Re: [Freesurfer] A problem about Freesurfer

[Douglas N. Greve]

no, humans only. Though if you google around you might find someone who 
has adapted it


On 6/4/2021 4:33 AM, 胡俊涛 wrote:


External Email - Use Caution

Can I use Freesurfer to process MRI image data of mice?

Thank you!






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[Freesurfer] A problem about Freesurfer

[胡俊涛]

External Email - Use Caution

Can I use Freesurfer to process MRI image data of mice?


Thank you!








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Re: [Freesurfer] A problem in publication (citation with freesurfer))

[Douglas N Greve]

You don't need to cite mri_label2vol, it is just a spatial transformation

On 08/02/2015 09:21 PM, jinyi wrote:
> Hello freesurfers
> I am working on a paper based on freesurfer and other images 
> process tools.
>
> I am wondering the citation problems, In the freesurfer wiki, a 
> help page 
> (http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&do=view&target=freesurfer_methods.doc)
>  
> is about it. But it is too short for me.
> On this page, The reconstrction technique details are from many 
> papers. So should I cite them all? And I mainly use recon-all to 
> reconstruction the brain and mri_label2vol  to extract some parts from 
> the 3D brain in my work, but the Wiki do not provide the papers about 
> mri_label2vol. What papers should I cite?
>
> Wating for your response.
>
> With personal regards.
>
>
> ___
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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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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[Freesurfer] A problem in publication (citation with freesurfer))

[jinyi]

Hello freesurfers
I am working on a paper based on freesurfer and other images process tools.

I am wondering the citation problems, In the freesurfer wiki, a help page 
(http://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferWiki?action=AttachFile&do=view&target=freesurfer_methods.doc)
 is about it. But it is too short for me.
On this page, The reconstrction technique details are from many papers. So 
should I cite them all? And I mainly use recon-all to reconstruction the brain 
and mri_label2vol  to extract some parts from the 3D brain in my work, but the 
Wiki do not provide the papers about mri_label2vol. What papers should I cite?

Wating for your response.

With personal regards. 
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Re: [Freesurfer] a problem

[Bruce Fischl]

Hi Ting

can you send us the commands that you used to establish correspondence and 
to map the vertices?

cheers
Bruce

On Thu, 
16 Oct 2014, Ting Li wrote:

> Hi, experts,
> I am trying to use the template fsaverage_sym and tried to map the same set
> of vertices onto the left and right pial surface. Surprisingly, these
> vertices on the two surfaces did not correspond to the same anatomical
> cortical regions. Sometimes, they correspond to each other very badly. For
> instance, one is mapped onto the lateral surface on the left pial surface,
> the other may be mapped onto the medial surface on the opposite hemisphere,
> I can not see their symmetry.
> Any comment?
> How can I establish the correspondence between the rh and lh pial surfaces?
> 
> Ting
> 
> 
> 
> 
>
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[Freesurfer] a problem

[Ting Li]

Hi, experts,
I am trying to use the template fsaverage_sym and tried to map the same set of 
vertices onto the left and right pial surface. Surprisingly, these vertices on 
the two surfaces did not correspond to the same anatomical cortical regions. 
Sometimes, they correspond to each other very badly. For instance, one is 
mapped onto the lateral surface on the left pial surface, the other may be 
mapped onto the medial surface on the opposite hemisphere, I can not see their 
symmetry.
Any comment?

How can I establish the correspondence between the rh and lh pial surfaces?

Ting


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Re: [Freesurfer] A problem while doing retinotopy by freesurfer

[Douglas Greve]

Hi Yufeng, it cannot handle only a single run. You must have both polar 
and eccen. You can "fool" it by copying your polar run into another run 
and calling it eccen.
doug
ps. Please remember to send email to the list and not to me personally. 
Thanks!



On 4/16/13 11:02 AM, yuf...@mail.ustc.edu.cn wrote:
> Hi Doug,
>   Thank you for your patient. I am doing retinotopy analysis by using 
> freesurfer 5.1 with the help of the webside 
> http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis . 
> And my problem is as followed while doing
> selxavg3-sess -s Sess01 -a fmcpr.sm5.self.lh.nii.gz
> My mmkanalysis-sess code is as followed:
> mmkanalysis-sess -fsd bold -stc odd -surface self lh -fwhm 5 -retinotopy 32 
> -paradigm rtopy.par -analysis fmcpr.sm5.self.lh.nii.gz -TR 2
>
> Error information
> Saving X matrix to 
> /usr/local/freesurfer/stable5/retinotopy_002/Sess01/bold/fmcpr.odd.sm5.fsaverage.lh.nii.gz/Xtmp.mat
> ??? Error using ==> svd
> Input to SVD must not contain NaN or Inf.
>
> Error in ==> cond at 40
> s = svd(A);
>
> Error in ==> fast_selxavg3 at 254
>XCond = cond(XtX);
>   
>>> --
> ERROR: fast_selxavg3() failed\n
>   
>   I just have one run and the rtopy.par is
> stimtype polar
>
> direction neg
>   
> I attach the analysis.info and Xtmp.mat on the email. Thanks very much.
>   
>Yours Yufeng
>   
> 

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Re: [Freesurfer] A problem about mri_glmfit result

[Douglas Greve]

It's a numerical issue having to due with adding very large numbers with 
very small ones. You don't get exactly the right number out, so there is 
a small error. Over many operations, these errors accumulate.


doug

On 5/4/11 7:17 AM, soft.join Huang wrote:

Oh, sorry, Greve. I misunderstood your suggestion.
Now I get the same resulte in both mri_glmfit and matlab. Thanks a lot!
But there is still a question about how it happened. Why I have to do 
so to get the correct result? There is nothing relevant between the 
number scale of one variable and the beta values of other variables 
theoretically. Is it any relevance to the data size of data structure 
in mri_glmfit?

