research and clinical 
studies. The position will allow for training opportunities in pulse 
sequence development, brain anatomy, and translational clinical 
research. The fellow is expected to be able to work independently as 
well as part of a multidisciplinary team with supervisory 
responsibilities of graduate student research. The fellow will support 
research MRI users, will have opportunities to develop new ideas and 
advance their own research interests in an international academic 
environment.

Requirements: Minimum qualifications are a doctoral degree in cognitive 
neurosciences, physics, engineering, computer sciences or related area, 
strong scientific publication record, and demonstrated expertise in MRI 
methods development and applications. The ideal candidates should be 
proficient in programming, such as C++, Matlab. Experience in pulse 
sequence design, particularly on Siemens platform, and/or image 
reconstruction will be a plus. Additional requirements include high 
self-motivation, ability of solving research problems independently, and 
excellent communication skills.

Contact: Interested candidates please contact Jorge Jovicich, Ph.D, 
MSc., Assistant Professor (jorge.jovic...@unitn.it).

-- 
Jorge Jovicich, Ph.D.

MR Lab Head
Center for Mind/Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: http://r.unitn.it/en/cimec/mri
CIMEC: http://www.cimec.unitn.it/

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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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Re: [Freesurfer] Test-retest reliability in longitudinal data

[Jovicich, Jorge]

Hi Amanda,


if I understand correctly the specific question of the reviewer, a 
potential response could be, almost quoting Reuter et al., 2012:


"The variability of the test-retest segmentations typically arises from 
three main sources: variability in the MRI acquisition (head position, 
head motion, scanner instabilities, etc.), anatomical variations in the 
subject such as hydration state, and variability intrinsic to the 
automated segmentation algorithms. The longitudinal Freesurfer analysis 
stream aims at minimizing this last factor (Reuter et al., 2012). 
Therefore, the test-retest segmentation variability when using the 
longitudinal stream represents the experimental error dominated by MRI 
acquisition and subject state factors."


Best,

     Jorge



On 04/10/2017 14:04, Worker, Amanda wrote:
>
> Hi,
>
>
> Thank you very much for your fast response. I had thought that it 
> would make sense to use the exact same pipeline, as I would be using 
> in a longitudinal study in future. If I could just be a bit more 
> specific about the details, as I have a publication under review at 
> the moment and one of the reviewers isn't happy about this approach. I 
> just wanted to check that we haven't misunderstood how the algorithm 
> works if that is ok?
>
>
> *Reviewer's comment*
>
> “It is unclear to me what is the value of establishing test-retest 
> reliability of applying FreeSurfer subfield segmentation to a 
> within-subject template constructed by the Reuter algorithm. Once this 
> template is constructed and mapped to the different time point images, 
> test-retest measures become meaningless because the segmentations are 
> not independent, but instead, highly dependent on each other.”
>
>
> *Our response*
>
> "our understanding is that the use of a within-subject’s template to 
> initialise the segmentation will minimise potential bias or inaccuracy 
> in segmentation in multi-session data. The segmentations are 
> themselves run independently, but with the template being used to 
> initialise (provide a starting point) for the nonlinear parameter 
> fitting. We don’t believe that this would be expected to, and does not 
> appear to, constrain the segmentation to the degree that it would 
> produce “identical” values, as the reviewer suggested in a previous 
> review. The alternative is to risk a biased segmentation which could 
> potentially give a false impression of poor reliability and increased 
> risk of false positive results. "
>
>
> Any thoughts appreciated.
>
>
> Thanks,
>
>
> Amanda
>
> 
> *From:* Jovicich, Jorge <jorge.jovic...@unitn.it>
> *Sent:* 20 September 2017 15:51:40
> *To:* Worker, Amanda
> *Cc:* Freesurfer support list
> *Subject:* Re: [Freesurfer] Test-retest reliability in longitudinal data
> Hi Amanda,
>
>
> I would recommend you to quantify reliability using the same processing
> pipeline you will use to test for longitudinal effects in your sample.
> Relevant literature include those listed below. For reliability you
> would want to evaluate subjects over a time period in which you do not
> expect the main effects of your study (e.g., disease related or learning
> related morphometric effects), but rather standard physiological and MRI
> system variability. Ideally this group also has the same age/gender
> representation of the group in which you later want to test for
> longitudinal effects.
>
>
> Cheers,
>
>  Jorge
>
>
> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpubmed%2F22430496=01%7C01%7Camanda.worker%40kcl.ac.uk%7Cb536198d4e48444c920908d5003722cd%7C8370cf1416f34c16b83c724071654356%7C0=5Zna%2FnZpaN62IpZVdWf%2FUE7MTSEjA0ygXQCUIIQP%2BuA%3D=0
>
> https://emea01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fpubmed%2F23668971=01%7C01%7Camanda.worker%40kcl.ac.uk%7Cb536198d4e48444c920908d5003722cd%7C8370cf1416f34c16b83c724071654356%7C0=yQaldU8xwFyenqpdPlZ%2FLDVu2aH7zpeWPVxfd5YqccQ%3D=0
>
>
>
> On 20/09/2017 15:00, Worker, Amanda wrote:
> >
> > Hi all,
> >
> >
> > I have a longitudinal dataset that I'd like to calculate test-retest
> > reliability for. However, I am not sure whether to calculate this for
> > the cross-sectionally processed data or longitudinal data? It would
> > seem to make sense to use the cross-sectional data, as the time points
> > are independent, but then it means that the test-retest results would
> > not be applicable in a dataset processed longitudinally. On the other
> > hand, calculating reliability metrics for 

