[Freesurfer] R: Re: R: Re: incomplete tracts

[stdp82]

No I did not try it. Now I'm trying to perform it.  


Thanks,

Stefano



Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 9-apr-2013 17.50
A: 
Cc: 
Ogg: Re: [Freesurfer] R: Re:  incomplete tracts


Hi Stefano - Did you try CVS for the inter-subject registration? It 
doesn't look like it from the configuration file.

a.y

On Tue, 9 Apr 2013, std...@virgilio.it wrote:

> Hi Anastasia,
> yes, I tried.I'm attacking the last configuration file that I used.
> 
> Thanks, 
> 
> 
> Stefano
> 
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 9-apr-2013 1.42
> A: 
> Cc: 
> Ogg: Re: [Freesurfer] incomplete tracts
> 
> 
> What registration methods are you using for the intra-subject and
> inter-subject registration? Have you tried the different options?
> 
> On Fri, 5 Apr 2013, std...@virgilio.it wrote:
> 
> > Yes, 5.2. Incomplete tracts are usually fmajor or cab. Rarely fminor.
> >
> > Messaggio originale
> > Da: ayend...@nmr.mgh.harvard.edu
> > Data: 5-apr-2013 18.57
> > A: 
> > Cc: "freesurfer@nmr.mgh.harvard.edu"
> > Ogg: Re: [Freesurfer] R: Re: R: Re:  incomplete tracts
> >
> >
> > What you say "again" you mean with 5.2?
> >
> > On Fri, 5 Apr 2013, std...@virgilio.it wrote:
> >
> > > Hi Anastasia,
> > > yes, for some subject the low-b volume is in the end.
> > > Some subjects have again incomplete tracts.
> > > I'm attacking an example of configuration file that I'm using.
> > > I hope that you can check it please.
> > >
> > > Thanks,
> > >
> > >
> > > Stefano
> > >
> > > Messaggio originale
> > > Da: ayend...@nmr.mgh.harvard.edu
> > > Data: 5-apr-2013 18.45
> > > A: 
> > > Cc: "freesurfer@nmr.mgh.harvard.edu"
> > > Ogg: Re: R: Re: [Freesurfer] incomplete tracts
> > >
> > >
> > > Hi Stefano - In your case we determined that the ones that had the low-b
> > > volume in the end didn't run correctly, right? In that case, I didn't
> need
> > > to see anything, you were going to try running 5.2.
> > >
> > > a.y
> > >
> > > On Fri, 5 Apr 2013, std...@virgilio.it wrote:
> > >
> > > > Hi Anastasia,
> > > > could I send you the data of a subject that I don't run correctly? 
> > > >
> > > > I still have some subjects with tracts incomplete and I do not know if
> > it depends
> > > from
> > > > my analysis or whether the images are not good.
> > > >
> > > > Thanks,
> > > >
> > > >
> > > > Stefano
> > > >
> > > >
> > > > Messaggio originale
> > > > Da: ayend...@nmr.mgh.harvard.edu
> > > > Data: 5-apr-2013 17.37
> > > > A: "Gerit Pfuhl"
> > > > Cc: "freesurfer@nmr.mgh.harvard.edu"
> > > > Ogg: Re: [Freesurfer] incomplete tracts
> > > >
> > > >
> > > > Hi Gerit - If it's not an issue with the gradient table but instead a
> > > > tractography initialization issue, I strongly recommend running 5.2
> with
> > > > bbregister for the registration (which is the default in 5.2 anyway).
> > > >
> > > > You can also upload an example data set with issues (include: dmri,
> > > > dmri.bedpostX, dlabel, dpath, scripts) here for me to take a look:
> > > > https://gate.nmr.mgh.harvard.edu/filedrop2/
> > > >
> > > > Hope this helps,
> > > > a.y
> > > >
> > > > On Fri, 5 Apr 2013, Gerit Pfuhl wrote:
> > > >
> > > > > Dear Anastasia,
> > > > >
> > > > > thanks for the help. There is also a line option in freeview.
> However
> > we still
> > > have
> > > > > brains with missing tracks, I rerun them with increasing the ncpts
> and
> > registering
> > > > to
> > > > > bbr (since that is default in Tracula 5.2.). We are reasonable
> > confident that our
> > > > bvel
> > > > > and bvac are correct, since we have roughly 20 cases out of 90
> > processed brains
> > > > where
> > > > > there are no missing tracts. Further sometimes only one tract is
> > missing,
> > > sometimes
> > > > it
> > > > > is more severe. We could not find any correlation with recon-all
> > problems or DTI
> > > raw
> > > > > data issues (all but one were without moving artefacts). Since we
> are
> > running
> > > > bedpostx
> > > > > outside of trac-all (i.e. trac-prep then bedpostx then trac-path)
> > might it be an
> > > > issue
> > > > > that is solved with installing the 5.2. version? Would that run in
> > freesurfer
> > > 5.1.0?
> > > > > I guess we need to change the dcmrirc files only a bit.
> > > > >
> > > > > Kind regards
> > > > > Gerit Pfuhl
> > > > >
> > > > >
> > > > > On 3 April 2013 16:59, Anastasia Yendiki
> >  wrote:
> > > > >
> > > > >   Hi Benjamin - I'd look in a coronal view to see if the lines
> in
> > the corpus
> > > > >   callosum follow the curvature of the corpus callosum, and in a
> > sagittal
> > > > >   view to see if the lines in the cingulum follow the curvature
> of
> > the
> > > > >   cingulum. Does this make sense?
> > > > >
> > > > >   a.y
> > > > >
> > > > >   On Wed, 3 Apr 2013, Roschinski, Benjamin wrote:
> > > > >
> > > > >   Dear Anastasia,
> > > > >
> > > > >   we dislpayed dtifit_V1 as lines, overlaid on dtifit_FA because
> > our
> > > 

[Freesurfer] question on GLM subgroup

[stdp82]

Hi list,
I'm performing cortical thickness among 3 groups by using GLM.
I created a group descriptor file with 3 groups and 2 covariates (age and mean 
thickness).
I performed 3 comparisons A-B, A-C, B-C.
Now, for one of 3 groups (group C) I have:
groups C=30 subjects; I'd like to divide it in some pairs. 
First pair: X (n=15) vs Y (n=15). Second pair: Z (n=15) vs W (n=15). Between 
first and second pair there isn't interactions.
X or Y subgroup can contain also subjects included in Z or W.
Z or W subgroup can contain also subjects included in X or Y. 
Design:
group A
group B   subgroup X vs subgroup Ygroup C  --<  
 subgroup Z vs subgroup W

I'm thinking to perform qdec for X-Y and Z-W. Is it correct?
What do you advise me?
Thanks,

Stefano ___
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Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

[Yang, Daniel]

Dear FreeSurfer Experts and Users,

Did anyone find similar things using FS 5.2 (please see my previous post
below)? That is, FS 5.2 is including more non-cortical "black spaces"
within pial surfaces, compared to FS 5.1?