Best Regards,
Lijie Huang
On Tue, May 3, 2011 at 10:55 PM, Douglas N Greve 
mailto:gr...@nmr.mgh.harvard.edu>> wrote:


sorry, I mean to do it for both the FSGD file and the matlab
script. I just tried it with your data and it works.

doug

soft.join Huang wrote:

Hi, doug.
 Thanks for your suggestion, but it does not seem to work.
After having divided the ICV by 1e6, I reculated the betas,
and got the similar results as before in Matlab, just the
beta4 -- correspondent to ICV -- multiplied a 10^6.
And then I computed the rank of matrix X that the value is 4,
indicating that each 2 variables in design matrix do not
highly correlated.
Also I have finished an regress analysis including one class
variable and one continuous variable using mri_glmfit, got the
same result in Matlab.
A wired situation...
Is it any additional constrains in mri_glmfit when doing
regression analysis?
 Lijie Huang

 On Mon, May 2, 2011 at 9:09 PM, Douglas N Greve
mailto:gr...@nmr.mgh.harvard.edu>
>> wrote:

   I think the problem may be that your data are "badly scaled"
   meaning that one column is much greater than another
column. Try
   dividing the ICV by 1e6 and see if you get more similar
results.

   doug

   soft.join Huang wrote:

   Doug,
Thanks for your reply.
   I recalculated the beta value and got the same results
as the
   Matlab does, but be different from the mri_glmfit's. I
can not
   figure out where the problem is.
   Details following:
   I use the command
mri_glmfit --table lh.volume.txt --fsgd
   volume.gender.fsgd doss --C gender.diff.mtx --glmdir
lh.vol.glmdir
   to finish regression analysis. and got the beta value (
   beta1 = 1.9781e+03, beta2 = 2.0639e+03, beta3 = 110.9220,
   beta4 = 5.1964e-04 ) from beta.mgh file.
   Using X.mat file and the same dependent variable
Y.mat as
   mri_glmfit's, I got totally different results in
Matlab( beta1
   = 5.19e+02, beta2 = 4.44e+02, beta3 = 90.32, beta4 =
0.0015 ).
   I don't know how it happened...
Hope for your reply.
   The data I used are all in the attachment.
Best Regrads,
Lijie Huang
   On Fri, Apr 29, 2011 at 9:45 PM,
mailto:gr...@nmr.mgh.harvard.edu>
>

 Hi all,
>
> I'm working on a group analysis using mri_glmfit.
>  In analysis directory, I got a X.mat file which
   containing the
  matrix X (
> size 50x4 ) used to regress analysis, also the beta value
   from
  beta.mgh
> file.
> Strangely, I loaded the X.mat in Matlab and recalculated the
  beta using
> function regress in matlab, but got a different result
   from that of
> mri_glmfit.
> I don't know where the problem is, is there any difference in
  algorithm
> between mri_glmfit and matlab function regress(
   regress(Y,X) )?
  or I made
> some mistakes during the procedure.
> The X.mat file and the dependent variable Y.mat are in the

Re: [Freesurfer] A problem about mri_glmfit result

[soft.join Huang]

Oh, sorry, Greve. I misunderstood your suggestion.
Now I get the same resulte in both mri_glmfit and matlab. Thanks a lot!
But there is still a question about how it happened. Why I have to do so to
get the correct result? There is nothing relevant between the number scale
of one variable and the beta values of other variables theoretically. Is it
any relevance to the data size of data structure in mri_glmfit?

Best Regards,
Lijie Huang

On Tue, May 3, 2011 at 10:55 PM, Douglas N Greve
wrote:

