------------------------------
Message: 9
Date: Thu, 11 Apr 2013 12:51:38 -0400
From: Douglas N Greve <greve@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] DTI: problems with (high) FA values
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <5166EA1A.8000701@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
That is a good value, so the regis not the problem. If you upload your
dt_recon folder as well as your recon-all folder for that subject I'll
take a look.
doug
On 04/11/2013 10:02 AM, Rotem Saar wrote:
> Hi Douge,
>
> In your last reply to my email (that contained questions regarding
> some really high FA values - see recent emails below), u asked me to
> write u the first value in register.dat.mincost -
> I'm copying the line I have:
>
> 0.280554 140.210312 156.795241 11.152485
>
> Does this takes us one step further towards understanding the problem
> and its solution ?
>
> Thanks for your time,
> Rotem
>
>
>
> On 04/07/2013 06:48 AM, Rotem Saar wrote:
> > Hi Doug,
> >
> > Thanks for your answer.
> > I changed the last step as u suggested, but I think I need to clarify
> > my question:
> > Indeed values of the CC looks OK, but don't u think other values, like
> > the ventricles are too high ?
> *_yes, the ventricles look too high_*
> >
> > When I first run the script, I got all values and looked the the CC -
> > it looked fine. Then, I wanted to validate with some other regions,
> > just to show that I got the appropriate (low) FA values for regions I
> > don't expect to see high values in - and things looked odd (too high).
> >
> > I remember Bruce also writing me that the values seems a little high,
> > but we didn't further discuss. I read the following this link:
> >
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalDtiIndividual
> >
> > "The CC has an average FA of about 0.75, gyral parcellations are about
> > 0.4, the left putamen is 0.27, and the ventricle is 0.2. This is as
> > expected because the CC is highly directional with no crossing fibers
> > so we would expect the CC to have the highest FA. The gyral white
> > matter is also directional but has fibers crossing in them, so one
> > expects the FA to be lower than CC. The gray matter (putamen) is still
> > lower. The ventricle has no fibers, so we expect it to have the lowest
> > FA".
> >
> > All my values are above 0.4....
> >
> > Additionally, if in the last step I'm writing --seg
> > /usr/local/freesurfer/
> subjects/Rotem_try/mri/wmparc.mgz
> >
> > why do I get 182 regions ? in my wmparc.stats I have only 70...
> The wmparc includes all the subcortical and cortical regions too, but
> only the WM regions are reported in the wmparc.stats file. *_To only
> report the WM regions, add to mri_segstats --ctab
> $FREESURFER_HOME/_**_WMParcStatsLUT.txt_*
> >
> > I'm probably doing something wrong, but I can't really point to the
> > problem, thus asking for your help.
> _*I don't know either. If I had to guess, I'd say it is a registration
> problem. What is the first value in register.dat.mincost?*_
> doug
> >
> > Attached is the table again,
> >
> > Thanks
> > Rotem
> >
> >
> > The values look about right in the table. Your pipeline looks ok,
> > thought the last step uses fa_FOLDER-NAME.mask.nii instead of the
> > output
> > of mri_vol2vol (fa_FOLDER-NAME.nii).
> > doug
> >
> >
> >
> > On 03/17/2013 02:16 AM, Rotem Saar wrote:
> > >
> > > Hi all,
> > > I run into somthing that seems odd to me and wanted to
> consult -
> > > I run the following script for getting the FA values from
> my DTI
> > > scans:
> > >
> > > 1) dt_recon --i
> > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s
> > > FOLDER-NAME --o
> > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b
> > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval
> > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec
> > > 2) tkregister2 --s fsaverage --surf white --reg
> > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg
> > > --mov
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii
> > > 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz
> > > -reg
> /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat
> > > -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii
> > > -fthresh 0.2 -fmax 1
> > > 4) mri_vol2vol --mov
> > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ
> > > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s
> > > FOLDER-NAME --interp nearest --o
> > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii
> > > --reg
> > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat
> > > 5) tkregister2 --mov
> > > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii
> > > --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz
> > > --reg
> > >
> > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg
> > > 6) mri_segstats --seg
> > > /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab
> > > $FREESURFER_HOME/FreeSurferColorLUT.txt --i
> > >
> > /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii
> > > --sum
> > >
> >
> /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME
> > >
> > >
> > > I got a table with all the FA values (see attached), for each
> > > segment, but I suspect a problem: I think that the values
> > are too
> > > high (I set the threshold to 0.2-1), am I right ?
> > > Can u guide me regarding what I can do to solve the
> problem ? in
> > > addition I attached a figure of the corpus-callosum, in
> > which I'm
> > > interested - i't seems that the green area in not big
> enough, is
> > > this fixable ?
