Re: [Freesurfer] Content of register.dof6.dat.param

2015-04-17 Thread pfannmoelj 
Hello Doug,

just a very last question. Where ist the origin of the coordinate system if the 
motion parameters are calculated using mc-afni2 and where is it if BBR is used? 
I mean the origin in the coordinate system of the input and output volume.

Yours pfannmoe


On Mon, 13 Apr 2015 10:36:02 -0400
Douglas Greve  wrote:

> yes
> 
> On 4/13/15 10:32 AM, pfannmo...@uni-greifswald.de wrote:
> > Just to make that point: Is it valid to apply "mcparams2extreg -mcfile 
> > fmc.mcdat -extreg mcextreg" after substitution of the numbers in
> > "register.dof6.dat.param" into "fmc.mcdat"? Is the result for the motion 
> > regressors valid?
> >
> >
> >
> > On Mon, 13 Apr 2015 10:15:08 -0400
> > Douglas Greve  wrote:
> >
> >> Those numbers do not have the same interpretation as as the ones in
> >> fmc.mcdat but they represent the same information. If you construct a
> >> new file with the same format as fmc.mcdat but with those numbers
> >> substituted in cols 2-7 then you should get pretty similar results.
> >>
> >>
> >> On 4/9/15 7:04 AM, pfannmo...@uni-greifswald.de wrote:
> >>> Sorry, I ment the first six numbers in "register.dof6.dat.param".
> >>>
> >>>
> >>>
> >>> On Thu, 9 Apr 2015 12:33:49 +0200
> >>> pfannmo...@uni-greifswald.de wrote:
> >>>
>  Dear Experts,
> 
>  is there a possibility to extract the "motion parameter" from a BBR 
>  registration? Possibly the first three numbers of the
> 
>  register.dof6.dat.param
> 
>  file are the same parameter as found in column 2 - 7 in:
> 
>  fmcpr.mcdat.
> 
>  If I have a series of "register.dof6.dat.param" can I use 
>  "mcdat2mcextreg" to calculate motion regressors from those 
>  transformations?
> 
>  Thanks pfannmoe
> 
> 
> 
> 
> 
>  -- 
>  Joerg Pfannmoeller 
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Re: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional

2015-04-17 Thread Martin Reuter 

Hi Pradeep,

is this the result of a single subject? In a single subject lot's of 
things can happen (e.g. motion artefacts can affect a single time point, 
other imaging or measurement noise will have effects). Also how far are 
the time points apart? Run the same thing with 20 subjects and you 
should see significantly reduced variablility in the longitudinal stream 
vs the cross sectional one.


Best, Martin

On 04/16/2015 01:12 PM, Pradeep wrote:

Hello All,

I have pre-processed a subject that has T1 scans at 3 time points 
using the freesurfer cross-sectional and longitudinal methods. The 
results show a lot of variability. I have attached the plots. Any 
advice would be much appreciated.


Thanks,
Pradeep

On Wed, Apr 15, 2015 at 5:26 PM, Pradeep > wrote:


Hello All,

I have pre-processed a subject that has T1 scans at 3 time using
the freesurfer cross-sectional and longitudinal methods. The
results show a lot of variability. I have attached the plots. Any
advice would be much appreciated.

Thanks,
Pradeep

On Wed, Jun 4, 2014 at 12:03 PM, Alexandru Hanganu
mailto:al.hang...@yahoo.ca>> wrote:

Thank you very much for your answer Bruce !

have a nice evening,

Alex.


Le 3 juin 14 7:6, Bruce Fischl a écrit :
> Hi Alex
>
> I would think that longitudinal analysis is still the way to
go as we try
> to improve both reliability and sensitivity using the fact
that we have
> multiple scans/subject.
>
> cheers
> Bruce
> On Tue, 3 Jun 2014, Alexandru Hanganu wrote:
>
>> Hello Everyone,
>>
>> could someone please give us an advice about which method
you consider is
>> the best for our study ?
>>
>> we have two groups with MRI at Time 1. Each group received
medication. After
>> this we performed another MRI at Time 2 after 2 weeks.
>>
>> The best method for this study is a longitudinal one or a
cross-sectional
>> GLM ?
>>
>> We consider that the distance between the time points is
too small, and the
>> longitudinal method is not the best choice. Hence, this
study should be
>> treated as a cross-sectional one. In this case we think
about performing a
>> simple GLM with the contrasts:
>> 0.5 0.5 0.5 0.5
>> or 1 -1 -1 1
>>
>> for the groups:
>> 1) grp 1 time 1
>> 2) grp 1 time 2
>> 3) grp 2 time 1
>> 4) grp 2 time 2
>>
>> we are searching to see whether medication had any impact
on the cortical
>> morphology in each group and between the groups.
>>
>> Thank you !
>> Best regards,
>> Alex.
>>
>>
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--
Dr. Martin Reuter