> sorry, I mean to do it for both the FSGD file and the matlab script. I just
> tried it with your data and it works.
>
> doug
>
> soft.join Huang wrote:
>
>> Hi, doug.
>>  Thanks for your suggestion, but it does not seem to work.
>> After having divided the ICV by 1e6, I reculated the betas, and got the
>> similar results as before in Matlab, just the beta4 -- correspondent to ICV
>> -- multiplied a 10^6.
>> And then I computed the rank of matrix X that the value is 4, indicating
>> that each 2 variables in design matrix do not highly correlated.
>> Also I have finished an regress analysis including one class variable and
>> one continuous variable using mri_glmfit, got the same result in Matlab.
>> A wired situation...
>> Is it any additional constrains in mri_glmfit when doing regression
>> analysis?
>>  Lijie Huang
>>
>>   On Mon, May 2, 2011 at 9:09 PM, Douglas N Greve <
>> gr...@nmr.mgh.harvard.edu > wrote:
>>
>>I think the problem may be that your data are "badly scaled"
>>meaning that one column is much greater than another column. Try
>>dividing the ICV by 1e6 and see if you get more similar results.
>>
>>doug
>>
>>soft.join Huang wrote:
>>
>>Doug,
>> Thanks for your reply.
>>I recalculated the beta value and got the same results as the
>>Matlab does, but be different from the mri_glmfit's. I can not
>>figure out where the problem is.
>>Details following:
>>I use the command
>> mri_glmfit --table lh.volume.txt --fsgd
>>volume.gender.fsgd doss --C gender.diff.mtx --glmdir lh.vol.glmdir
>>to finish regression analysis. and got the beta value (
>>beta1 = 1.9781e+03, beta2 = 2.0639e+03, beta3 = 110.9220,
>>beta4 = 5.1964e-04 ) from beta.mgh file.
>>Using X.mat file and the same dependent variable Y.mat as
>>mri_glmfit's, I got totally different results in Matlab( beta1
>>= 5.19e+02, beta2 = 4.44e+02, beta3 = 90.32, beta4 = 0.0015 ).
>>I don't know how it happened...
>> Hope for your reply.
>>The data I used are all in the attachment.
>> Best Regrads,
>> Lijie Huang
>>On Fri, Apr 29, 2011 at 9:45 PM, >
>>>>> wrote:
>>
>>   Lijie,
>>
>>   I don't know what the matlab regress() function does.
>>mri_glmfit
>>   is just
>>   solving the GLM equation, which you can do easily in matlab:
>>
>>   beta = inv(X'*X)*X'*y;
>>
>>   try that and see if you get the same as mri_glmfit.
>>
>>   doug
>>
>>
>>   > Hi all,
>>   >
>>   > I'm working on a group analysis using mri_glmfit.
>>   >  In analysis directory, I got a X.mat file which
>>containing the
>>   matrix X (
>>   > size 50x4 ) used to regress analysis, also the beta value
>>from
>>   beta.mgh
>>   > file.
>>   > Strangely, I loaded the X.mat in Matlab and recalculated the
>>   beta using
>>   > function regress in matlab, but got a different result
>>from that of
>>   > mri_glmfit.
>>   > I don't know where the problem is, is there any difference in
>>   algorithm
>>   > between mri_glmfit and matlab function regress(
>>regress(Y,X) )?
>>   or I made
>>   > some mistakes during the procedure.
>>   > The X.mat file and the dependent variable Y.mat are in the
>>   attachment.
>>   >
>>   > Thanks in advance
>>   >
>>   > Lijie Huang
>>   > ___
>>   > 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 Hel

Re: [Freesurfer] A problem about mri_glmfit result

[Douglas N Greve]

sorry, I mean to do it for both the FSGD file and the matlab script. I 
just tried it with your data and it works.
doug

soft.join Huang wrote:
> Hi, doug.
>  
> Thanks for your suggestion, but it does not seem to work.
> After having divided the ICV by 1e6, I reculated the betas, and got 
> the similar results as before in Matlab, just the beta4 -- 
> correspondent to ICV -- multiplied a 10^6.
> And then I computed the rank of matrix X that the value is 4, 
> indicating that each 2 variables in design matrix do not highly 
> correlated.
> Also I have finished an regress analysis including one class variable 
> and one continuous variable using mri_glmfit, got the same result in 
> Matlab.
> A wired situation...
> Is it any additional constrains in mri_glmfit when doing regression 
> analysis?
>  
> Lijie Huang
>
>  
> On Mon, May 2, 2011 at 9:09 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> I think the problem may be that your data are "badly scaled"
> meaning that one column is much greater than another column. Try
> dividing the ICV by 1e6 and see if you get more similar results.
>
> doug
>
> soft.join Huang wrote:
>
> Doug,
>  Thanks for your reply.
> I recalculated the beta value and got the same results as the
> Matlab does, but be different from the mri_glmfit's. I can not
> figure out where the problem is.
> Details following:
> I use the command
>  mri_glmfit --table lh.volume.txt --fsgd
> volume.gender.fsgd doss --C gender.diff.mtx --glmdir lh.vol.glmdir
> to finish regression analysis. and got the beta value (
> beta1 = 1.9781e+03, beta2 = 2.0639e+03, beta3 = 110.9220,
> beta4 = 5.1964e-04 ) from beta.mgh file.
> Using X.mat file and the same dependent variable Y.mat as
> mri_glmfit's, I got totally different results in Matlab( beta1
> = 5.19e+02, beta2 = 4.44e+02, beta3 = 90.32, beta4 = 0.0015 ).
> I don't know how it happened...
>  Hope for your reply.
> The data I used are all in the attachment.
>  Best Regrads,
>  Lijie Huang
> On Fri, Apr 29, 2011 at 9:45 PM,  
>  >> wrote:
>
>Lijie,
>
>I don't know what the matlab regress() function does.
> mri_glmfit
>is just
>solving the GLM equation, which you can do easily in matlab:
>
>beta = inv(X'*X)*X'*y;
>
>try that and see if you get the same as mri_glmfit.
>
>doug
>
>
>> Hi all,
>>
>> I'm working on a group analysis using mri_glmfit.
>>  In analysis directory, I got a X.mat file which
> containing the
>matrix X (
>> size 50x4 ) used to regress analysis, also the beta value
> from
>beta.mgh
>> file.
>> Strangely, I loaded the X.mat in Matlab and recalculated the
>beta using
>> function regress in matlab, but got a different result
> from that of
>> mri_glmfit.
>> I don't know where the problem is, is there any difference in
>algorithm
>> between mri_glmfit and matlab function regress(
> regress(Y,X) )?
>or I made
>> some mistakes during the procedure.
>> The X.mat file and the dependent variable Y.mat are in the
>attachment.
>>
>> Thanks in advance
>>
>> Lijie Huang
>> ___
>> 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.
>
>
>
> -- 
> 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
> 

Re: [Freesurfer] A problem about mri_glmfit result

[soft.join Huang]

Hi, doug.

