Re: [Freesurfer] Does data orientation (Neurological Vs. Radiological) produces different results

2018-12-15 Thread Bruce Fischl 

Hi Meena

hmmm, I'm not sure what to tell you. The borders of the accumbens are not 
very well defined (one reason the CMA called it "accumbens area" instead of 
just "accumbens"). I guess we can check our atlas data to see if there is 
any asymmetry there


Bruce

On Sat, 15 Dec 2018, Meena M. Makary wrote:



External Email - Use Caution

Thank you Bruce for your reply and the helpful information. Our data never went 
through Analyze
format (we converted the data from dcm > NIFTI using mricron). FreeView reads 
the data appropriately
(confirmed by attaching a Vitamin D pill to one of our subject's right side).  

Thanks again;
--Meena

On Fri, Dec 14, 2018 at 5:59 PM Bruce Fischl  wrote:
  when you bring it up in freeview does it properly show left and right? If
  it ever went through analyze as a format you will have lost the
  information that lets us distinguish left from right

  cheers
  Bruce
  On Fri, 14 Dec 2018,
  Geha, Paul wrote:

  > It is NIFTI format.  
  > ——
  > Paul Geha, MD
  > Assistant Professor of Psychiatry
  > Yale School of Medicine
  > Assistant Fellow, The John B. Pierce Laboratory
  > Email: paul.g...@yale.edu
  > Tel:(203)903-4334
  >
  >
  >
  >       On Dec 14, 2018, at 10:53 AM, Bruce Fischl 
 wrote:
  >
  > what is your input data format?
  > On Fri, 14 Dec 2018, Geha, Paul wrote:
  >
  >       Dear Bruce,
  >
  >       Thank you for your reply.
  >
  >       However, we are obtaining an odd result with FreeSurfer when we 
examine the
  volume
  >       of the left and right accumbens.  In the UK  BioBank data >20K 
subjects
  freesurfer
  >       segmentations the left accumbens is clearly significantly larger 
than the right
  >       
accumbens(https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiobank.ctsu.ox.ac.uk%2Fcrystal%2Fl
  a
  
>bel.cgi%3Fid%3D110data=02%7C01%7Cpaul.geha%40yale.edu%7C6fe7514e6a064d661e6608d661dc40ef%7Cdd8c

  
>bebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636803995945018317sdata=Iq5%2FMtaNTPUbuvdXnDnRVGPV6NOnMN

  >      
MMSLiAGyXq734%3Dreserved=0abel.cgi%3Fid%3D110data=02%7C01%7Cpaul.geha%40yale.edu%7C6fe7514e6a064d661e6608d661dc40ef%7Cdd8

  
>cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636803995945018317sdata=Iq5%2FMtaNTPUbuvdXnDnRVGPV6NOnM

  >       NMMSLiAGyXq734%3Dreserved=0>). Also, the attached paper used 
freesurfer and
  >       found left accumbens > right.  In our hands, and in  2 different 
data sets
  >       collected in two different sites,  we obtain the opposite with 
FreeSurfer (right
  >       accumbens > left accumbens).
  >
  >       Furthermore, when we segment these same data sets with FIRST from 
FSL we do
  obtain
  >       Left accumbens > right Accumbens in both data sets in agreement 
with the
  >       literature.
  >
  >       Any help in solving this discrepancy is much appreciated.
  >
  >       Regards,
  >       Paul
  >       ——
  >       Paul Geha, MD
  >       Assistant Professor of Psychiatry
  >       Yale School of Medicine
  >       Assistant Fellow, The John B. Pierce Laboratory
  >       Email: paul.g...@yale.edu
  >       Tel:(203)903-4334
  >
  >
  >
  >             On Dec 13, 2018, at 3:49 PM, Bruce Fischl 