I'm not interested in nitpicking but I feel this is a rather serious
issue, so I would like to raise it again before it's completely forgotten.

At the meantime I keep receiving Emails from people asking me this issue.

Thanks!
Daniel

-- 
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454






On 3/19/13 7:07 AM, "Yang, Daniel"  wrote:

>
>Posting one of the brains.
>
>https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn
>
>
>It seems to me that neither version is perfect; however, 5.2.0 is
>capturing more "black spaces" in the region I'm looking at.
>
>It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20).
>
>Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the
>region I examined with my samples, it's not a systematic "predictable"
>bias.
>
>Any solution?
>
>-- 
>Yung-Jui "Daniel" Yang, PhD
>Postdoctoral Researcher
>Yale Child Study Center
>New Haven, CT
>(203) 737-5454
>
>
>
>
>
>
>On 3/18/13 6:27 PM, "Matt Glasser"  wrote:
>
>>Do the surfaces look correct in these regions?  You might post some
>>screenshots of subjects who have a big difference between 5.1 and 5.2
>>with
>>the 5.1 and 5.2 white and pial surfaces on volume slices that highlight
>>the difference.  Without this kind of info, its hard to know which was
>>more correct, 5.1 or 5.2.
>>
>>Peace,
>>
>>Matt.
>>
>>On 3/18/13 5:13 PM, "Ritobrato Datta"  wrote:
>>
>>>I concur. I have seen similar results in primary visual cortex from ~40
>>>subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to
>>>1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3.
>>>
>>>Ritobrato Datta, Ph.D.
>>>Post Doctoral Researcher
>>>Department of Neurology
>>>University of Pennsylvania School of Medicine
>>>3rd Floor, Room 312
>>>3710 Hamilton Walk (Goddard Laboratories)
>>>Philadelphia, PA 19104-6241
>>>email - rida...@mail.med.upenn.edu
>>> 
>>>
>>>- Original Message -
>>>From: Daniel Yang 
>>>To: freesurfer@nmr.mgh.harvard.edu
>>>Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT)
>>>Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0
>>>
>>>Dear FreeSurfer Experts,
>>>
>>>I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161
>>>subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in
>>>particular.
>>>
>>>Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in
>>>5.2.0. They are significantly different, t(160) = 56.71.
>>>
>>>The correlation between the two versions is r = .33
>>>
>>>Is this something possible?? I can't see what went wrong in my
>>>procedures.
>>>
>>>Thanks!
>>>Daniel
>>>
>>>--
>>>Yung-Jui "Daniel" Yang, PhD
>>>Postdoctoral Researcher
>>>Yale Child Study Center
>>>New Haven, CT
>>>(203) 737-5454
>>>
>>>___
>>>Freesurfer mailing list
>>>Freesurfer@nmr.mgh.harvard.edu
>>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>>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
>>>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.
>>>
>>
>>
>


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Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

[Bruce Fischl]

We are investigating it. I did fix one thing that you can try if you want - 
give us your hardware/software info and we will send you a new version of 
mris_make_surfaces
Bruce

P.s. you can also upload and we will take a look



On Apr 10, 2013, at 6:11 AM, "Yang, Daniel"  wrote:

> Dear FreeSurfer Experts and Users,
> 
> Did anyone find similar things using FS 5.2 (please see my previous post
> below)? That is, FS 5.2 is including more non-cortical "black spaces"
> within pial surfaces, compared to FS 5.1?
> 
> I'm not interested in nitpicking but I feel this is a rather serious
> issue, so I would like to raise it again before it's completely forgotten.
> 
> At the meantime I keep receiving Emails from people asking me this issue.
> 
> Thanks!
> Daniel
> 
> -- 
> Yung-Jui "Daniel" Yang, PhD
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> (203) 737-5454
> 
> 
> 
> 
> 
> 
> On 3/19/13 7:07 AM, "Yang, Daniel"  wrote:
> 
>> 
>> Posting one of the brains.
>> 
>> https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn
>> 
>> 
>> It seems to me that neither version is perfect; however, 5.2.0 is
>> capturing more "black spaces" in the region I'm looking at.
>> 
>> It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20).
>> 
>> Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the
>> region I examined with my samples, it's not a systematic "predictable"
>> bias.
>> 
>> Any solution?
>> 
>> -- 
>> Yung-Jui "Daniel" Yang, PhD
>> Postdoctoral Researcher
>> Yale Child Study Center
>> New Haven, CT
>> (203) 737-5454
>> 
>> 
>> 
>> 
>> 
>> 
>> On 3/18/13 6:27 PM, "Matt Glasser"  wrote:
>> 
>>> Do the surfaces look correct in these regions?  You might post some
>>> screenshots of subjects who have a big difference between 5.1 and 5.2
>>> with
>>> the 5.1 and 5.2 white and pial surfaces on volume slices that highlight
>>> the difference.  Without this kind of info, its hard to know which was
>>> more correct, 5.1 or 5.2.
>>> 
>>> Peace,
>>> 
>>> Matt.
>>> 
>>> On 3/18/13 5:13 PM, "Ritobrato Datta"  wrote:
>>> 
 I concur. I have seen similar results in primary visual cortex from ~40
 subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to
 1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3.
 
 Ritobrato Datta, Ph.D.
 Post Doctoral Researcher
 Department of Neurology
 University of Pennsylvania School of Medicine
 3rd Floor, Room 312
 3710 Hamilton Walk (Goddard Laboratories)
 Philadelphia, PA 19104-6241
 email - rida...@mail.med.upenn.edu
 
 
 - Original Message -
 From: Daniel Yang 
 To: freesurfer@nmr.mgh.harvard.edu
 Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT)
 Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0
 
 Dear FreeSurfer Experts,
 
 I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161
 subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in
 particular.
 
 Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in
 5.2.0. They are significantly different, t(160) = 56.71.
 
 The correlation between the two versions is r = .33
 
 Is this something possible?? I can't see what went wrong in my
 procedures.
 
 Thanks!
 Daniel
 
 --
 Yung-Jui "Daniel" Yang, PhD
 Postdoctoral Researcher
 Yale Child Study Center
 New Haven, CT
 (203) 737-5454
 
 ___
 Freesurfer mailing list
 Freesurfer@nmr.mgh.harvard.edu
 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
 
 
 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
 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.
 
>>> 
>>> 
>> 
> 
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 

___
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Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

[Pedro Paulo de Magalhães Oliveira Junior]

I have processed more that 600 brains with both versions in the last weeks
and the only difference I'm seeing between version 5.2.0 and 5.1, besides
the obvious new features, is processing time.

Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance.

Besides that there's no visible difference in terms of cortical thickness,
volumes, etc.

If you have access to computer resources to spare you can run recon-all of
both versions in some well known database of images and do a more formal
test.