Thanks for your suggestion, but it does not seem to work.
After having divided the ICV by 1e6, I reculated the betas, and got the
similar results as before in Matlab, just the beta4 -- correspondent to ICV
-- multiplied a 10^6.
And then I computed the rank of matrix X that the value is 4, indicating
that each 2 variables in design matrix do not highly correlated.
Also I have finished an regress analysis including one class variable and
one continuous variable using mri_glmfit, got the same result in Matlab.
A wired situation...
Is it any additional constrains in mri_glmfit when doing regression
analysis?

Lijie Huang


On Mon, May 2, 2011 at 9:09 PM, Douglas N Greve
wrote:

> I think the problem may be that your data are "badly scaled" meaning that
> one column is much greater than another column. Try dividing the ICV by 1e6
> and see if you get more similar results.
>
> doug
>
> soft.join Huang wrote:
>
>> Doug,
>>  Thanks for your reply.
>> I recalculated the beta value and got the same results as the Matlab does,
>> but be different from the mri_glmfit's. I can not figure out where the
>> problem is.
>> Details following:
>> I use the command
>>  mri_glmfit --table lh.volume.txt --fsgd volume.gender.fsgd doss
>> --C gender.diff.mtx --glmdir lh.vol.glmdir
>> to finish regression analysis. and got the beta value ( beta1 =
>> 1.9781e+03, beta2 = 2.0639e+03, beta3 = 110.9220, beta4 = 5.1964e-04 ) from
>> beta.mgh file.
>> Using X.mat file and the same dependent variable Y.mat as
>> mri_glmfit's, I got totally different results in Matlab( beta1 = 5.19e+02,
>> beta2 = 4.44e+02, beta3 = 90.32, beta4 = 0.0015 ).
>> I don't know how it happened...
>>  Hope for your reply.
>> The data I used are all in the attachment.
>>  Best Regrads,
>>  Lijie Huang
>>  On Fri, Apr 29, 2011 at 9:45 PM, > gr...@nmr.mgh.harvard.edu>> wrote:
>>
>>Lijie,
>>
>>I don't know what the matlab regress() function does. mri_glmfit
>>is just
>>solving the GLM equation, which you can do easily in matlab:
>>
>>beta = inv(X'*X)*X'*y;
>>
>>try that and see if you get the same as mri_glmfit.
>>
>>doug
>>
>>
>>> Hi all,
>>>
>>> I'm working on a group analysis using mri_glmfit.
>>>  In analysis directory, I got a X.mat file which containing the
>>matrix X (
>>> size 50x4 ) used to regress analysis, also the beta value from
>>beta.mgh
>>> file.
>>> Strangely, I loaded the X.mat in Matlab and recalculated the
>>beta using
>>> function regress in matlab, but got a different result from that of
>>> mri_glmfit.
>>> I don't know where the problem is, is there any difference in
>>algorithm
>>> between mri_glmfit and matlab function regress( regress(Y,X) )?
>>or I made
>>> some mistakes during the procedure.
>>> The X.mat file and the dependent variable Y.mat are in the
>>attachment.
>>>
>>> Thanks in advance
>>>
>>> Lijie Huang
>>> ___
>>> 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
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>>sender and properly
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> --
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> MGH-NMR Center
>
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358 Fax: 617-726-7422
>
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Re: [Freesurfer] A problem about mri_glmfit result

[Douglas N Greve]

I think the problem may be that your data are "badly scaled" meaning 
that one column is much greater than another column. Try dividing the 
ICV by 1e6 and see if you get more similar results.

doug

soft.join Huang wrote:
> Doug,
>  
> Thanks for your reply.
> I recalculated the beta value and got the same results as the Matlab 
> does, but be different from the mri_glmfit's. I can not figure out 
> where the problem is.
> Details following:
>  I use the command
>   mri_glmfit --table lh.volume.txt --fsgd volume.gender.fsgd 
> doss --C gender.diff.mtx --glmdir lh.vol.glmdir
>  to finish regression analysis. and got the beta value ( beta1 = 
> 1.9781e+03, beta2 = 2.0639e+03, beta3 = 110.9220, beta4 = 5.1964e-04 ) 
> from beta.mgh file.
>  Using X.mat file and the same dependent variable Y.mat as 
> mri_glmfit's, I got totally different results in Matlab( beta1 = 
> 5.19e+02, beta2 = 4.44e+02, beta3 = 90.32, beta4 = 0.0015 ).
> I don't know how it happened...
>  
> Hope for your reply.
> The data I used are all in the attachment.
>  
> Best Regrads,
>  
> Lijie Huang
> On Fri, Apr 29, 2011 at 9:45 PM,  > wrote:
>
> Lijie,
>
> I don't know what the matlab regress() function does. mri_glmfit
> is just
> solving the GLM equation, which you can do easily in matlab:
>
> beta = inv(X'*X)*X'*y;
>
> try that and see if you get the same as mri_glmfit.
>
> doug
>
>
> > Hi all,
> >
> > I'm working on a group analysis using mri_glmfit.
> >  In analysis directory, I got a X.mat file which containing the
> matrix X (
> > size 50x4 ) used to regress analysis, also the beta value from
> beta.mgh
> > file.
> > Strangely, I loaded the X.mat in Matlab and recalculated the
> beta using
> > function regress in matlab, but got a different result from that of
> > mri_glmfit.
> > I don't know where the problem is, is there any difference in
> algorithm
> > between mri_glmfit and matlab function regress( regress(Y,X) )?
> or I made
> > some mistakes during the procedure.
> > The X.mat file and the dependent variable Y.mat are in the
> attachment.
> >
> > Thanks in advance
> >
> > Lijie Huang
> > ___
> > 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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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422

