Dear Doug,
I have uploaded the files to the "filedrop" (file name: Rotem_try.tar.gz) and activated the link (I hope I did it OK). I will appreciate your help as I'm stuck - can't see the problem...:)
Thanks for all your help !!
Rotem
------------------------------
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 toconsult -
> I run the following script for getting the FA values frommy 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 -segwmparc.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 theproblem ? in
> addition I attached a figure of the corpus-callosum, in which I'm > interested - i't seems that the green area in not bigenough, is
> this fixable ? > > Thanks ! > > Rotem
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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.edumailto:yung-jui.yang@yale.edu> Cc: Bruce Fischl <fischl@nmr.mgh.harvard.edumailto: fischl@nmr.mgh.harvard.edu>, "freesurfer@nmr.mgh.harvard.edumailto: freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto: 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.brhttp://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) 737-5454tel:%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.edumailto: fischl@nmr.mgh.harvard.edu> Cc: Daniel Yang <yung-jui.yang@yale.edumailto:yung-jui.yang@yale.edu>, " freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" < freesurfer@nmr.mgh.harvard.edumailto: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.brhttp://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.brmailto: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.brhttp://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) 737-5454tel:%28203%29%20737-5454
On 3/19/13 7:07 AM, "Yang, Daniel" <yung-jui.yang@yale.edumailto: 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) 737-5454tel:%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.edumailto: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) 737-5454tel:%28203%29%20737-5454
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Dear Doug,
I have uploaded the files to the "filedrop" (file name: Rotem_try.tar.gz) and activated the link (I hope I did it OK). I will appreciate your help as I'm stuck - can't see the problem...:)
Thanks for all your help !!
Rotem
------------------------------
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 toconsult -
> I run the following script for getting the FA values frommy 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 -segwmparc.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 theproblem ? in
> addition I attached a figure of the corpus-callosum, in which I'm > interested - i't seems that the green area in not bigenough, is
> this fixable ? > > Thanks ! > > Rotem
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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/
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-- 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/
Hi Rotem, I don't think I ever got an email notifying me. Did you use www.nmr.mgh.harvard.edu/facility/filedrop/index.html http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html ? Can you upload it again, and make sure to put my email in the contact list.
doug
On 4/29/13 9:08 PM, Rotem Saar wrote:
Dear Doug,
I have uploaded the files to the "filedrop" (file name: Rotem_try.tar.gz) and activated the link (I hope I did it OK). I will appreciate your help as I'm stuck - can't see the problem...:)
Thanks for all your help !!
Rotem
------------------------------ Message: 9 Date: Thu, 11 Apr 2013 12:51:38 -0400 From: Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] DTI: problems with (high) FA values To: freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> Message-ID: <5166EA1A.8000701@nmr.mgh.harvard.edu <mailto: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> <mailto: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> <mailto: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> > <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> > <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 <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/
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Douglas Greve -
Rotem Saar