> > >
> > > Thanks !
> > >
> > > Rotem
> >
> >
> >
> >
> > _______________________________________________
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://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/
>
>
>
>
>
> _______________________________________________
> 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
greve@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/
------------------------------
Message: 10
Date: Thu, 11 Apr 2013 17:47:14 +0000
From: "Yang, Daniel" <yung-jui.yang@yale.edu>
Subject: Re: [Freesurfer] Very different results between 5.1.0 and
5.2.0
To: Pedro Paulo de Magalh?es Oliveira Junior <ppj@netfilter.com.br>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <CD8C6E39.1A7E1%yung-jui.yang@yale.edu>
Content-Type: text/plain; charset="windows-1252"
Hi PPJ and all,
I found that the 5.2 ? 5.1 difference is primarily seen in the cortical thickness, and much less so in the aseg.volume.
Here, I picked right-amygdala volume as an example of aseg.volume and rh_bankssts_thickness as an example of rh.aparc.thickness.
While the correlation between the two versions of right-amygdala is r = .92 (n = 161), that of the rh_bankssts_thickness is r = .45.
Presumably I believe the correlation should be > .90 for a strong continuity between the two versions?
Do you have anything in the cortical thickness?
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
From: Pedro Paulo de Magalh?es Oliveira Junior <ppj@netfilter.com.br<mailto:ppj@netfilter.com.br>>
Date: Wednesday, April 10, 2013 11:07 AM
To: Daniel Yang <yung-jui.yang@yale.edu<mailto:yung-jui.yang@yale.edu>>
Cc: Bruce Fischl <fischl@nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>>, "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.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
Ok, I'll try to put together a stat from aparc too.
---------------------------------------------------------------------
Pedro Paulo de Magalh?es Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br<http://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 <yung-jui.yang@yale.edu<mailto:yung-jui.yang@yale.edu>> 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<tel:%28203%29%20737-5454>
From: Pedro Paulo de Magalh?es Oliveira Junior <ppj@netfilter.com.br<mailto:ppj@netfilter.com.br>>
Date: Wednesday, April 10, 2013 10:49 AM
To: Bruce Fischl <fischl@nmr.mgh.harvard.edu<mailto:fischl@nmr.mgh.harvard.edu>>
Cc: Daniel Yang <yung-jui.yang@yale.edu<mailto:yung-jui.yang@yale.edu>>, "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.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 Magalh?es Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br<http://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 <fischl@nmr.mgh.harvard.edu<mailto:fischl@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 Magalh?es Oliveira Junior<ppj@netfilter.com.br<mailto:ppj@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 Magalh?es Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br<http://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 <yung-jui.yang@yale.edu<mailto:yung-jui.yang@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<tel:%28203%29%20737-5454>
On 3/19/13 7:07 AM, "Yang, Daniel" <yung-jui.yang@yale.edu<mailto:yung-jui.yang@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<tel:%28203%29%20737-5454>
>
>
>
>
>
>
>On 3/18/13 6:27 PM, "Matt Glasser" <matt@ma-tea.com<mailto:matt@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" <ridatta@mail.med.upenn.edu<mailto:ridatta@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 - ridatta@mail.med.upenn.edu<mailto:ridatta@mail.med.upenn.edu>
>>>
>>>
>>>----- Original Message -----
>>>From: Daniel Yang <yung-jui.yang@yale.edu<mailto:yung-jui.yang@yale.edu>>
>>>To: freesurfer@nmr.mgh.harvard.edu<mailto: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<tel:%28203%29%20737-5454>
>>>
>>>_______________________________________________
>>>Freesurfer mailing list
>>>Freesurfer@nmr.mgh.harvard.edu<mailto: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
>>>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
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
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Message: 11
Date: Thu, 11 Apr 2013 14:28:34 -0400
From: nicolas guizard <n.guizard@gmail.com>
Subject: [Freesurfer] Fwd: Sample size estimation from LME models
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<CADT1u3D79B1Odo2cD_Zt3aaWHuw2WwqAyR-DgeqHrdOWxX3eHA@mail.gmail.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi,
I am new to Freesurfer and the Linear Mixed Effects (LME) Models packages.
And I would like to compute sample size from volumetric measures for 2
groups.