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Re: [Freesurfer] A problem about mri_glmfit result

[soft.join Huang]

Doug,

Thanks for your reply.
I recalculated the beta value and got the same results as the Matlab does,
but be different from the mri_glmfit's. I can not figure out where the
problem is.
Details following:
 I use the command
  mri_glmfit --table lh.volume.txt --fsgd volume.gender.fsgd doss
--C gender.diff.mtx --glmdir lh.vol.glmdir
 to finish regression analysis. and got the beta value ( beta1 =
1.9781e+03, beta2 = 2.0639e+03, beta3 = 110.9220, beta4 = 5.1964e-04 ) from
beta.mgh file.
 Using X.mat file and the same dependent variable Y.mat as mri_glmfit's,
I got totally different results in Matlab( beta1 = 5.19e+02, beta2 =
4.44e+02, beta3 = 90.32, beta4 = 0.0015 ).
I don't know how it happened...

Hope for your reply.
The data I used are all in the attachment.

Best Regrads,

Lijie Huang
On Fri, Apr 29, 2011 at 9:45 PM,  wrote:

> Lijie,
>
> I don't know what the matlab regress() function does. mri_glmfit is just
> solving the GLM equation, which you can do easily in matlab:
>
> beta = inv(X'*X)*X'*y;
>
> try that and see if you get the same as mri_glmfit.
>
> doug
>
>
> > Hi all,
> >
> > I'm working on a group analysis using mri_glmfit.
> >  In analysis directory, I got a X.mat file which containing the matrix X
> (
> > size 50x4 ) used to regress analysis, also the beta value from beta.mgh
> > file.
> > Strangely, I loaded the X.mat in Matlab and recalculated the beta using
> > function regress in matlab, but got a different result from that of
> > mri_glmfit.
> > I don't know where the problem is, is there any difference in algorithm
> > between mri_glmfit and matlab function regress( regress(Y,X) )? or I made
> > some mistakes during the procedure.
> > The X.mat file and the dependent variable Y.mat are in the attachment.
> >
> > Thanks in advance
> >
> > Lijie Huang
> > ___
> > 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.
>
>
lh.aparc.volume lh_bankssts_volume
S0295   2613
S0057   3172
S0138   3267
S0139   2962
S0104   3071
S0230   2852
S0032   3434
S0165   3181
S0338   2629
S0099   2891
S0004   3382
S0296   3208
S0105   2067
S0036   2826
S0279   3148
S0140   3162
S0085   2364
S0311   2723
S0037   2085
S0166   2223
S0038   1999
S0231   2429
S0232   3004
S0167   1964
S0108   2850
S0141   2949
S0135   2213
S0322   2053
S0142   1983
S0098   2608
S0282   2047
S0101   2652
S0005   3261
S0299   2793
S0143   2478
S0109   2956
S0312   3468
S0271   2669
S0168   3649
S0323   3097
S0283   2921
S0144   1560
S0284   3081
S0255   2717
S0001   2880
S0324   2771
S0285   2989
S0256   3164
S0111   4366
S0233   2446


gender.diff.mtx
Description: Binary data


volume.gender.fsgd
Description: Binary data


X.mat
Description: Binary data


Y.mat
Description: Binary data
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Re: [Freesurfer] A problem about mri_glmfit result

[greve]

Lijie,

I don't know what the matlab regress() function does. mri_glmfit is just
solving the GLM equation, which you can do easily in matlab:

beta = inv(X'*X)*X'*y;

try that and see if you get the same as mri_glmfit.

doug


> Hi all,
>
> I'm working on a group analysis using mri_glmfit.
>  In analysis directory, I got a X.mat file which containing the matrix X (
> size 50x4 ) used to regress analysis, also the beta value from beta.mgh
> file.
> Strangely, I loaded the X.mat in Matlab and recalculated the beta using
> function regress in matlab, but got a different result from that of
> mri_glmfit.
> I don't know where the problem is, is there any difference in algorithm
> between mri_glmfit and matlab function regress( regress(Y,X) )? or I made
> some mistakes during the procedure.
> The X.mat file and the dependent variable Y.mat are in the attachment.
>
> Thanks in advance
>
> Lijie Huang
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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[Freesurfer] A problem about mri_glmfit result

[soft.join Huang]

Hi all,

I'm working on a group analysis using mri_glmfit.
 In analysis directory, I got a X.mat file which containing the matrix X (
size 50x4 ) used to regress analysis, also the beta value from beta.mgh
file.
Strangely, I loaded the X.mat in Matlab and recalculated the beta using
function regress in matlab, but got a different result from that of
mri_glmfit.
I don't know where the problem is, is there any difference in algorithm
between mri_glmfit and matlab function regress( regress(Y,X) )? or I made
some mistakes during the procedure.
The X.mat file and the dependent variable Y.mat are in the attachment.