-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441



On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel wrote:

> Dear FreeSurfer Experts and Users,
>
> Did anyone find similar things using FS 5.2 (please see my previous post
> below)? That is, FS 5.2 is including more non-cortical "black spaces"
> within pial surfaces, compared to FS 5.1?
>
> I'm not interested in nitpicking but I feel this is a rather serious
> issue, so I would like to raise it again before it's completely forgotten.
>
> At the meantime I keep receiving Emails from people asking me this issue.
>
> Thanks!
> Daniel
>
> --
> Yung-Jui "Daniel" Yang, PhD
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> (203) 737-5454
>
>
>
>
>
>
> On 3/19/13 7:07 AM, "Yang, Daniel"  wrote:
>
> >
> >Posting one of the brains.
> >
> >https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn
> >
> >
> >It seems to me that neither version is perfect; however, 5.2.0 is
> >capturing more "black spaces" in the region I'm looking at.
> >
> >It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20).
> >
> >Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the
> >region I examined with my samples, it's not a systematic "predictable"
> >bias.
> >
> >Any solution?
> >
> >--
> >Yung-Jui "Daniel" Yang, PhD
> >Postdoctoral Researcher
> >Yale Child Study Center
> >New Haven, CT
> >(203) 737-5454
> >
> >
> >
> >
> >
> >
> >On 3/18/13 6:27 PM, "Matt Glasser"  wrote:
> >
> >>Do the surfaces look correct in these regions?  You might post some
> >>screenshots of subjects who have a big difference between 5.1 and 5.2
> >>with
> >>the 5.1 and 5.2 white and pial surfaces on volume slices that highlight
> >>the difference.  Without this kind of info, its hard to know which was
> >>more correct, 5.1 or 5.2.
> >>
> >>Peace,
> >>
> >>Matt.
> >>
> >>On 3/18/13 5:13 PM, "Ritobrato Datta" 
> wrote:
> >>
> >>>I concur. I have seen similar results in primary visual cortex from ~40
> >>>subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to
> >>>1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3.
> >>>
> >>>Ritobrato Datta, Ph.D.
> >>>Post Doctoral Researcher
> >>>Department of Neurology
> >>>University of Pennsylvania School of Medicine
> >>>3rd Floor, Room 312
> >>>3710 Hamilton Walk (Goddard Laboratories)
> >>>Philadelphia, PA 19104-6241
> >>>email - rida...@mail.med.upenn.edu
> >>>
> >>>
> >>>- Original Message -
> >>>From: Daniel Yang 
> >>>To: freesurfer@nmr.mgh.harvard.edu
> >>>Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT)
> >>>Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0
> >>>
> >>>Dear FreeSurfer Experts,
> >>>
> >>>I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161
> >>>subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in
> >>>particular.
> >>>
> >>>Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in
> >>>5.2.0. They are significantly different, t(160) = 56.71.
> >>>
> >>>The correlation between the two versions is r = .33
> >>>
> >>>Is this something possible?? I can't see what went wrong in my
> >>>procedures.
> >>>
> >>>Thanks!
> >>>Daniel
> >>>
> >>>--
> >>>Yung-Jui "Daniel" Yang, PhD
> >>>Postdoctoral Researcher
> >>>Yale Child Study Center
> >>>New Haven, CT
> >>>(203) 737-5454
> >>>
> >>>___
> >>>Freesurfer mailing list
> >>>Freesurfer@nmr.mgh.harvard.edu
> >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
> >>>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
> >>>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.
> >>>
> >>
> >>
> >
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
___
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Freesurfer@nmr.m

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

[Bruce Fischl]

Hi PPJ
That's exactly what we are doing. Good to hear its stable for you
Bruce



On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalhães Oliveira 
Junior wrote:

> I have processed more that 600 brains with both versions in the last weeks 
> and the only difference I'm seeing between version 5.2.0 and 5.1, besides the 
> obvious new features, is processing time.
> 
> Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance.
> 
> Besides that there's no visible difference in terms of cortical thickness, 
> volumes, etc.
> 
> If you have access to computer resources to spare you can run recon-all of 
> both versions in some well known database of images and do a more formal test.
> 
> 
> 
> 
> 
> 
> -
> Pedro Paulo de Magalhães Oliveira Junior
> Netfilter & SpeedComm Telecom
> -- www.netfilter.com.br
> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
> 
> 
> 
> On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel  wrote:
> Dear FreeSurfer Experts and Users,
> 
> Did anyone find similar things using FS 5.2 (please see my previous post
> below)? That is, FS 5.2 is including more non-cortical "black spaces"
> within pial surfaces, compared to FS 5.1?
> 
> I'm not interested in nitpicking but I feel this is a rather serious
> issue, so I would like to raise it again before it's completely forgotten.
> 
> At the meantime I keep receiving Emails from people asking me this issue.
> 
> Thanks!
> Daniel
> 
> --
> Yung-Jui "Daniel" Yang, PhD
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> (203) 737-5454
> 
> 
> 
> 
> 
> 
> On 3/19/13 7:07 AM, "Yang, Daniel"  wrote:
> 
> >
> >Posting one of the brains.
> >
> >https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn
> >
> >
> >It seems to me that neither version is perfect; however, 5.2.0 is
> >capturing more "black spaces" in the region I'm looking at.
> >
> >It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20).
> >
> >Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the
> >region I examined with my samples, it's not a systematic "predictable"
> >bias.
> >
> >Any solution?
> >
> >--
> >Yung-Jui "Daniel" Yang, PhD
> >Postdoctoral Researcher
> >Yale Child Study Center
> >New Haven, CT
> >(203) 737-5454
> >
> >
> >
> >
> >
> >
> >On 3/18/13 6:27 PM, "Matt Glasser"  wrote:
> >
> >>Do the surfaces look correct in these regions?  You might post some
> >>screenshots of subjects who have a big difference between 5.1 and 5.2
> >>with
> >>the 5.1 and 5.2 white and pial surfaces on volume slices that highlight
> >>the difference.  Without this kind of info, its hard to know which was
> >>more correct, 5.1 or 5.2.
> >>
> >>Peace,
> >>
> >>Matt.
> >>
> >>On 3/18/13 5:13 PM, "Ritobrato Datta"  wrote:
> >>
> >>>I concur. I have seen similar results in primary visual cortex from ~40
> >>>subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to
> >>>1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3.
> >>>
> >>>Ritobrato Datta, Ph.D.
> >>>Post Doctoral Researcher
> >>>Department of Neurology
> >>>University of Pennsylvania School of Medicine
> >>>3rd Floor, Room 312
> >>>3710 Hamilton Walk (Goddard Laboratories)
> >>>Philadelphia, PA 19104-6241
> >>>email - rida...@mail.med.upenn.edu
> >>>
> >>>
> >>>- Original Message -
> >>>From: Daniel Yang 
> >>>To: freesurfer@nmr.mgh.harvard.edu
> >>>Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT)
> >>>Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0
> >>>
> >>>Dear FreeSurfer Experts,
> >>>
> >>>I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161
> >>>subjects, and I'm interested in rh_superior_temporal_sulcus_thickness in
> >>>particular.
> >>>
> >>>Previously, the mean thickness is 2.24 mm in 5.1.0; now it is 3.28 mm in
> >>>5.2.0. They are significantly different, t(160) = 56.71.
> >>>
> >>>The correlation between the two versions is r = .33
> >>>
> >>>Is this something possible?? I can't see what went wrong in my
> >>>procedures.
> >>>
> >>>Thanks!
> >>>Daniel
> >>>
> >>>--
> >>>Yung-Jui "Daniel" Yang, PhD
> >>>Postdoctoral Researcher
> >>>Yale Child Study Center
> >>>New Haven, CT
> >>>(203) 737-5454
> >>>
> >>>___
> >>>Freesurfer mailing list
> >>>Freesurfer@nmr.mgh.harvard.edu
> >>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >>>
> >>>
> >>>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
> >>>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.
> >>>
> >>
> >>
> >
> 
> 
> ___