Re: [Freesurfer] Test-retest reliability in longitudinal data

[Jovicich, Jorge]

Hi Amanda,


I would recommend you to quantify reliability using the same processing 
pipeline you will use to test for longitudinal effects in your sample. 
Relevant literature include those listed below. For reliability you 
would want to evaluate subjects over a time period in which you do not 
expect the main effects of your study (e.g., disease related or learning 
related morphometric effects), but rather standard physiological and MRI 
system variability. Ideally this group also has the same age/gender 
representation of the group in which you later want to test for 
longitudinal effects.


Cheers,

     Jorge


https://www.ncbi.nlm.nih.gov/pubmed/22430496

https://www.ncbi.nlm.nih.gov/pubmed/23668971



On 20/09/2017 15:00, Worker, Amanda wrote:
>
> Hi all,
>
>
> I have a longitudinal dataset that I'd like to calculate test-retest 
> reliability for. However, I am not sure whether to calculate this for 
> the cross-sectionally processed data or longitudinal data? It would 
> seem to make sense to use the cross-sectional data, as the time points 
> are independent, but then it means that the test-retest results would 
> not be applicable in a dataset processed longitudinally. On the other 
> hand, calculating reliability metrics for data processed in the exact 
> same way as will be used in further studies seems to make sense also, 
> but would calculating test-retest on the longitudinally processed data 
> bias the results, as the data points are not fully independent?
>
>
> Does anyone have any idea of the best way forward?
>
>
> Thanks,
>
>
> A
>
>
>
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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
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> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.

-- 
Jorge Jovicich, Ph.D.

MR Lab Head
Center for Mind/Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: http://r.unitn.it/en/cimec/mri
CIMEC: http://www.cimec.unitn.it/

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Re: [Freesurfer] Freesurfer longitudinal analysis accuracy

[Jovicich, Jorge]

Hello Gabor,

a few quick comments:

i) Although we typically aim for maximizing both, accuracy and 
reproducibility are different things. In a longitudinal study you are 
often particularly interested in the reproducibility of the findings, in 
the sense of their repeatability across different time points if there 
are no significant biological changes in your sample. T


ii) Ideally you would have included in your experimental design a group 
of controls that you expect to not show longitudinal effects, and used 
them to measure and estimate the test-retest reproducibility error of 
your experimental setup (i.e., acquisition + analyses pipeline). This 
information can then be used to estimate a lower limit of the effect 
size you may be able to measure with your setup.


iii) We have looked at reproducibility errors of the longitudinal 
Freesurfer cortex in healthy elderly volunteers from standard 3T MPRAGE 
and found that it was generally above 2% in the structures we looked at 
(https://www.ncbi.nlm.nih.gov/pubmed/23668971, Table 7). We did not look 
at the cerebellum, but I imagine its reproducibility will not be higher. 
However, if your acquisition protocol and subject population are very 
different then these results might not apply well as reference for you.


Cheers,
jorge

On 13/12/2016 11:41, Gabor Perlaki wrote:
I've found the article "Within-subject template estimation for 
unbiased longitudinal image analysis" by Reuter et al. It only 
examines a limited number of structures for the reproducibility of 
longitudinal Freesurfer. Are there any other paper that examines the 
cerebellum as well? Any suggestion from the authors of Freesurfer 
about accuracy of longitudinal Freesurfer for the cerebellum in 
healthy subjects?


Best,
Gabor

2016-12-06 11:44 GMT+01:00 Gabor Perlaki >:


Dear all,

We've run longitudinal Freesurfer on 30 healthy subjects. We have
two subgroups (n=15) and we found a significant longitudinal
change in the left and right cerebellar cortex in one of our
subgroups. However, this change is very small: mean=0.67% range:
-1.61-2.3% for the right cerebellar cortex; mean=0.86% range:
-1.64-3.7% for the left cerebellar cortex. Although statistics
indicate significant cerebellar cortex increase, we are sceptical
that Freesurfer's accuracy allows reliable detection of such small
differences. Is there any article on how accurate the longitudinal
Freesurfer for cerebellum segmentation or any suggestion on how to
decide whether our results are reliable?