Thanks in advance

Lijie Huang


X.mat
Description: Binary data


Y.mat
Description: Binary data
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Re: [Freesurfer] A problem about average curvature value

[Douglas N Greve]

It is iterative. The heat kernel stuff does not actually work.

doug

Zhangyuanchao wrote:

Thanks a lot!
 
what do you mean by iterative smoothing, is it heat kernel smoothing?
 
Attached is a paper about curvature of UCLA, in which I highlight some 
part of it.
 
firstly, they average the mean curvature within 3mm, then obtain its 
absolute value,
Then they further smoothed the absolute mean curvature using heat 
kernel smoothing.
 
I do not know what is the difference between averaging and iterative 
smoothing.
 
By the way, can I get the absolute value of a curv file using build-in 
function rather than load it into matlab and then write it back to 
binary files?
 
yczhang
 
 
 
Thanks


--- *09年6月1日，周一, Bruce Fischl //* 写道：


发件人: Bruce Fischl 
主题: Re: [Freesurfer] A problem about average curvature value
收件人: "Zhangyuanchao" 
抄送: "freesurfer" 
日期: 2009年6月1日,周一,下午10:36

Hi yczhang,

yes, mris_average_curvature will do this on the surfae. It uses
iterative averaging, but this converges to a Gaussian. Doug: can
you post the formula that translates number of iterations into fwhm?

thanks
Bruce

p.s. remember to include the -w switch otherwise it won't write
out the results.


On Mon, 1 Jun 2009, Zhangyuanchao wrote:

> Is there any build-in function that I can average a curvature
file with Radius of 4mm on the surface, for example, lh.pial.H.crv
file. in addition, lh.curv are smoothed in some way, is it
smoothed simply by averaging the values?
>  
> Thanks!
>  
> Best Regards,

> yczhang
>
>
>  ___
>  ÿÿ
> http://card.mail.cn.yahoo.com/



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Fax: 617-726-7422


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Re: [Freesurfer] A problem about average curvature value

[Douglas N Greve]

you can just use mri_surf2surf with the --fwhm option

Bruce Fischl wrote:

Hi yczhang,

yes, mris_average_curvature will do this on the surfae. It uses 
iterative averaging, but this converges to a Gaussian. Doug: can you 
post the formula that translates number of iterations into fwhm?


thanks
Bruce

p.s. remember to include the -w switch otherwise it won't write out 
the results.



On Mon, 1 Jun 2009, Zhangyuanchao wrote:

Is there any build-in function that I can average a curvature file 
with Radius of 4mm on the surface, for example, lh.pial.H.crv file. 
in addition, lh.curv are smoothed in some way, is it smoothed simply 
by averaging the values?
 
Thanks!
 
Best Regards,

yczhang


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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 
Fax: 617-726-7422


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Re: [Freesurfer] A problem about average curvature value

[Rudolph Pienaar]

Zhangyuanchao wrote:
 
By the way, can I get the absolute value of a curv file using build-in 
function rather than load it into matlab and then write it back to 
binary files?
 


$>mris_calc -o lh.abs.curv lh.curv abs

This will calculate the absolute value of the curv file 'lh.curv' and 
save to 'lh.abs.curv'.




--
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MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
149 (2301) 13th Street, Charlestown, MA 02129 USA
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Re: [Freesurfer] A problem about average curvature value

[Bruce Fischl]

Hi yczhang,

yes, mris_average_curvature will do this on the surfae. It uses iterative 
averaging, but this converges to a Gaussian. Doug: can you post the formula 
that translates number of iterations into fwhm?


thanks
Bruce

p.s. remember to include the -w switch otherwise it won't write out the 
results.



On Mon, 1 Jun 2009, Zhangyuanchao 
wrote:



Is there any build-in function that I can average a curvature file with Radius 
of 4mm on the surface, for example, lh.pial.H.crv file. in addition, lh.curv 
are smoothed in some way, is it smoothed simply by averaging the values?
 
Thanks!
 
Best Regards,
yczhang


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[Freesurfer] A problem about average curvature value

[Zhangyuanchao]

Is there any build-in function that I can average a curvature file with Radius 
of 4mm on the surface, for example, lh.pial.H.crv file. in addition, lh.curv 
are smoothed in some way, is it smoothed simply by averaging the values?
 
Thanks!
 
Best Regards,
yczhang


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Re: [Freesurfer] A problem on groupanalysis

[Doug Greve]

Have you looked at my presentation on group analysis? The slides are here:

http://surfer.nmr.mgh.harvard.edu/docs/ftp/pub/docs/freesurfer.groupanalysis.pdf

There's a very similar design on slides 23 and 24.

doug



Zhangyuanchao wrote:

> Dear Mr or Ms,
> I have read the FreeSurfer Tutorial: Group Analysis, but there are
> still something I do not quite understand. I want to make comparison
> of lgi between two groups, namely, normal control groupand patient
> group. I want to regress out gender and age.For example,if I have 4
> subjects:nc1 male age=30,nc2 female age=31,patient1 male age=32,
> patient2 female age=30, how should I create the FSGD file?How should I
> design the constrast vector? What kind of test does Freesurfer
> use,F-test or t-test to detect difference regionof thickness orlgion
> the surface? What should I do if I want to use t-test to detect the
> difference between two groups? How should I set the option of the
> command mri_glmfit --sim nulltype nsim thresh csdbasename if I want to
> set the p-value threshold 0.05?
> Sorry for the trouble!
> Thank you very much!
> Yuanchao Zhang
>
> 
> 雅虎邮箱，您的终生邮箱！ 
>
>
>
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MGH-NMR Center
[EMAIL PROTECTED]
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Fax: 617-726-7422