I followed the longitudinal example provided in the wiki (
http://surfer.nmr.mgh.harvard.edu/fswiki/LinearMixedEffectsModels#a.29Univariate),
with the ADNI example. But I am not sure what to use for the "common random
effect design matrix" Zi and "column" ZiCol with the
lme_plannedSampleSize(Zi,ZiCol,Dhat,phisqhat,effsz,dr,pw,alpha,gr_pr)
function:
Here is what I do in matlab:
> load('ADNI791_Hipp_and_Entorh.mat')
> total_hipp_vol_stats = lme_fit_EM(X_Hipp,[1,2],Y(:,1)+Y(:,2),ni);
> lme_plannedSampleSize(total_hipp_vol_stats.X,[1,2]
,total_hipp_vol_stats.Dhat,total_hipp_vol_stats.phisqhat,1,.2,.8,0.05)
> ans =
1.0e+07 *
1.3584 0.0154
0.0154 0.0100
Is that right?
Regards,
Nicolas
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Message: 12
Date: Thu, 11 Apr 2013 18:33:37 +0000
From: "Yang, Daniel" <yung-jui.yang@yale.edu>
Subject: Re: [Freesurfer] Very different results between 5.1.0 and
5.2.0
To: Nick Schmansky <nicks@nmr.mgh.harvard.edu>
Cc: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <CD8C7A19.1A879%yung-jui.yang@yale.edu>
Content-Type: text/plain; charset="us-ascii"
Thanks Nick! I have uploaded the relevant files to you.
Thanks,
Daniel
--
Yung-Jui "Daniel" Yang, PhD
Postdoctoral Researcher
Yale Child Study Center
New Haven, CT
(203) 737-5454
On 4/10/13 1:19 PM, "Nick Schmansky" <nicks@nmr.mgh.harvard.edu> wrote:
>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
>regions....its still handy to see where hippocampus sits).
>
>Nick
>
>
>On Wed, 2013-04-10 at 11:11 +0000, 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
>>
>
>
>
>
>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
>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.
------------------------------
Message: 13
Date: Thu, 11 Apr 2013 14:43:23 -0400
From: Daniel Haehn <daniel.haehn@childrens.harvard.edu>
Subject: Re: [Freesurfer] Transform SMOOTHWM to DTI B0
To: Satrajit Ghosh <satra@mit.edu>
Cc: Freesurfer Mailing List <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAPDjdmbXBR-LeKLKOfmShzdsuObp8YCTwTEiJaoSarHqQLYTuA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Thanks, Satra! This is helpful!!
On Thu, Apr 11, 2013 at 12:32 PM, Satrajit Ghosh <satra@mit.edu> wrote:
> hi all,
>
> here you go:
>
> https://gist.github.com/satra/1451812
>
> this goes from trackvis streamlines to freesurfer surface space. you
> would do the inverse of this transform to go the other way.
>
> cheers,
>
> satra
>
> On Thu, Apr 11, 2013 at 12:26 PM, Daniel Haehn <
> daniel.haehn@childrens.harvard.edu> wrote:
>
>> Hi Satra et al,
>>
>> thanks a lot and it would be great if you could find some code!
>>
>> In the meantime, I tried the following based on information from Kiho
>> Im:
>>
>> # we have to first remove transformation of 'vertex to RAS' embedded in
>> smoothwm surface.
>> mris_transform lh.smoothwm identity.xfm ./lh.smoothwm.clean
>>
>> # then use the flirt T1-to-b0 matrix converted from .mat to .xfm format
>> to transform the surface
>> mris_transform lh.smoothwm.clean T1-to-b0.xfm lh.b0.smoothwm
>>
>> And of course: it didn't work.. In the attached screenshot, the red
>> surface is the original one which kind of fits the b0 image but not very
>> well (it obviously fits the original T1 very well). The blue is the
>> transformed surface (lh.b0.smoothwm) and is completely off.
>>
>> [image: Inline image 1]
>>
>> Do you know what I could be doing wrong? I also attached both
>> tranforms. Maybe I just converted them wrong.
>>
>> Thanks!!
>> Daniel
>>
>>
>> On Thu, Apr 11, 2013 at 10:53 AM, Satrajit Ghosh <satra@mit.edu> wrote:
>>
>>> hi dan,
>>>
>>> if you use bbregister to match the DTI b0 to freesurfer space, then
>>> you can transform the surface back (no guarantees on the tesselations
>>> though i think). the only additional component here would be a tkr
>>> transform that's based on the conformed space. i might even have some
>>> python code lying around to do this. i'll take a look.
>>>
>>> cheers,
>>>
>>> satra
>>>
>>> On Thu, Apr 11, 2013 at 10:40 AM, Daniel Haehn <
>>> daniel.haehn@childrens.harvard.edu> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I want to transform the Freesurfer Smoothwm surfaces to DTI B0 space.
>>>>
>>>> I found
>>>> http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferTrackVisTransformsbut this describes transforming the B0 to T1 space and then match the
>>>> surfaces. I don't want to change the DTI B0 image.