  >             wrote:
  >
  >             Hi Meena
  >
  >             it shouldn't. We reorient everything to radiological
  >
  >             cheers
  >             Bruce
  >             On Thu, 13 Dec 2018, Meena M. Makary wrote:
  >
  >                  External Email - Use Caution
  >                   Hi;
  >                   I am wondering if the orientation of the input data to
  >                   recon-all (i.e. Neurological Vs. Radiological)
  >                   produces different results in terms of laterality 
(right
  >                   vs. left)?
  >                   Thanks;
  >                   --Meena
  >                   —
  >                   Meena M. Makary, Ph.D.
  >                   Assistant Professor | Cairo University
  >                   Postdoctoral Fellow | Yale University School of 
Medicine
  >                   Postdoctoral Associate |  The John B. Pierce 
Laboratory
  >                   Postdoc Committee Chair | The John B. Pierce 
Laboratory
  >                   Career Development and Mentoring Manager Elect | OHBM
  >                   Student and Postdoc SIG
  >                   290 Congress Avenue, New Haven, CT 06519
  >                   +1 (475) 731-5592
  >
  >
  >
  >

Re: [Freesurfer] Does data orientation (Neurological Vs. Radiological) produces different results

2018-12-14 Thread Meena M. Makary 
External Email - Use Caution

Thank you Bruce for your reply and the helpful information. Our data never
went through Analyze format (we converted the data from dcm > NIFTI using
mricron). FreeView reads the data appropriately (confirmed by attaching a
Vitamin D pill to one of our subject's right side).

Thanks again;
--Meena

On Fri, Dec 14, 2018 at 5:59 PM Bruce Fischl 
wrote:

> when you bring it up in freeview does it properly show left and right? If
> it ever went through analyze as a format you will have lost the
> information that lets us distinguish left from right
>
> cheers
> Bruce
> On Fri, 14 Dec 2018,
> Geha, Paul wrote:
>
> > It is NIFTI format.
> > ——
> > Paul Geha, MD
> > Assistant Professor of Psychiatry
> > Yale School of Medicine
> > Assistant Fellow, The John B. Pierce Laboratory
> > Email: paul.g...@yale.edu
> > Tel:(203)903-4334
> >
> >
> >
> >   On Dec 14, 2018, at 10:53 AM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
> >
> > what is your input data format?
> > On Fri, 14 Dec 2018, Geha, Paul wrote:
> >
> >   Dear Bruce,
> >
> >   Thank you for your reply.
> >
> >   However, we are obtaining an odd result with FreeSurfer when we
> examine the volume
> >   of the left and right accumbens.  In the UK  BioBank data >20K
> subjects freesurfer
> >   segmentations the left accumbens is clearly significantly larger
> than the right
> >   accumbens (
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiobank.ctsu.ox.ac.uk%2Fcrystal%2Fla
> > bel.cgi%3Fid%3D110data=02%7C01%7Cpaul.geha%40yale.edu
> %7C6fe7514e6a064d661e6608d661dc40ef%7Cdd8c
> >
> bebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636803995945018317sdata=Iq5%2FMtaNTPUbuvdXnDnRVGPV6NOnMN
> >   MMSLiAGyXq734%3Dreserved=0<
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiobank.ctsu.ox.ac.uk%2Fcrystal%2Fl
> > abel.cgi%3Fid%3D110data=02%7C01%7Cpaul.geha%40yale.edu
> %7C6fe7514e6a064d661e6608d661dc40ef%7Cdd8
> >
> cbebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636803995945018317sdata=Iq5%2FMtaNTPUbuvdXnDnRVGPV6NOnM
> >   NMMSLiAGyXq734%3Dreserved=0>). Also, the attached paper used
> freesurfer and
> >   found left accumbens > right.  In our hands, and in  2 different
> data sets
> >   collected in two different sites,  we obtain the opposite with
> FreeSurfer (right
> >   accumbens > left accumbens).
> >
> >   Furthermore, when we segment these same data sets with FIRST from
> FSL we do obtain
> >   Left accumbens > right Accumbens in both data sets in agreement
> with the
> >   literature.
> >
> >   Any help in solving this discrepancy is much appreciated.
> >
> >   Regards,
> >   Paul
> >   ——
> >   Paul Geha, MD
> >   Assistant Professor of Psychiatry
> >   Yale School of Medicine
> >   Assistant Fellow, The John B. Pierce Laboratory
> >   Email: paul.g...@yale.edu
> >   Tel:(203)903-4334
> >
> >
> >
> > On Dec 13, 2018, at 3:49 PM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu>
> > wrote:
> >
> > Hi Meena
> >
> > it shouldn't. We reorient everything to radiological
> >
> > cheers
> > Bruce
> > On Thu, 13 Dec 2018, Meena M. Makary wrote:
> >
> >  External Email - Use Caution
> >   Hi;
> >   I am wondering if the orientation of the input data to
> >   recon-all (i.e. Neurological Vs. Radiological)
> >   produces different results in terms of laterality
> (right
> >   vs. left)?
> >   Thanks;
> >   --Meena
> >   —
> >   Meena M. Makary, Ph.D.
> >   Assistant Professor | Cairo University
> >   Postdoctoral Fellow | Yale University School of
> Medicine
> >   Postdoctoral Associate |  The John B. Pierce Laboratory
> >   Postdoc Committee Chair | The John B. Pierce Laboratory
> >   Career Development and Mentoring Manager Elect | OHBM
> >   Student and Postdoc SIG
> >   290 Congress Avenue, New Haven, CT 06519
> >   +1 (475) 731-5592
> >
> >
> >
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer



-- 
—
*Meena M. Makary, Ph.D.*
Assistant Professor | Cairo University 
Postdoctoral Fellow | Yale University School of Medicine

Postdoctoral Associate |  The John B. Pierce Laboratory

Postdoc Committee Chair | The John B. Pierce Laboratory

Career Development and Mentoring Manager Elect | OHBM Student and

Re: [Freesurfer] Does data orientation (Neurological Vs. Radiological) produces different results

2018-12-14 Thread Bruce Fischl 
when you bring it up in freeview does it properly show left and right? If 
it ever went through analyze as a format you will have lost the 
information that lets us distinguish left from right


cheers
Bruce
On Fri, 14 Dec 2018, 
Geha, Paul wrote:



It is NIFTI format.  
——
Paul Geha, MD
Assistant Professor of Psychiatry
Yale School of Medicine
Assistant Fellow, The John B. Pierce Laboratory
Email: paul.g...@yale.edu
Tel:(203)903-4334



  On Dec 14, 2018, at 10:53 AM, Bruce Fischl  
wrote:

what is your input data format?
On Fri, 14 Dec 2018, Geha, Paul wrote:

  Dear Bruce,

  Thank you for your reply.

  However, we are obtaining an odd result with FreeSurfer when we examine 
the volume
  of the left and right accumbens.  In the UK  BioBank data >20K subjects 
freesurfer
  segmentations the left accumbens is clearly significantly larger than the 
right
  accumbens 
(https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiobank.ctsu.ox.ac.uk%2Fcrystal%2Fla
bel.cgi%3Fid%3D110data=02%7C01%7Cpaul.geha%40yale.edu%7C6fe7514e6a064d661e6608d661dc40ef%7Cdd8c
bebb21394df8b4114e3e87abeb5c%7C0%7C0%7C636803995945018317sdata=Iq5%2FMtaNTPUbuvdXnDnRVGPV6NOnMN
  
MMSLiAGyXq734%3Dreserved=0). Also, the attached paper used 
freesurfer and
  found left accumbens > right.  In our hands, and in  2 different data sets
  collected in two different sites,  we obtain the opposite with FreeSurfer 
(right
  accumbens > left accumbens).

  Furthermore, when we segment these same data sets with FIRST from FSL we 
do obtain
  Left accumbens > right Accumbens in both data sets in agreement with the
  literature.

  Any help in solving this discrepancy is much appreciated.

  Regards,
  Paul
  ——
  Paul Geha, MD
  Assistant Professor of Psychiatry
  Yale School of Medicine
  Assistant Fellow, The John B. Pierce Laboratory
  Email: paul.g...@yale.edu
  Tel:(203)903-4334



On Dec 13, 2018, at 3:49 PM, Bruce Fischl 

wrote:

Hi Meena

it shouldn't. We reorient everything to radiological

cheers
Bruce
On Thu, 13 Dec 2018, Meena M. Makary wrote:

     External Email - Use Caution
  Hi;
  I am wondering if the orientation of the input data to
  recon-all (i.e. Neurological Vs. Radiological)
  produces different results in terms of laterality (right
  vs. left)?
  Thanks;
  --Meena
  —
  Meena M. Makary, Ph.D.
  Assistant Professor | Cairo University
  Postdoctoral Fellow | Yale University School of Medicine
  Postdoctoral Associate |  The John B. Pierce Laboratory
  Postdoc Committee Chair | The John B. Pierce Laboratory
  Career Development and Mentoring Manager Elect | OHBM
  Student and Postdoc SIG
  290 Congress Avenue, New Haven, CT 06519
  +1 (475) 731-5592




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Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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Re: [Freesurfer] Does data orientation (Neurological Vs. Radiological) produces different results

2018-12-14 Thread Bruce Fischl 

what is your input data format?
On Fri, 14 Dec 2018, Geha, Paul wrote:


Dear Bruce,

Thank you for your reply.