Re: [Freesurfer] tracula FS 5.2

[Anastasia Yendiki]

Hi Daria - How much memory does your system have? Were you ever able to 
run trac-all from the 5.1 version on the same system?

a.y

On Wed, 10 Apr 2013, Antonenko, Daria wrote:

> Hi FS experts,
> I tried to run Tracula with the new FS 5.2 release and came across memory 
> allocation problems in the preprocessing step and would appreciate some 
> advice on solving them:
>
> MRIalloc(218, 182, 182): could not allocate 158704 bytes for 98th slice
> Cannot allocate memory
> Linux daria-Think 3.5.0-17-generic #28-Ubuntu SMP Tue Oct 9 19:32:08 UTC 2012 
> i686 i686 i686 GNU/Linux
> trac-preproc exited with ERRORS at Tue Apr  9 22:21:43 CEST 2013
>
> I attached the log-file.
> Let me know if you need further information about my system.
> Thank you in advance, Daria
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Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

[Yang, Daniel]

Hi PPJ,

Thanks! It looks interesting. I also found FS 5.2 is faster. Is there any 
chance you could also provide the cortical thickness of the 2009 atlas (e.g., 
rh)?

I will take a look into the aseg.volume in my data too.

Best,
Daniel


--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454

From: Pedro Paulo de Magalhães Oliveira Junior 
mailto:p...@netfilter.com.br>>
Date: Wednesday, April 10, 2013 10:49 AM
To: Bruce Fischl mailto:fis...@nmr.mgh.harvard.edu>>
Cc: Daniel Yang mailto:yung-jui.y...@yale.edu>>, 
"freesurfer@nmr.mgh.harvard.edu" 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

You'll find attached some preliminary data of the comparison we did among 
versions.

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441



On Wed, Apr 10, 2013 at 10:42 AM, Bruce Fischl 
mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi PPJ
That's exactly what we are doing. Good to hear its stable for you
Bruce



On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalhães Oliveira 
Juniormailto:p...@netfilter.com.br>> wrote:

I have processed more that 600 brains with both versions in the last weeks and 
the only difference I'm seeing between version 5.2.0 and 5.1, besides the 
obvious new features, is processing time.

Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance.

Besides that there's no visible difference in terms of cortical thickness, 
volumes, etc.

If you have access to computer resources to spare you can run recon-all of both 
versions in some well known database of images and do a more formal test.






-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441



On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel 
mailto:yung-jui.y...@yale.edu>> wrote:
Dear FreeSurfer Experts and Users,

Did anyone find similar things using FS 5.2 (please see my previous post
below)? That is, FS 5.2 is including more non-cortical "black spaces"
within pial surfaces, compared to FS 5.1?

I'm not interested in nitpicking but I feel this is a rather serious
issue, so I would like to raise it again before it's completely forgotten.

At the meantime I keep receiving Emails from people asking me this issue.

Thanks!
Daniel

--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454






On 3/19/13 7:07 AM, "Yang, Daniel" 
mailto:yung-jui.y...@yale.edu>> wrote:

>
>Posting one of the brains.
>
>https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn
>
>
>It seems to me that neither version is perfect; however, 5.2.0 is
>capturing more "black spaces" in the region I'm looking at.
>
>It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20).
>
>Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the
>region I examined with my samples, it's not a systematic "predictable"
>bias.
>
>Any solution?
>
>--
>Yung-Jui "Daniel" Yang, PhD
>Postdoctoral Researcher
>Yale Child Study Center
>New Haven, CT
>(203) 737-5454
>
>
>
>
>
>
>On 3/18/13 6:27 PM, "Matt Glasser" mailto:m...@ma-tea.com>> 
>wrote:
>
>>Do the surfaces look correct in these regions?  You might post some
>>screenshots of subjects who have a big difference between 5.1 and 5.2
>>with
>>the 5.1 and 5.2 white and pial surfaces on volume slices that highlight
>>the difference.  Without this kind of info, its hard to know which was
>>more correct, 5.1 or 5.2.
>>
>>Peace,
>>
>>Matt.
>>
>>On 3/18/13 5:13 PM, "Ritobrato Datta" 
>>mailto:rida...@mail.med.upenn.edu>> wrote:
>>
>>>I concur. I have seen similar results in primary visual cortex from ~40
>>>subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to
>>>1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3.
>>>
>>>Ritobrato Datta, Ph.D.
>>>Post Doctoral Researcher
>>>Department of Neurology
>>>University of Pennsylvania School of Medicine
>>>3rd Floor, Room 312
>>>3710 Hamilton Walk (Goddard Laboratories)
>>>Philadelphia, PA 19104-6241
>>>email - rida...@mail.med.upenn.edu
>>>
>>>
>>>- Original Message -
>>>From: Daniel Yang mailto:yung-jui.y...@yale.edu>>
>>>To: freesurfer@nmr.mgh.harvard.edu
>>>Sent: Mon, 18 Mar 2013 17:44:44 -0400 (EDT)
>>>Subject: [Freesurfer] Very different results between 5.1.0 and 5.2.0
>>>
>>>Dear FreeSurfer Experts,
>>>
>>>I ran FreeSurfer 5.1.0 and FreeSurfer 5.2.0 on identical set of 161
>>>subjects, and I'm interested in rh_superior_temporal_sulcu

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

[Pedro Paulo de Magalhães Oliveira Junior]

Ok, I'll try to put together a stat from aparc too.