>>>>
>>>> What is the best way to do that?
>>>>
>>>> Thank you very much!
>>>> Daniel
>>>>
>>>> --
>>>> Daniel Haehn
>>>> FNNDSC / BCH
>>>> +1.857.218.5140
>>>>
>>>> _______________________________________________
>>>> 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
>>>> 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.
>>>>
>>>>
>>>
>>
>>
>> --
>> Daniel Haehn
>> FNNDSC / BCH
>> +1.857.218.5140
>>
>
>
--
Daniel Haehn
FNNDSC / BCH
+1.857.218.5140
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Message: 14
Date: Thu, 11 Apr 2013 15:31:19 -0400
From: "Marco Loggia, PhD" <marco@nmr.mgh.harvard.edu>
Subject: [Freesurfer] "final" skull-stripped file?
To: freesurfer@nmr.mgh.harvard.edu
Message-ID: <FEF69FD2-88B1-4193-9D2C-7079A6619B15@nmr.mgh.harvard.edu>
Content-Type: text/plain; charset="us-ascii"
Dear all,
what is the 'best' skull stripped file produced by freesurfer? From what I see, it would seem to be 'brainmask'. However this file -if I understand correctly- is produced in the very first stages of recon-all, and therefore does not take advantage of the detailed reconstruction of the brain 'borders' which is achieved in the subsequent stages of recon-all. For this reason, I have been masking my brainmask.mgz file with a binary file created using the aparc+aseg file (which labels only the brain), slightly smoothed to be conservative in the stripping.
Or is there already a file skull-stripped this way?
Thanks,
Marco
______________________________
Marco L. Loggia, PhD
Instructor in Radiology
Harvard Medical School
Massachusetts General Hospital
149 Thirteenth Street, Room 2301
Charlestown, MA 02129
Phone: (617) 643-7267
Fax: (617) 726-7422
marco@nmr.mgh.harvard.edu
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Message: 15
Date: Thu, 11 Apr 2013 20:39:16 +0100 (BST)
From: Lucille Deroche <lucillederoche@yahoo.fr>
Subject: Re: [Freesurfer] Autoreg-sess and mri_surf2vol
To: Douglas N Greve <greve@nmr.mgh.harvard.edu>,
"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<1365709156.28353.YahooMailNeo@web171802.mail.ir2.yahoo.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi,?
I did the command:?
mri_surf2vol --surfval $SUBJECTS_DIR/Patient1/surf/rh.pial --hemi rh --identity Patient1.?
ERROR: cannot recognize the type of /home/lucille/Freesurfer/freesurfer/subjects/Patient1/surf/rh.pial
The name of my subject is ' Patient1'.?
Did I do a wrong entery at the --surfval argument ??
Cheers
Lucille
________________________________
De?: Douglas N Greve <greve@nmr.mgh.harvard.edu>
??: freesurfer@nmr.mgh.harvard.edu
Envoy? le : Jeudi 11 avril 2013 12h49
Objet?: Re: [Freesurfer] Autoreg-sess and mri_surf2vol
Hi Lucile, don't use autoreg-sess (that is an old program and was for
fMRI). Use mri_surf2vol with --identity subjectname instead of --reg
doug
On 04/11/2013 11:45 AM, Lucille Deroche wrote:
> Hi Bruce,
>
>? In fact, have 2 differents? surfaces? of pial surface. I would like
> to save my surfaces in volume to be able to calculate the dice score
> between the two.
>
> Cheers
>
> Lucille
> ------------------------------------------------------------------------
> *De :* Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> *? :* Lucille Deroche <lucillederoche@yahoo.fr>
> *Cc :* "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> *Envoy? le :* Jeudi 11 avril 2013 11h18
> *Objet :* Re: [Freesurfer] Autoreg-sess and mri_surf2vol
>
> Hi Lucille
>
> what do you mean by converting a surface to the volume? What do you want
> to do with it? What volume would you like to convert it to?
>
> cheers
> Bruce
> On Thu, 11 Apr
> 2013, Lucille Deroche wrote:
>
> > Hi,
> > My name is Lucille and I'm really new? with Freesurfer : My
> questions are very basic, sorry.
> > I just start a project in segmentation of cerebrum.
> >? For converting a surface in volume. I would like to use
> mri_surf2vol but for that I need a
> >? volume registration file . For creating that file, I would use
> autoreg-sess.
> > In documentation, it is said that : 'The volume registration file
> contains the matrix that
> > maps XYZ in the reference anatomical to XYZ in the functional volume'
> > My question is : what here, represent the anatomical reference ? The
> functionnal volume ?