Best,
Gabor




--
Gabor Perlaki
research associate
Diagnostic Center of Pécs
H-7623 Pécs, Rét str. 2.
Tel.: 0036-30-2084367
E-mail: petzinger.ga...@gmail.com 


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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.


--
Jorge Jovicich, Ph.D.

MR Lab Head
Center for Mind Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: http://r.unitn.it/en/cimec/mri
CIMEC: http://www.cimec.unitn.it/

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Re: [Freesurfer] FLAIR for hippo subfield segmentation with an additional scan

[Jovicich, Jorge]

Hi Eugenio,

just to confirm I understand the currently available options. There are 
two multispectral strategies (MPRAGE + high res 2D T2, or MPRAGE + 3D 
FLAIR). It would be great to see if the combo option improves things 
even further for the subfields (MPRAGE + high res 2D T2 + 3D FLAIR). Is 
that option at all possible with the available FS version or in the works?


Best,

Jorge


On 05/09/2016 16:13, Iglesias, Eugenio wrote:

The same one; just change the input file and the analysis ID

- T2:   recon-all -s mySubject -hippocampal-subfields-T1T2 
myT2scan.nii.gz  T2


- FLAIR: recon-all -s mySubject -hippocampal-subfields-T1T2 
myFLAIRscan.nii.gz  FLAIR


Cheers,

/Eugenio

Juan Eugenio Iglesias
Senior Research Fellow
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 5 Sep 2016, at 15:10, Vaz pandolfo, Renata > wrote:


Dear FS experts,
I have a question about the "segmentation with an additional scan - 
multispectral segmentation" on the hippocampal sf segmentation, FS 
dev. 6.0.
For controls on which I had already run recon-all -all, I added the 
T2 sequence with the following command:

recon-all -s  \
-hippocampal-subfields-T1T2  

Now, if I want to do the same thing with FLAIR as the additional 
input, which flag should I use? Thank you,

Renata




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--
Jorge Jovicich, Ph.D.

MR Lab Head
Center for Mind/Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: http://r.unitn.it/en/cimec/mri
CIMEC: http://www.cimec.unitn.it/

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Re: [Freesurfer] volumetric difference between 1.5 T and 3.0 T...

[Jovicich, Jorge]

Hi Gonzalo,

indeed, here are the references Bruce is refering to:
http://www.ncbi.nlm.nih.gov/pubmed/19233293
http://www.ncbi.nlm.nih.gov/pubmed/16651008

Image contrast to noise ratio per unit time of acquisition is different 
because of different T1s and lower SNR. Different scan durations will 
also give different head motion biases. Then differences can also 
increase depending on protocol and scanner model/vendor differences. It 
is in general cleaner to not mix data from multiple fields. If you have 
large numbers and well balanced cohorts you can test for differences in 
healthy controls.


Jorge

On 06/06/2016 17:40, Bruce Fischl wrote:

Hi Gonzalo

we seek to minimize these explicitly, but given the difference in T1s 
at different field strength it's pretty hard to get rid of them 
completely. Xiao Han wrote a paper on this, and I think Jorge Jovicich 
did as well


cheers
Bruce


 On Mon, 6 Jun 2016, Gonzalo Rojas Costa wrote:


Hi:

 There exist any difference between the volumetric values obtained
using 1.5T and 3.0T images ? Any paper about it ?

 Sincerely,

Gonzalo Rojas Costa
Laboratory for Advanced Medical Image Processing
Department of Radiology
Clínica las Condes
Lo Fontecilla 441, Las Condes, Santiago, Chile.
Tel: 56-2-2105170
Cel: 56-9-97771785
www.clc.cl

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--
Jorge Jovicich, Ph.D.

MR Lab Head
Center for Mind Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: http://r.unitn.it/en/cimec/mri
CIMEC: http://www.cimec.unitn.it/

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[Freesurfer] Cognitive & Brain Sciences PhD opening call, University of Trento, Italy

[Jovicich, Jorge]

Dear All,

We are pleased to announce the opening of a call for 14 fellowships for 
our international PhD Program in Cognitive and Brain Sciences (CIMeC), 
commencing in November 2016 at the University of Trento, Italy. As you 
will see from the links below, the PhD call is open to several fields of 
cognitive neuroscience research. Interested candidates should feel free 
to contact the PIs that might have topics of interest to them.