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441



On Wed, Apr 10, 2013 at 12:04 PM, Yang, Daniel wrote:

>  Hi PPJ,
>
>  Thanks! It looks interesting. I also found FS 5.2 is faster. Is there
> any chance you could also provide the cortical thickness of the 2009 atlas
> (e.g., rh)?
>
>  I will take a look into the aseg.volume in my data too.
>
>  Best,
> Daniel
>
>
>  --
>  Yung-Jui "Daniel" Yang, PhD
> Postdoctoral Researcher
> Yale Child Study Center
> New Haven, CT
> (203) 737-5454
>
>   From: Pedro Paulo de Magalhães Oliveira Junior 
> Date: Wednesday, April 10, 2013 10:49 AM
> To: Bruce Fischl 
> Cc: Daniel Yang , "freesurfer@nmr.mgh.harvard.edu"
> 
> Subject: Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0
>
>   You'll find attached some preliminary data of the comparison we did
> among versions.
>
> -
> Pedro Paulo de Magalhães Oliveira Junior
> Netfilter & SpeedComm Telecom
> -- www.netfilter.com.br
> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
>
>
>
> On Wed, Apr 10, 2013 at 10:42 AM, Bruce Fischl  > wrote:
>
>>  Hi PPJ
>> That's exactly what we are doing. Good to hear its stable for you
>>  Bruce
>>
>>
>>
>> On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalhães Oliveira Junior<
>> p...@netfilter.com.br> wrote:
>>
>>   I have processed more that 600 brains with both versions in the last
>> weeks and the only difference I'm seeing between version 5.2.0 and 5.1,
>> besides the obvious new features, is processing time.
>>
>>  Version 5.2 is 10% faster than 5.1 in an Amazon EC2 instance.
>>
>>  Besides that there's no visible difference in terms of cortical
>> thickness, volumes, etc.
>>
>>  If you have access to computer resources to spare you can run recon-all
>> of both versions in some well known database of images and do a more formal
>> test.
>>
>>
>>
>>
>>
>>
>> -
>> Pedro Paulo de Magalhães Oliveira Junior
>> Netfilter & SpeedComm Telecom
>> -- www.netfilter.com.br
>> -- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
>>
>>
>>
>> On Wed, Apr 10, 2013 at 8:11 AM, Yang, Daniel wrote:
>>
>>> Dear FreeSurfer Experts and Users,
>>>
>>> Did anyone find similar things using FS 5.2 (please see my previous post
>>> below)? That is, FS 5.2 is including more non-cortical "black spaces"
>>> within pial surfaces, compared to FS 5.1?
>>>
>>> I'm not interested in nitpicking but I feel this is a rather serious
>>> issue, so I would like to raise it again before it's completely
>>> forgotten.
>>>
>>> At the meantime I keep receiving Emails from people asking me this issue.
>>>
>>> Thanks!
>>> Daniel
>>>
>>> --
>>> Yung-Jui "Daniel" Yang, PhD
>>> Postdoctoral Researcher
>>> Yale Child Study Center
>>> New Haven, CT
>>> (203) 737-5454
>>>
>>>
>>>
>>>
>>>
>>>
>>>  On 3/19/13 7:07 AM, "Yang, Daniel"  wrote:
>>>
>>> >
>>> >Posting one of the brains.
>>> >
>>> >https://yalesurvey.qualtrics.com/SE/?SID=SV_ddwW7I9yMQuCtPn
>>> >
>>> >
>>> >It seems to me that neither version is perfect; however, 5.2.0 is
>>> >capturing more "black spaces" in the region I'm looking at.
>>> >
>>> >It's in the right hemisphere, TAL coordinate about ~ (44, -46, 20).
>>> >
>>> >Given that the correlation between 5.1.0 and 5.2.0 is r = .33 in the
>>> >region I examined with my samples, it's not a systematic "predictable"
>>> >bias.
>>> >
>>> >Any solution?
>>> >
>>> >--
>>> >Yung-Jui "Daniel" Yang, PhD
>>> >Postdoctoral Researcher
>>> >Yale Child Study Center
>>> >New Haven, CT
>>> >(203) 737-5454
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >
>>> >On 3/18/13 6:27 PM, "Matt Glasser"  wrote:
>>> >
>>> >>Do the surfaces look correct in these regions?  You might post some
>>> >>screenshots of subjects who have a big difference between 5.1 and 5.2
>>> >>with
>>> >>the 5.1 and 5.2 white and pial surfaces on volume slices that highlight
>>> >>the difference.  Without this kind of info, its hard to know which was
>>> >>more correct, 5.1 or 5.2.
>>> >>
>>> >>Peace,
>>> >>
>>> >>Matt.
>>> >>
>>> >>On 3/18/13 5:13 PM, "Ritobrato Datta" 
>>> wrote:
>>> >>
>>> >>>I concur. I have seen similar results in primary visual cortex from
>>> ~40
>>> >>>subjects. While fs 5.1 estimated mean thickness in the range of 1.5 to
>>> >>>1.9 in V1, fs 5.2 is giving me V1 thickness in the range of 2 to 2.3.
>>> >>>
>>> >>>Ritobrato Datta, Ph.D.
>>> >>>Post Doctoral Researcher
>>> >>>Department of Neurology
>>> >>>University of Pennsylvania School of Medicine
>>> >>>3rd Floor, Room 312
>>> >>>3710 Hamilton Walk (Goddard Laboratories)
>>> >>>Philadelphia, PA 19104-6241
>>> >>>email - rida...@mail.med.upenn.edu
>>> >>>
>>> >>>
>>> >>>- Original Mes

[Freesurfer] freesurfer 5.1 vs 5.2

[Gonzalo Rojas Costa]

Hi:

  How can install version 5.2 in a computer without uninstalling
version 5.1 ?...

  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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Re: [Freesurfer] freesurfer 5.1 vs 5.2

[Louis Nicholas Vinke]

Hi Gonzalo,
You can untar the 5.2 files in a separate directory, and then just source 
the SetUpFreeSurfer.csh from the directory of the version of FreeSurfer 
you want to use.  You can run 'which recon-all' to check which version you 
have sourced.

-Louis

On Wed, 10 Apr 2013, Gonzalo Rojas Costa wrote:


Hi:

 How can install version 5.2 in a computer without uninstalling
version 5.1 ?...