However, we are obtaining an odd result with FreeSurfer when we examine the volume of the left 
and right accumbens.  In the UK  BioBank data >20K subjects freesurfer segmentations the 
left accumbens is clearly significantly larger than the right accumbens ( 
http://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=110 
). Also, the attached paper used 
freesurfer and found left accumbens > right.  In our hands, and in  2 different data sets 
collected in two different sites,  we obtain the opposite with FreeSurfer (right accumbens 
> left accumbens).

Furthermore, when we segment these same data sets with FIRST from FSL we do obtain 
Left accumbens > right Accumbens in both data sets in agreement with the 
literature.

Any help in solving this discrepancy is much appreciated.

Regards,
Paul
——
Paul Geha, MD
Assistant Professor of Psychiatry
Yale School of Medicine
Assistant Fellow, The John B. Pierce Laboratory
Email: paul.g...@yale.edu
Tel:(203)903-4334




On Dec 13, 2018, at 3:49 PM, Bruce Fischl  wrote:

Hi Meena

it shouldn't. We reorient everything to radiological

cheers
Bruce
On Thu, 13 Dec 2018, Meena M. Makary wrote:


External Email - Use Caution
Hi;
I am wondering if the orientation of the input data to recon-all (i.e. 
Neurological Vs. Radiological)
produces different results in terms of laterality (right vs. left)?
Thanks;
--Meena
—
Meena M. Makary, Ph.D.
Assistant Professor | Cairo University
Postdoctoral Fellow | Yale University School of Medicine
Postdoctoral Associate |  The John B. Pierce Laboratory
Postdoc Committee Chair | The John B. Pierce Laboratory
Career Development and Mentoring Manager Elect | OHBM Student and Postdoc SIG
290 Congress Avenue, New Haven, CT 06519
+1 (475) 731-5592


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Re: [Freesurfer] Does data orientation (Neurological Vs. Radiological) produces different results

2018-12-13 Thread Bruce Fischl 

Hi Meena

it shouldn't. We reorient everything to radiological

cheers
Bruce
On Thu, 13 Dec 2018, 
Meena M. Makary wrote:




External Email - Use Caution

Hi;

I am wondering if the orientation of the input data to recon-all (i.e. 
Neurological Vs. Radiological)
produces different results in terms of laterality (right vs. left)?

Thanks;
--Meena
—
Meena M. Makary, Ph.D.
Assistant Professor | Cairo University 
Postdoctoral Fellow | Yale University School of Medicine
Postdoctoral Associate |  The John B. Pierce Laboratory
Postdoc Committee Chair | The John B. Pierce Laboratory
Career Development and Mentoring Manager Elect | OHBM Student and Postdoc SIG

290 Congress Avenue, New Haven, CT 06519
+1 (475) 731-5592

___
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Freesurfer@nmr.mgh.harvard.edu
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[Freesurfer] Does data orientation (Neurological Vs. Radiological) produces different results

2018-12-13 Thread Meena M. Makary 
External Email - Use Caution

Hi;

I am wondering if the orientation of the input data to recon-all (i.e.
Neurological Vs. Radiological) produces different results in terms of
laterality (right vs. left)?

Thanks;
--Meena
—
*Meena M. Makary, Ph.D.*
Assistant Professor | Cairo University 
Postdoctoral Fellow | Yale University School of Medicine

Postdoctoral Associate |  The John B. Pierce Laboratory

Postdoc Committee Chair | The John B. Pierce Laboratory

Career Development and Mentoring Manager Elect | OHBM Student and Postdoc
SIG 

290 Congress Avenue, New Haven, CT 06519
+1 (475) 731-5592 <+1%20475-731-5592>
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