[Freesurfer] neuroimaging postdoc position available

2019-09-11 Thread Keith Schneider 
External Email - Use Caution

A post-doctoral position is available with Keith Schneider at the University of 
Delaware http://keith.psych.udel.edu . The 
position is funded by NEI/NIH to study the subcortical mechanisms of vision, 
audition, attention and dyslexia.

The successful candidate will join a thriving neuroimaging community at the 
University of Delaware.  The Center for Biomedical & Brain Imaging includes a 
Siemens Prisma 3T MRI scanner, simultaneous EEG, TMS, eye-tracking, and a 
Bruker 9.4 T scanner for small animals.

I am looking for a scientist who:

* has experience with fMRI
* has programming experience (e.g. Matlab or Python)
* has an interest in attention, sensory systems, reading and/or neuroimaging 
methods development (acquisition or analysis)

This position is initially for one year but can be renewed as mutually agreed. 
The start date is flexible but can begin immediately.  To inquire, e-mail your 
CV and a PDF of a first-authored journal article to keit...@udel.edu.

The University of Delaware is located in Newark, Delaware, a small college 
town, located along the Northeast Corridor, within 2 hours of New York and 
Washington, DC, and within an hour of Philadelphia and Baltimore.

-
Keith Schneider
Director, Center for Biomedical & Brain Imaging
Associate Professor, Department of Psychological & Brain Sciences
University of Delaware

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Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed}

2019-09-11 Thread Ruopeng Wang 
The scalar bar display for overlay in stable 6.0 is broken. If you can 
install the latest dev build, you should be able to see the scalar bar:


https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview

Best,
Ruopeng

On 9/11/19 9:57 AM, Caspar M. Schwiedrzik wrote:


External Email - Use Caution

Hi Doug and Ruopeng,
thanks a lot for your advice!
Is there a way to display a meaningful legend? In tksurfer/rtview, we 
get a linear legend that does not seem to make much sense and in 
freeview we typically do not get anything when we choose color wheel 
and then click on the legend button.

Thanks! Caspar


Am Di., 10. Sept. 2019 um 17:23 Uhr schrieb Greve, Douglas N.,Ph.D. 
mailto:dgr...@mgh.harvard.edu>>:


When you run rtview, it will run tksurfer. To get to the color wheel,
open View->Configure->Overlay, then select "Color Wheel" under the
"Color Scale" tab.

On 9/10/19 4:03 AM, Caspar M. Schwiedrzik wrote:
>
> External Email - Use Caution
>
> Hi Doug and Roupeng,
> did you already have the chance to look into the question how to
> display the color wheel with rtview and/or freeview?
> Thank you! Caspar
>
> Am Sa., 7. Sept. 2019 um 13:13 Uhr schrieb Caspar M. Schwiedrzik
> mailto:cschwie...@mail.rockefeller.edu>
> >>:
>
>     External Email - Use Caution
>
>     Hi Doug and Ruopeng,
>     it would be amazing if you could dig out the information on
how to
>     display the color wheel.
>     Looking forward to what you find!
>     Caspar
>
>
>     Am Fr., 6. Sept. 2019 um 17:14 Uhr schrieb Greve, Douglas
N.,Ph.D.
>     mailto:dgr...@mgh.harvard.edu>
>>:
>
>         Hi Caspar, sorry for the delay. I have not used the
retinotoy
>         stream in a long, long time so I don't know off the top
of my
>         head. I'll have to look into it. tksurfer (from rtview) does
>         have a way to display using the color wheel, but I don't
>         remember how to do it.
>
>         Ruopeng, can freeview display using a color wheel?
>
>         On 9/6/2019 6:16 AM, Caspar M. Schwiedrzik wrote:
>>
>>         External Email - Use Caution
>>
>>         Hi!
>>         I wanted to ask again whether there is a way to display the
>>         color wheel in rtview and/or freeview. We are debugging our
>>         analyses and it would be immensely helpful to have a legend
>>         that specifies the color assignments.
>>         Thank you,
>>         Caspar
>>
>>         On Wed, Sep 4, 2019 at 14:30 Caspar M. Schwiedrzik
>>         mailto:cschwie...@rockefeller.edu>
>>         >> wrote:
>>
>>             Hi!
>>             I am following up on this thread trying to
understand how
>>             to make the color wheel visible in rtview, or, if
>>             necessary, in freeview.
>>             Thank you! Caspar
>>
>>
>>  ___
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Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed}

2019-09-11 Thread Caspar M. Schwiedrzik 
External Email - Use Caution

Hi Doug and Ruopeng,
thanks a lot for your advice!
Is there a way to display a meaningful legend? In tksurfer/rtview, we get a
linear legend that does not seem to make much sense and in freeview we
typically do not get anything when we choose color wheel and then click on
the legend button.
Thanks! Caspar


Am Di., 10. Sept. 2019 um 17:23 Uhr schrieb Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu>:

> When you run rtview, it will run tksurfer. To get to the color wheel,
> open View->Configure->Overlay, then select "Color Wheel" under the
> "Color Scale" tab.
>
> On 9/10/19 4:03 AM, Caspar M. Schwiedrzik wrote:
> >
> > External Email - Use Caution
> >
> > Hi Doug and Roupeng,
> > did you already have the chance to look into the question how to
> > display the color wheel with rtview and/or freeview?
> > Thank you! Caspar
> >
> > Am Sa., 7. Sept. 2019 um 13:13 Uhr schrieb Caspar M. Schwiedrzik
> >  > >:
> >
> > External Email - Use Caution
> >
> > Hi Doug and Ruopeng,
> > it would be amazing if you could dig out the information on how to
> > display the color wheel.
> > Looking forward to what you find!
> > Caspar
> >
> >
> > Am Fr., 6. Sept. 2019 um 17:14 Uhr schrieb Greve, Douglas N.,Ph.D.
> > mailto:dgr...@mgh.harvard.edu>>:
> >
> > Hi Caspar, sorry for the delay. I have not used the retinotoy
> > stream in a long, long time so I don't know off the top of my
> > head. I'll have to look into it. tksurfer (from rtview) does
> > have a way to display using the color wheel, but I don't
> > remember how to do it.
> >
> > Ruopeng, can freeview display using a color wheel?
> >
> > On 9/6/2019 6:16 AM, Caspar M. Schwiedrzik wrote:
> >>
> >> External Email - Use Caution
> >>
> >> Hi!
> >> I wanted to ask again whether there is a way to display the
> >> color wheel in rtview and/or freeview. We are debugging our
> >> analyses and it would be immensely helpful to have a legend
> >> that specifies the color assignments.
> >> Thank you,
> >> Caspar
> >>
> >> On Wed, Sep 4, 2019 at 14:30 Caspar M. Schwiedrzik
> >>  >> > wrote:
> >>
> >> Hi!
> >> I am following up on this thread trying to understand how
> >> to make the color wheel visible in rtview, or, if
> >> necessary, in freeview.
> >> Thank you! Caspar
> >>
> >>
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[Freesurfer] multiple comparisons correction for brain-behaviour correlations

2019-09-11 Thread Annelies Vant Westeinde 
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Dear members,

I have run several analyses in which we correlate cognitive performance with 
vertex-wise cortical surface area, thickness and volume. We ran monte carlo 
simulation for each correlation. However, we would like to correct the outcome 
for the number of associations we did, that is for the for 10 different 
cognitive scales that we tested. How can this be done? We would rather not use 
bonferroni correction, as it is so strict, but would prefer fdr. Do we need to 
somehow get the p-values of the cluster peaks that correlated with the 
cognitive scales and do FDR on those? Or should we adjust the monte carlo 
simulation threshold to account for the 10 different tests?

Thank you in advance,

Annelies

Annelies van't Westeinde | PHD Candidate
Department of Women's and Children's Health | Karolinska Institutet
171 77 Solna | Karolinskavägen 37A
+46 760967499
annelies.vant.westei...@ki.se | ki.se
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Re: [Freesurfer] Additional scans in hippocampal subfields segmentation

2019-09-11 Thread Bruce Fischl 
yes, that seems reasonable and should help avoid the dura. Eugenio can 
commend on the subfields

cheers
Bruce

On Wed, 11 Sep 2019, Rovai Antonin wrote:


   External Email - Use Caution

Hi Bruce,

What are the relevant parameters you need? It’s a pretty standard T2FLAIR with 
spacing 0.7mm x 1mm x 1mm with inversion time 2247ms, TR of 8502ms and TE of 
137ms.

Thanks for you help

Antonin

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer


On 5 Sep 2019, at 15:53, Bruce Fischl  wrote:

Hi Antonin

can you give us the details of your T2-FLAIR? Certainly it helps us generate 
more accurate pial surfaces by avoiding dura. For the subfields I defer to 
Eugenio

cheers
Bruce
On Thu, 5 Sep 2019, Rovai Antonin wrote:


  External Email - Use Caution

I’m resending this request as I really would like to know what you 
think :-)


Best

Antonin

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer


On 30 Aug 2019, at 11:00, Rovai Antonin  wrote:

Hello

I’d like to know if there is any advantage in having a T2 FLAIR as 
additional scan (in addition to our 1mm isotropic T1 scans) when using 
the hippocampal subfield segmentation tool. We do not have T2 nor PD 
available.


Thanks for you help

Antonin Rovai



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Re: [Freesurfer] Additional scans in hippocampal subfields segmentation

2019-09-11 Thread Rovai Antonin 
External Email - Use Caution

Hi Bruce,

What are the relevant parameters you need? It’s a pretty standard T2FLAIR with 
spacing 0.7mm x 1mm x 1mm with inversion time 2247ms, TR of 8502ms and TE of 
137ms.

Thanks for you help

Antonin

Hôpital Erasme - ULB
Cliniques universitaires de Bruxelles
Route de Lennik 808 - B - 1070 Bruxelles
S www.erasme.ulb.ac.be

Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer

> On 5 Sep 2019, at 15:53, Bruce Fischl  wrote:
>
> Hi Antonin
>
> can you give us the details of your T2-FLAIR? Certainly it helps us generate 
> more accurate pial surfaces by avoiding dura. For the subfields I defer to 
> Eugenio
>
> cheers
> Bruce
> On Thu, 5 Sep 2019, Rovai Antonin wrote:
>
>>   External Email - Use Caution
>>
>> I’m resending this request as I really would like to know what you think :-)
>>
>> Best
>>
>> Antonin
>>
>> Hôpital Erasme - ULB
>> Cliniques universitaires de Bruxelles
>> Route de Lennik 808 - B - 1070 Bruxelles
>> S www.erasme.ulb.ac.be
>>
>> Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer
>>
>>> On 30 Aug 2019, at 11:00, Rovai Antonin  
>>> wrote:
>>>
>>> Hello
>>>
>>> I’d like to know if there is any advantage in having a T2 FLAIR as 
>>> additional scan (in addition to our 1mm isotropic T1 scans) when using the 
>>> hippocampal subfield segmentation tool. We do not have T2 nor PD available.
>>>
>>> Thanks for you help
>>>
>>> Antonin Rovai
>>
>>
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