 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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[Freesurfer] Finding adjacent vertices/labels

[Chris McNorgan]

Hello Freesurfers,

I was wondering if there is information embedded in the annotation/label 
files that could be used to determine whether two labels represent 
anatomically adjacent regions? For example, I have parcellated a bunch 
of participants using connectomemapper into 1000 ROIs. I was just now 
reading Power et al. (2011), who looked at functional connectivity, but 
specifically excluded connections between spheroid ROIs that were less 
than 20mm apart. Analogously, I might wish to exclude connections 
between adjacent labels, but it seemed that manually creating an 
adjacency matrix for 1000 regions would be impractical, and a good 
candidate for an automated approach. I'm just not clear what information 
such an approach might have to work with. Can the adjacency between two 
vertices be determined based on their values? If so, one approach might be:

for each pair of labels (A,B):
get set of vertices within A
get set of vertices within B
 for each vertex pair (Ai, Bj)
 if Ai and Bj are adjacent, stop, and mark A and B as adjacent

Cheers,
Chris
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[Freesurfer] merging dti data

[Jon Wieser]

we captured some dti data. there were 2 runs. we acquired in the axial plane, 
2mm slice thickness the first run captured the lower half of the brain, slice 
locations: I56-S20, and the second run captured the upper half of the brain 
S16-S92. i have made briks from each of these runs.
I can convert the briks to nifti files
I want to merge the nifti files together to analyze the data in tracula

In the past i have merged data from two dti runs, but each run have covered the 
entire brain,  with the following commands

mri_convert MJ0001dti1+orig.BRIK MJ0001dti1.nii.gz
mri_convert MJ0001dti2+orig.BRIK MJ0001dti2.nii.gz
mri_concat --i MJ0001dti1.nii.gz MJ0001dti2.nii.gz --o MJ0001dti12.nii.gz


would it work to concat the two half brain niftis into one file and analyze 
that with tracula?
(I will concat the bvec and bvals files too)
would this cause problems doing it this way?
Thanks
Jon

-- 
Jon Wieser
Research Specialist
UW-Milwaukee
Psychology Department, Pearse Hall Rm 366
2441 East Hartford Ave
Milwaukee, WI 53211
Phone: 414-229-7145
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Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

[Nick Schmansky]

Daniel,

We're repeating our paired-analysis of thickness measures between 5.1
and 5.2.  In the meantime, to check for correctness, open the
brain.finalsurfs.mgz file with the surfaces overlayed, and check the
intensity value of the voxels which appear to be non-cortical 'black
spaces', relative to neighboring gm voxels.  ignore the aseg.mgz gm
voxels, as those are not accurate (ie, dont load aseg.mgz when
inspecting surfaces, or at least turn if off when inspecting gm
regionsits still handy to see where hippocampus sits).  

Nick


On Wed, 2013-04-10 at 11:11 +, Yang, Daniel wrote:
> Dear FreeSurfer Experts and Users,
> 
> Did anyone find similar things using FS 5.2 (please see my previous post
> below)? That is, FS 5.2 is including more non-cortical "black spaces"
> within pial surfaces, compared to FS 5.1?
> 
> I'm not interested in nitpicking but I feel this is a rather serious
> issue, so I would like to raise it again before it's completely forgotten.
> 
> At the meantime I keep receiving Emails from people asking me this issue.
> 
> Thanks!
> Daniel
> 


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[Freesurfer] FS-FAST motion correction / register

[preciado]

One of my subjects exhibited motion during the middle time point of one
the functional scans. FS-FAST then reads all other time points as having a
significant amount of motion because the subject was out of place during
the point that is marked as the origin. Is there some way that I can set a
different time point? I am worried that there will be some over-correction
for motion that isn't really there because my middle time point it out of
an anomaly.


-Ronny



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Re: [Freesurfer] FS-FAST motion correction / register

[Douglas N Greve]

Hi Ronny, the time point used to as the template is hard-coded to be the 
middle time point. If this is just the case for one subject, a silly but 
simple solution is to remove the last two time points from the time 
series. This will cause the "middle" time point to shift to an earlier 
time point. Would this work?
doug



On 04/10/2013 01:48 PM, preci...@nmr.mgh.harvard.edu wrote:
> One of my subjects exhibited motion during the middle time point of one
> the functional scans. FS-FAST then reads all other time points as having a
> significant amount of motion because the subject was out of place during
> the point that is marked as the origin. Is there some way that I can set a
> different time point? I am worried that there will be some over-correction
> for motion that isn't really there because my middle time point it out of
> an anomaly.
>
>
> -Ronny
>
>
>
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] FS-FAST motion correction / register

[preciado]

If anything I was thinking of removing the first two time points, as those
are going to get nixed anyway. I was hoping it wouldn't come to that but i
f that's the only way...

-Ronny

> Hi Ronny, the time point used to as the template is hard-coded to be the
> middle time point. If this is just the case for one subject, a silly but
> simple solution is to remove the last two time points from the time
> series. This will cause the "middle" time point to shift to an earlier
> time point. Would this work?
> doug
>
>
>
> On 04/10/2013 01:48 PM, preci...@nmr.mgh.harvard.edu wrote:
>> One of my subjects exhibited motion during the middle time point of one
>> the functional scans. FS-FAST then reads all other time points as having
>> a
>> significant amount of motion because the subject was out of place during
>> the point that is marked as the origin. Is there some way that I can set
>> a
>> different time point? I am worried that there will be some
>> over-correction
>> for motion that isn't really there because my middle time point it out
>> of
>> an anomaly.
>>
>>
>> -Ronny
>>
>>
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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>
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>
>
>

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Re: [Freesurfer] FS-FAST motion correction / register

[Douglas N Greve]

You can do that, but you'll need to change the paradigm file to reflect 
the new timing.
doug
On 04/10/2013 01:57 PM, preci...@nmr.mgh.harvard.edu wrote:
> If anything I was thinking of removing the first two time points, as those
> are going to get nixed anyway. I was hoping it wouldn't come to that but i
> f that's the only way...
>
> -Ronny
>
>> Hi Ronny, the time point used to as the template is hard-coded to be the
>> middle time point. If this is just the case for one subject, a silly but
>> simple solution is to remove the last two time points from the time
>> series. This will cause the "middle" time point to shift to an earlier
>> time point. Would this work?
>> doug
>>
>>
>>
>> On 04/10/2013 01:48 PM, preci...@nmr.mgh.harvard.edu wrote:
>>> One of my subjects exhibited motion during the middle time point of one
>>> the functional scans. FS-FAST then reads all other time points as having
>>> a
>>> significant amount of motion because the subject was out of place during
>>> the point that is marked as the origin. Is there some way that I can set
>>> a
>>> different time point? I am worried that there will be some
>>> over-correction
>>> for motion that isn't really there because my middle time point it out
>>> of
>>> an anomaly.
>>>
>>>
>>> -Ronny
>>>
>>>
>>>
>>>
>>>
>>> ___
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] Comparing HRF undershoots between conditions

[SHAHIN NASR]

Hi,
 I want to generate a map to show the significant difference between
HRF undershoot  (negative peak of activity) between two conditions
independent from the positive peak. Is there anyway, to generate this map?

P.S.: Please note that I need a map and not a time course graph.


-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] Comparing HRF undershoots between conditions

[Douglas N Greve]

Hi Shahin, there are several ways that you could do it. The one that 
immediately comes to mind is to use an FIR and then test for a 
difference at a particular post stimulus time point.
doug



On 04/10/2013 03:54 PM, SHAHIN NASR wrote:
> Hi,
>  I want to generate a map to show the significant difference 
> between HRF undershoot  (negative peak of activity) between two 
> conditions independent from the positive peak. Is there anyway, to 
> generate this map?
>
> P.S.: Please note that I need a map and not a time course graph.
>
>
> -- 
> Shahin Nasr
>
> PhD in Cognitive Neuroscience
> Martinos Imaging Center, MGH
> Harvard Medical School

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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[Freesurfer] Fwd: Comparing HRF undershoots between conditions

[SHAHIN NASR]

That's the problem Doug. I have already generated the FIR model but how can
I show the sig MAP for one "particulat time point".  What are the other
ways?