Instructor in Neurology
  Harvard Medical School
Assistant in Neuroscience
  Dept. of Radiology, Massachusetts General Hospital
  Dept. of Neurology, Massachusetts General Hospital
Research Affiliate
  Computer Science and Artificial Intelligence Lab,
  Dept. of Electrical Engineering and Computer Science,
  Massachusetts Institute of Technology

A.A.Martinos Center for Biomedical Imaging
149 Thirteenth Street, Suite 2301
Charlestown, MA 02129

Phone: +1-617-724-5652
Email:
   mreu...@nmr.mgh.harvard.edu
   reu...@mit.edu
Web  : http://reuter.mit.edu

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Re: [Freesurfer] Advice - best method, longitudinal vs. cross-sectional

2015-04-17 Thread Bruce Fischl 
you should also plot them on the same axes (or at the very least with the 
same limits)

On Fri, 17 Apr 2015, Martin Reuter wrote:


Hi Pradeep,

is this the result of a single subject? In a single subject lot's of things
can happen (e.g. motion artefacts can affect a single time point, other
imaging or measurement noise will have effects). Also how far are the time
points apart? Run the same thing with 20 subjects and you should see
significantly reduced variablility in the longitudinal stream vs the cross
sectional one.

Best, Martin

On 04/16/2015 01:12 PM, Pradeep wrote:
  Hello All, 
I have pre-processed a subject that has T1 scans at 3 time points
using the freesurfer cross-sectional and longitudinal methods. The
results show a lot of variability. I have attached the plots. Any
advice would be much appreciated. 
Thanks,
Pradeep

On Wed, Apr 15, 2015 at 5:26 PM, Pradeep  wrote:
  Hello All, 
I have pre-processed a subject that has T1 scans at 3 time using
the freesurfer cross-sectional and longitudinal methods. The
results show a lot of variability. I have attached the plots.
Any advice would be much appreciated. 
Thanks,
Pradeep

On Wed, Jun 4, 2014 at 12:03 PM, Alexandru Hanganu
 wrote:
  Thank you very much for your answer Bruce !

  have a nice evening,

  Alex.


  Le 3 juin 14 7:6, Bruce Fischl a écrit :
  > Hi Alex
  >
  > I would think that longitudinal analysis is still
  the way to go as we try
  > to improve both reliability and sensitivity using
  the fact that we have
  > multiple scans/subject.
  >
  > cheers
  > Bruce
  > On Tue, 3 Jun 2014, Alexandru Hanganu wrote:
  >
  >> Hello Everyone,
  >>
  >> could someone please give us an advice about
  which method you consider is
  >> the best for our study ?
  >>
  >> we have two groups with MRI at Time 1. Each group
  received medication. After
  >> this we performed another MRI at Time 2 after 2
  weeks.
  >>
  >> The best method for this study is a longitudinal
  one or a cross-sectional
  >> GLM ?
  >>
  >> We consider that the distance between the time
  points is too small, and the
  >> longitudinal method is not the best choice.
  Hence, this study should be
  >> treated as a cross-sectional one. In this case we
  think about performing a
  >> simple GLM with the contrasts:
  >> 0.5 0.5 0.5 0.5
  >> or 1 -1 -1 1
  >>
  >> for the groups:
  >> 1) grp 1 time 1
  >> 2) grp 1 time 2
  >> 3) grp 2 time 1
  >> 4) grp 2 time 2
  >>
  >> we are searching to see whether medication had
  any impact on the cortical
  >> morphology in each group and between the groups.
  >>
  >> Thank you !
  >> Best regards,
  >> Alex.
  >>
  >>
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  > addressed. If you believe this e-mail was sent to
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Re: [Freesurfer] Is the linux centos package compiled with openmp enabled?

2015-04-17 Thread Z K 
It is compiled with the "-fopenmp" flag.

-Zeke

On 04/16/2015 09:01 PM, jupiter wrote:
> Hi,
>
> I've installed FreeSurfer from a binary package
> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0.tar.gz., does that
> package was compiled witn ---enable-openmp?
>
> Thank you.
>
> Kind regards,
>
> - j
>
>
>
>
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[Freesurfer] adjust pial surface outward for abnormally thick cortex

2015-04-17 Thread Jonathan DuBois 
Hi Freesurfers,

I am having trouble manually correcting the surface of brain with an
abnorally thick cortex due to a malformation. It seems as though there is a
thickness threshold that constrains the pial surface reconstruction. I have
added control points to the white matter but the problem seems to be due to
the adnormally thick cortex or the abnormal gyrification. Is there an
option I can change when running recon-all or a manual edit I can make in
these cases? I understand that it may not be perfect but I would like to
get it good as possible.

Thanks in advance,
Jonathan

[image: Inline image 1]
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