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[Freesurfer] A problem on groupanalysis

[Zhangyuanchao]

Dear Mr or Ms,
  I have read the FreeSurfer Tutorial: Group Analysis, but there are still 
something  I do not quite understand. I want to make comparison of lgi between 
two groups, namely, normal control group and patient group. I want to regress 
out gender and age.For example,if I have 4 subjects: nc1 male age=30,nc2 female 
age=31,patient1 male age=32, patient2 female age=30, how should I create the 
FSGD file?How should I design the constrast vector? What kind of test does 
Freesurfer use,F-test or t-test to detect difference region of thickness or lgi 
on the surface? What should I do if I want to use t-test to detect the 
difference between two groups? How should I set the option of the command 
mri_glmfit --sim nulltype nsim thresh csdbasename if I want to set the p-value 
threshold 0.05?
  Sorry for the trouble!
  Thank you very much!
  Yuanchao Zhang

   
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[Freesurfer] a problem

[yczhang]

Using lgi or thickness,how could I know the anatomical correspondence for a  
statistical difference area which had been found between patients and controls. 
I have to report the significant regions ,for example ,postcentral sulcus or 
posterior cingulate
Thanks!




yczhang
2008-05-21
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[Freesurfer] a problem

[yczhang]

Using lgi or thickness,how could I know the anatomical correspondence for a  
statistical difference area which had been found between patients and controls.
Thanks!




yczhang
2008-05-21
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Re: [Freesurfer] A problem with Deflate compression of tif format

[Nick Schmansky]

Jiefeng Jiang,

I can't say I have seen that problem, but we use libtiff.so.3 here, so
you may want to try installing that version of libtiff, rather than
linking libtiff.so.4 to libtiff.so.3 (if I understand correctly, you
have libtiff.so.4).

Nick

ps. I did find this message by googling the error:

Problem: Trying to produce a zip/deflate compressed file produces the
message "Deflate compression support is not configured."

Solution: Your TIFF library was not compiled with ZIP support.  The
standard libtiff is almost never distributed with ZIP="yes" in the
config.site file, so you will need to recompile it yourself if
you want to build drgtools which support zip from the source code.



On Wed, 2008-01-02 at 19:06 +0800, Jiefeng Jiang wrote:
> Hi, 
>  
> I met the problem of "Deflate compression support is not configured.
> TiffWrite: TIFFWriteScanline returned error" when I used
> mris_make_template. Currently I use libtiff4 for tiff interface and
> zlib1g for deflate compression. In addition, I linked libtiff.so.3 to
> libtiff.so.4. I also tested the two libs by opening and saving a
> sample tiff image and they worked well. I have no idea how to solve
> this, maybe I need to establish another link for deflate
> compression... Could somebody give me some advices?
>  
> Thank you in advance!
>  
>  
> Jiefeng Jiang
>  
> Medical image computing
> National lab of pattern recognition
> Institute of automation, CAS
> Beijing, China
> +86 10 62659278
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[Freesurfer] A problem with Deflate compression of tif format

[Jiefeng Jiang]

Hi, 

I met the problem of "Deflate compression support is not configured. TiffWrite: 
TIFFWriteScanline returned error" when I used mris_make_template. Currently I 
use libtiff4 for tiff interface and zlib1g for deflate compression. In 
addition, I linked libtiff.so.3 to libtiff.so.4. I also tested the two libs by 
opening and saving a sample tiff image and they worked well. I have no idea how 
to solve this, maybe I need to establish another link for deflate 
compression... Could somebody give me some advices?

Thank you in advance!


Jiefeng Jiang

Medical image computing
National lab of pattern recognition
Institute of automation, CAS
Beijing, China
+86 10 62659278___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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RE: [Freesurfer] A problem occurred while running recon-all in thenew dev version

[Nick Schmansky]

Shen-Mou,

In older freesurfer installations, which did not include the MINC tools
directly, but were included in a separate download, we recommended
installing that separate download in the same path as that which exists
at our center, which is /usr/pubsw/packages/mni/current/.

A goal of the new freesurfer installation is to make it totally self-
contained, and able to be installed in any directory, and not require
admin priveledges.  So now the MINC tools are included in the
freesurfer/lib/mni directory, and do not need to be installed
in /usr/pubsw/packages/mni/current (although there is still an issue
with certain mni tools looking for perl in the path /usr/pubsw/bin, but
that is being resolved soon, and the installation instructions describe
the temporary hack of creating a symbolic link).

So, the easiest way to confirm that your installation is correct is,
after sourcing SetUpFreeSurfer.csh, check that all the path names point
into your new installation, and running 'which nu_correct' should also
point into your new installation.