On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
wrote:

> Hi Shahin, there are several ways that you could do it. The one that
> immediately comes to mind is to use an FIR and then test for a difference
> at a particular post stimulus time point.
> doug
>
>
>
>
> On 04/10/2013 03:54 PM, SHAHIN NASR wrote:
>
>> Hi,
>>  I want to generate a map to show the significant difference between
>> HRF undershoot  (negative peak of activity) between two conditions
>> independent from the positive peak. Is there anyway, to generate this map?
>>
>> P.S.: Please note that I need a map and not a time course graph.
>>
>>
>> --
>> Shahin Nasr
>>
>> PhD in Cognitive Neuroscience
>> Martinos Imaging Center, MGH
>> Harvard Medical School
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: 
> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
> FileDrop: 
> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
> greve/ 
>
>
>


-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School



-- 
Shahin Nasr

PhD in Cognitive Neuroscience
Martinos Imaging Center, MGH
Harvard Medical School
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Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

[shahin]

I think I figured it out but I want to double check. I am generating
group-average map for my subjects using isxconcat-sess command which
generates ces maps for each time frame. I think these maps are what I
wanted. Right?
   If you still have other solutions that you think may generate more
reliable results, I am eager to know. For instance, is there anyway to
fit a model as we do for spmhrf or fslhrf, but just for the negative
peak?

Regards

> That's the problem Doug. I have already generated the FIR model but how
> can
> I show the sig MAP for one "particulat time point".  What are the other
> ways?
>
>
> On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
> wrote:
>
>> Hi Shahin, there are several ways that you could do it. The one that
>> immediately comes to mind is to use an FIR and then test for a
>> difference
>> at a particular post stimulus time point.
>> doug
>>
>>
>>
>>
>> On 04/10/2013 03:54 PM, SHAHIN NASR wrote:
>>
>>> Hi,
>>>  I want to generate a map to show the significant difference
>>> between
>>> HRF undershoot  (negative peak of activity) between two conditions
>>> independent from the positive peak. Is there anyway, to generate this
>>> map?
>>>
>>> P.S.: Please note that I need a map and not a time course graph.
>>>
>>>
>>> --
>>> Shahin Nasr
>>>
>>> PhD in Cognitive Neuroscience
>>> Martinos Imaging Center, MGH
>>> Harvard Medical School
>>>
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs:
>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
>> FileDrop:
>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
>> greve/ 
>>
>>
>>
>
>
> --
> Shahin Nasr
>
> PhD in Cognitive Neuroscience
> Martinos Imaging Center, MGH
> Harvard Medical School
>
>
>
> --
> Shahin Nasr
>
> PhD in Cognitive Neuroscience
> Martinos Imaging Center, MGH
> Harvard Medical School
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] Rejoindre mon réseau sur LinkedIn

[Sima Chalavi]

LinkedIn





Sima Chalavi souhaite se connecter à vous sur LinkedIn :
  

--

Je vous invite à faire partie de mon réseau professionnel en ligne sur le site 
LinkedIn.

Accepter l'invitation de Sima Chalavi
http://www.linkedin.com/e/-qq80um-hfd0ug20-5o/qaAr-Z_86TRZ5lXG-dA9kZQ49qSe59qYFaT9QmQ47Ub3yw/blk/I427517471_65/3wOtCVFbmdxnSVFbm8JrnpKqlZJrmZzbmNJpjRQnOpBtn9QfmhBt71BoSd1p65Lr6lOfPkSnP4Td3sNdjsOd4ALen1Fsmx4en4Ldz0TcPAPdjoPcz4LrCBxbOYWrSlI/eml-comm_invm-b-in_ac-inv28/?hs=false&tok=1BZKYjafcQj5I1

Voir le profil de Sima Chalavi
http://www.linkedin.com/e/-qq80um-hfd0ug20-5o/rso/245935493/G7CW/name/66471168_I427517471_65/?hs=false&tok=3vNr3vrw4Qj5I1
--
Vous recevez des invitations par e-mail.


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Re: [Freesurfer] Comparing HRF undershoots between conditions

[Douglas N Greve]

If you run tkmedit-sess, then open the overlay configuration window, 
then advance the time point to the delay you want. Otherwise, you can 
create a contrast where you just look at the delay you want. To do this, 
run mkcontrast-sess with -setwdelays and specify 0 for all delays and 1 
for the delay you want to see.

doug


On 04/10/2013 04:15 PM, SHAHIN NASR wrote:
> That's the problem Doug. I have already generated the FIR model but 
> how can I show the sig MAP for one "particulat time point".  What are 
> the other ways?
>
>
> On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> Hi Shahin, there are several ways that you could do it. The one
> that immediately comes to mind is to use an FIR and then test for
> a difference at a particular post stimulus time point.
> doug
>
>
>
>
> On 04/10/2013 03:54 PM, SHAHIN NASR wrote:
>
> Hi,
>  I want to generate a map to show the significant
> difference between HRF undershoot  (negative peak of activity)
> between two conditions independent from the positive peak. Is
> there anyway, to generate this map?
>
> P.S.: Please note that I need a map and not a time course graph.
>
>
> -- 
> Shahin Nasr
>
> PhD in Cognitive Neuroscience
> Martinos Imaging Center, MGH
> Harvard Medical School
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu 
> Phone Number: 617-724-2358 
> Fax: 617-726-7422 
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> 
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
>
>
> -- 
> Shahin Nasr
>
> PhD in Cognitive Neuroscience
> Martinos Imaging Center, MGH
> Harvard Medical School

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

[Douglas N Greve]

yes, that is what you want. The only other way that comes to mind is to 
model each event type as two event types one delayed relative to the 
other. Then model the responseto each as a gamma. If the delay is right, 
then the first gamma should model the main positive response and the 
second gamma will model the negative response. both will be independent 
from the other.

doug

On 04/10/2013 05:00 PM, sha...@nmr.mgh.harvard.edu wrote:
> I think I figured it out but I want to double check. I am generating
> group-average map for my subjects using isxconcat-sess command which
> generates ces maps for each time frame. I think these maps are what I
> wanted. Right?
> If you still have other solutions that you think may generate more
> reliable results, I am eager to know. For instance, is there anyway to
> fit a model as we do for spmhrf or fslhrf, but just for the negative
> peak?
>
> Regards
>
>> That's the problem Doug. I have already generated the FIR model but how
>> can
>> I show the sig MAP for one "particulat time point".  What are the other
>> ways?
>>
>>
>> On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
>> wrote:
>>
>>> Hi Shahin, there are several ways that you could do it. The one that
>>> immediately comes to mind is to use an FIR and then test for a
>>> difference
>>> at a particular post stimulus time point.
>>> doug
>>>
>>>
>>>
>>>
>>> On 04/10/2013 03:54 PM, SHAHIN NASR wrote:
>>>
 Hi,
   I want to generate a map to show the significant difference
 between
 HRF undershoot  (negative peak of activity) between two conditions
 independent from the positive peak. Is there anyway, to generate this
 map?