> > Secondly, for autoreg-sess, the arguments are the subject name and
> the subject directory. I
> > think the registration I need to create must be between my 2
> volumes, so should I use the
> > subject name and subject directory for my 2 subjects ?
> >
> > Sorry,I am really messed...
> >
> > Cheers
> > Lucille
> >
> >
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu <mailto: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
> 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
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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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------------------------------
Message: 16
Date: Thu, 11 Apr 2013 14:52:51 -0500
From: Michael Harms <mharms@conte.wustl.edu>
Subject: Re: [Freesurfer] Autoreg-sess and mri_surf2vol
To: Lucille Deroche <lucillederoche@yahoo.fr>, Douglas N Greve
<greve@nmr.mgh.harvard.edu>, "freesurfer@nmr.mgh.harvard.edu"
<freesurfer@nmr.mgh.harvard.edu>
Message-ID: <CD8C7D8E.12B8B%mharms@conte.wustl.edu>
Content-Type: text/plain; charset="iso-8859-1"
Try:
mri_surf2vol --surf pial --mkmask --hemi lh --identity <subjid> --template
<subjid>/mri/norm.mgz --o <subjid>/mri/pial_in_vol.mgz
FWIW, I'm not sure if sampling two surfaces to the volume, and then
computing a dice coefficient is really the best way to "compare" two
surfaces. I would instead compare the two surfaces directly -- e.g., the
rms distance between matched vertices.
cheers,
-MH
--
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO 63110 Email: mharms@wustl.edu
From: Lucille Deroche <lucillederoche@yahoo.fr>
Reply-To: Lucille Deroche <lucillederoche@yahoo.fr>
Date: Thursday, April 11, 2013 2:39 PM
To: Doug Greve <greve@nmr.mgh.harvard.edu>,
"freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Autoreg-sess and mri_surf2vol
Hi,
I did the command:
mri_surf2vol --surfval $SUBJECTS_DIR/Patient1/surf/rh.pial --hemi rh
--identity Patient1.
ERROR: cannot recognize the type of
/home/lucille/Freesurfer/freesurfer/subjects/Patient1/surf/rh.pial
The name of my subject is ' Patient1'.
Did I do a wrong entery at the --surfval argument ?
Cheers
Lucille
De : Douglas N Greve <greve@nmr.mgh.harvard.edu>
? : freesurfer@nmr.mgh.harvard.edu
Envoy? le : Jeudi 11 avril 2013 12h49
Objet : Re: [Freesurfer] Autoreg-sess and mri_surf2vol
Hi Lucile, don't use autoreg-sess (that is an old program and was for
fMRI). Use mri_surf2vol with --identity subjectname instead of --reg
doug
On 04/11/2013 11:45 AM, Lucille Deroche wrote:
> Hi Bruce,
>
> In fact, have 2 differents surfaces of pial surface. I would like
> to save my surfaces in volume to be able to calculate the dice score
> between the two.
>
> Cheers
>
> Lucille
> ------------------------------------------------------------------------
> *De :* Bruce Fischl <fischl@nmr.mgh.harvard.edu>
> *? :* Lucille Deroche <lucillederoche@yahoo.fr>
> *Cc :* "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
> *Envoy? le :* Jeudi 11 avril 2013 11h18
> *Objet :* Re: [Freesurfer] Autoreg-sess and mri_surf2vol
>
> Hi Lucille
>
> what do you mean by converting a surface to the volume? What do you want
> to do with it? What volume would you like to convert it to?
>
> cheers
> Bruce
> On Thu, 11 Apr
> 2013, Lucille Deroche wrote:
>
> > Hi,
> > My name is Lucille and I'm really new with Freesurfer : My
> questions are very basic, sorry.
> > I just start a project in segmentation of cerebrum.
> > For converting a surface in volume. I would like to use
> mri_surf2vol but for that I need a
> > volume registration file . For creating that file, I would use
> autoreg-sess.
> > In documentation, it is said that : 'The volume registration file
> contains the matrix that
> > maps XYZ in the reference anatomical to XYZ in the functional volume'
> > My question is : what here, represent the anatomical reference ? The
> functionnal volume ?
> > Secondly, for autoreg-sess, the arguments are the subject name and
> the subject directory. I
> > think the registration I need to create must be between my 2
> volumes, so should I use the
> > subject name and subject directory for my 2 subjects ?
> >
> > Sorry,I am really messed...
> >
> > Cheers
> > Lucille
> >
> >
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu <mailto: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
> 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
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@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
_______________________________________________ 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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End of Freesurfer Digest, Vol 110, Issue 20
*******************************************