PhD areas outline: 
http://web.unitn.it/en/drcimec/37990/32nd-cycle-research-topics-2016-call
PhD Application summary: 
http://web.unitn.it/en/drcimec/10141/application-summary-and-process

PhD Application link: https://webapps.unitn.it/Apply/en/Web/Home/dott
*PhD Application deadline: Tuesday May 10, 2016, at 4pm ECT*
CIMeC: http://web.unitn.it/en/cimec

Supplementary information about CIMEC's doctoral program:
-CIMeC ranked 1^st in Italy for Quality of Research 2013 

-2014-2015 UNITrento ranks 1st in Italy in the rankings of THE - Times 
Higher Education 

-3-yr program: Nov. 1, 2016- Oct. 31, 2019
-Courses are given in English
-14 positions, 100% funded
-Salary: starting at €1.100/mo., tax-free
-Winners receive a €2800 tax-free research/mobility budget
-Winners are eligible for a €150/month residential contribution
-Why choose UniTrento 


- FAQ: http://www.unitn.it/en/drcimec/10142/frequently-asked-questions
- More information: phd.ci...@unitn.it 

--
Jorge Jovicich, Ph.D.

MR Lab Head
Center for Mind Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: http://r.unitn.it/en/cimec/mri
CIMEC: http://www.cimec.unitn.it/

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[Freesurfer] Director Position, Center for Mind/Brain Sciences, University of Trento, Italy

[Jovicich, Jorge]

 Director, Center for Mind-Brain Sciences (CIMeC) : Trento, Italy

http://www.nature.com/naturejobs/science/jobs/534333-director-center-for-mind-brain-sciences-cimec

The University of Trento, Italy, invites expressions of interest from 
highly motivated scholars for the position of Director of the Center for 
Mind-Brain Sciences (CIMeC):http://web.unitn.it/en/cimec


The CIMeC's purpose is to foster cutting-edge research on the neural 
underpinnings of cognition and to support the dissemination of these 
findings internationally and within the local community. As an 
interdisciplinary research and teaching center, the center draws on 
faculty from several departments, including Psychology and Cognitive 
Science, Humanities and Philosophy, Physics, Mathematics, and 
Information Engineering and Computer Science. Its faculty originates 
from Italy, Germany, The Netherlands, Belgium,USA, Canada, Argentina, 
Israel and beyond. Researchers study brain organization via the analysis 
of its functional, structural and physiological characteristics, in both 
normal and pathological conditions. Top-of-the-line instrumentation 
includes research-dedicatedMRI,MEG,EEG,NIRS,TMSand eye tracking 
solutions, as well as systems for studying kinematics. In addition, the 
affiliated Center for Neurocognitive Rehabilitation (CERiN) is 
specialized in the study of clinical cases.


In the last 5 years CIMeC faculty have won many competitive national and 
international grants, including 1 European Research Council (ERC) 
advanced grant, 1ERCconsolidator grant, 6ERCstarting grants, other 
European Framework grants and highly competitive grants awarded by the 
local province. The center has recently been ranked the leading 
cognitive neuroscience research unit in Italy.
The University of Trento is interested in applications from candidates 
with an excellent research record and experience in the area of 
cognitive neuroscience.


*Candidate profile*
Candidates must have an excellent research and teaching record in the 
area of Cognitive Neuroscience.
They must be able to work individually and as part of a team in a 
multidisciplinary and international environment. They would be expected 
to contribute to the Center’s overall goal of developing cutting-edge 
research in the area of Cognitive Neuroscience. Applicants must have:


 * Internationally-recognized research experience
 * The rank of tenured full professor
 * Research/academic administrative experience such as directing a
   research center or chairing a department
 * Proven skills in fund-raising from (public or private) national, EU
   and international sources
 * Some fluency in Italian

In addition, experience in areas of interaction between clinical 
neurology and basic research in cognitive neuroscience is desirable.


The University of Trento is committed to providing equal opportunities 
regardless of gender and race.


Applicants should submit their expression of interest by providing a 
statement addressing their suitability for appointment (max 2 pages) and 
a CV to the Rector:recruitm...@unitn.it mailto:recruitm...@unitn.it


The deadline for applications is*Wednesday, 30 September 2015.*

Applications will be evaluated confidentially by an International 
Advisory Committee appointed by the Academic Senate of the University of 
Trento.
The Director's mandate shall last three years. The appointment will be 
renewable.


The contract between the Director and the University of Trento shall be 
defined according to the status of the chosen candidate. The salary 
shall be negotiable, abiding by the Italian University Regulations.


--
Jorge Jovicich, Ph.D.

MR Lab Head
Center for Mind Brain Sciences
University of Trento,
Via delle Regole, 101
38100 Mattarello (TN)
Italy

Telephone: +39-0461-28 3064
Fax: +39-0461-28-3066
Email: jorge.jovic...@unitn.it
MRI Methods Group: http://r.unitn.it/en/cimec/mri
CIMEC: http://www.cimec.unitn.it/

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