 P.S.: Please note that I need a map and not a time course graph.


 --
 Shahin Nasr

 PhD in Cognitive Neuroscience
 Martinos Imaging Center, MGH
 Harvard Medical School

>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>>
>>> Bugs:
>>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
>>> FileDrop:
>>> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
>>> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
>>> greve/ 
>>>
>>>
>>>
>>
>> --
>> Shahin Nasr
>>
>> PhD in Cognitive Neuroscience
>> Martinos Imaging Center, MGH
>> Harvard Medical School
>>
>>
>>
>> --
>> Shahin Nasr
>>
>> PhD in Cognitive Neuroscience
>> Martinos Imaging Center, MGH
>> Harvard Medical School
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Finding adjacent vertices/labels

[Bruce Fischl]

Hi Chris

the easiest way would be to load the surfaces and parcellation in in matlab 
and look for adjacency that way

Bruce
On Wed, 10 Apr 2013, Chris McNorgan wrote:

> Hello Freesurfers,
>
> I was wondering if there is information embedded in the annotation/label
> files that could be used to determine whether two labels represent
> anatomically adjacent regions? For example, I have parcellated a bunch
> of participants using connectomemapper into 1000 ROIs. I was just now
> reading Power et al. (2011), who looked at functional connectivity, but
> specifically excluded connections between spheroid ROIs that were less
> than 20mm apart. Analogously, I might wish to exclude connections
> between adjacent labels, but it seemed that manually creating an
> adjacency matrix for 1000 regions would be impractical, and a good
> candidate for an automated approach. I'm just not clear what information
> such an approach might have to work with. Can the adjacency between two
> vertices be determined based on their values? If so, one approach might be:
>
> for each pair of labels (A,B):
>get set of vertices within A
>get set of vertices within B
> for each vertex pair (Ai, Bj)
> if Ai and Bj are adjacent, stop, and mark A and B as adjacent
>
> Cheers,
> Chris
> ___
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>
>
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Re: [Freesurfer] merging dti data

[Douglas Greve]

Hi Jon, I don't know how to make this work, but I'm sure that those 
commands will not do it. Sorry:(
doug




On 4/10/13 1:13 PM, Jon Wieser wrote:
> we captured some dti data. there were 2 runs. we acquired in the axial plane, 
> 2mm slice thickness the first run captured the lower half of the brain, slice 
> locations: I56-S20, and the second run captured the upper half of the brain 
> S16-S92. i have made briks from each of these runs.
> I can convert the briks to nifti files
> I want to merge the nifti files together to analyze the data in tracula
>
> In the past i have merged data from two dti runs, but each run have covered 
> the entire brain,  with the following commands
>
> mri_convert MJ0001dti1+orig.BRIK MJ0001dti1.nii.gz
> mri_convert MJ0001dti2+orig.BRIK MJ0001dti2.nii.gz
> mri_concat --i MJ0001dti1.nii.gz MJ0001dti2.nii.gz --o MJ0001dti12.nii.gz
>
>
> would it work to concat the two half brain niftis into one file and analyze 
> that with tracula?
> (I will concat the bvec and bvals files too)
> would this cause problems doing it this way?
> Thanks
> Jon
>

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Re: [Freesurfer] Fwd: Comparing HRF undershoots between conditions

[SHAHIN NASR]

Sorry that I keep on asking questions but I want to know if using a model
can significantly increase the chance of getting a significant response.
  As far as I see for the positive peak, when I use a model (e.g. gamma
model or spmhrf), I see a more significant response compared to when I use
the FIR model. Is it correct? If true, then the same might be correct for
the negative peak.

P.S.: To be more clear, I am talking about the response maps relative to
the baseline.
On Apr 10, 2013 6:46 PM, "Douglas N Greve" 
wrote:

>
> yes, that is what you want. The only other way that comes to mind is to
> model each event type as two event types one delayed relative to the other.
> Then model the responseto each as a gamma. If the delay is right, then the
> first gamma should model the main positive response and the second gamma
> will model the negative response. both will be independent from the other.
>
> doug
>
> On 04/10/2013 05:00 PM, sha...@nmr.mgh.harvard.edu wrote:
>
>> I think I figured it out but I want to double check. I am generating
>> group-average map for my subjects using isxconcat-sess command which
>> generates ces maps for each time frame. I think these maps are what I
>> wanted. Right?
>> If you still have other solutions that you think may generate more
>> reliable results, I am eager to know. For instance, is there anyway to
>> fit a model as we do for spmhrf or fslhrf, but just for the negative
>> peak?
>>
>> Regards
>>
>>  That's the problem Doug. I have already generated the FIR model but how
>>> can
>>> I show the sig MAP for one "particulat time point".  What are the other
>>> ways?
>>>
>>>
>>> On Wed, Apr 10, 2013 at 4:05 PM, Douglas N Greve
>>> **wrote:
>>>
>>>  Hi Shahin, there are several ways that you could do it. The one that
 immediately comes to mind is to use an FIR and then test for a
 difference
 at a particular post stimulus time point.
 doug




 On 04/10/2013 03:54 PM, SHAHIN NASR wrote:

  Hi,
>   I want to generate a map to show the significant difference
> between
> HRF undershoot  (negative peak of activity) between two conditions
> independent from the positive peak. Is there anyway, to generate this
> map?
>
> P.S.: Please note that I need a map and not a time course graph.
>
>
> --
> Shahin Nasr
>
> PhD in Cognitive Neuroscience
> Martinos Imaging Center, MGH
> Harvard Medical School
>
>  --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422

 Bugs:
 surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 
 >
 FileDrop:
 www.nmr.mgh.harvard.edu/facility/filedrop/index.html
 http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
 >
 Outgoing: ftp://surfer.nmr.mgh.harvard.***
 *edu/transfer/outgoing/flat/**
 greve/ 
 >




>>> --
>>> Shahin Nasr
>>>
>>> PhD in Cognitive Neuroscience
>>> Martinos Imaging Center, MGH
>>> Harvard Medical School
>>>
>>>
>>>
>>> --
>>> Shahin Nasr
>>>
>>> PhD in Cognitive Neuroscience
>>> Martinos Imaging Center, MGH
>>> Harvard Medical School
>>> __**_
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
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>>>
>>
>>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: 
> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting
> FileDrop: 
> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**
> greve/ 
>
>
>
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