Nick

On Wed, 2005-09-21 at 16:33 -0400, Hsu, Shen-Mou wrote: 
> Many thanks Nick!
> 
> It is working now after changing setenv MINC_BIN_DIR 
> /usr/pubsw/packages/mni/current/bin (the default) into setenv MINC_BIN_DIR 
> /home/riobravo/freesurfer/lib/mni/bin (the home directory). Then, I got the 
> latest version of nu_correct. Is there any possibility that my installization 
> went wrong? I reckon that in principle, the MINC tool should be store in the 
> /usr/pubsw/packages/mni/current/bin?
> 
> thanks again! Shen-Mou
> 
> 
> -Original Message-
> From: Nick Schmansky [mailto:[EMAIL PROTECTED]
> Sent: Wed 9/21/2005 1:14 PM
> To: Hsu, Shen-Mou
> Cc: Brian T. Quinn; Freesurfer Mailing List
> Subject: RE: [Freesurfer] A problem occurred while running recon-all in 
> thenewdev version
>  
> Hsu,
> 
> The MINC toolkit is now included in the Freesurfer distribution, and
> nu_correct should be version 1.10.  
> 
> Since you say that nu_correct returns a version 1.04, its my guess that
> you have an older version of the MINC toolkit installed somewhere in
> your path.  Remove any setup commands to older MINC toolkits in
> your .cshrc file.  
> 
> The new $FREESURFER_HOME/FreeSurferEnv.csh script (called by
> SetUpFreeSurfer.csh) will setup the paths to the newly installed MINC
> toolkit for you.
> 
> You can confirm which tools are used by typing:
> 
>   which nu_correct
> 
> and
> 
>   which nu_estimate_np_and_em
> 
> These binaries should be in a subdirectory of your new FreeSurfer
> installation.  Also type:
> 
>   echo $PERL5LIB
> 
> and confirm that the path points to your new installation.
> 
> Nick
>  
> 
> On Wed, 2005-09-21 at 13:00 -0400, Hsu, Shen-Mou wrote:
> > Dear All,
> > 
> > The problem is fixed as Brian suggested (Thanks Brian), but there is a new 
> > problem while running the recon-all. Nu_correct somehow crashes during the 
> > proceesing. The follows are the details. Could anyone give me an idea?
> > 
> > Thanks a lot in advance!
> > 
> > p.s. nu_correct seems fine while typing nuc_correct, it returns vesion info 
> > (1.04).
> > 
> > [EMAIL PROTECTED] ~/freesurfer]$ recon-all -autorecon1 -subjid Sub05
> > INFO: SUBJECTS_DIR is /home/riobravo/freesurfer/subjects
> > Actual FREESURFER_HOME /home/riobravo/freesurfer
> > Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 
> > i686 i686 i386 GNU/Linux
> > 
> > program versions used
> > $Id: recon-all-nmr,v 1.104 2005/09/07 15:59:46 greve Exp $
> > $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $
> > mri_convert --version
> >  $
> > $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 
> > 6.3 1999/10/19 14:45:31 neelin Exp $
> > minctracc.c
> > $Header: 
> > /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 
> > 2000/03/15 08:42:41 stever Exp $
> > $Header: 
> > /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 
> > 1999/10/19 14:45:27 neelin Exp $
> > $Header: 
> > /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 6.1 
> > 1999/10/19 14:45:18 neelin Exp $
> > $Id: talairach2,v 1.8 2005/09/06 13:54:17 nicks Exp $
> > mri_convert --version
> >  $
> > # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $
> > Program nu_correct, built from:
> > Package MNI N3, version 1.04, compiled by [EMAIL PROTECTED] 
> > (i686-pc-linux-gnu) on 2001-08-09 at 10:52:16
> > ProgramName: mri_normalize ProgramArgumen

RE: [Freesurfer] A problem occurred while running recon-all in thenew dev version

[Hsu, Shen-Mou]

Many thanks Nick!

It is working now after changing setenv MINC_BIN_DIR 
/usr/pubsw/packages/mni/current/bin (the default) into setenv MINC_BIN_DIR 
/home/riobravo/freesurfer/lib/mni/bin (the home directory). Then, I got the 
latest version of nu_correct. Is there any possibility that my installization 
went wrong? I reckon that in principle, the MINC tool should be store in the 
/usr/pubsw/packages/mni/current/bin?

thanks again! Shen-Mou


-Original Message-
From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Wed 9/21/2005 1:14 PM
To: Hsu, Shen-Mou
Cc: Brian T. Quinn; Freesurfer Mailing List
Subject: RE: [Freesurfer] A problem occurred while running recon-all in thenew  
dev version
 
Hsu,

The MINC toolkit is now included in the Freesurfer distribution, and
nu_correct should be version 1.10.  

Since you say that nu_correct returns a version 1.04, its my guess that
you have an older version of the MINC toolkit installed somewhere in
your path.  Remove any setup commands to older MINC toolkits in
your .cshrc file.  

The new $FREESURFER_HOME/FreeSurferEnv.csh script (called by
SetUpFreeSurfer.csh) will setup the paths to the newly installed MINC
toolkit for you.

You can confirm which tools are used by typing:

  which nu_correct

and

  which nu_estimate_np_and_em

These binaries should be in a subdirectory of your new FreeSurfer
installation.  Also type:

  echo $PERL5LIB

and confirm that the path points to your new installation.

Nick
 

On Wed, 2005-09-21 at 13:00 -0400, Hsu, Shen-Mou wrote:
> Dear All,
> 
> The problem is fixed as Brian suggested (Thanks Brian), but there is a new 
> problem while running the recon-all. Nu_correct somehow crashes during the 
> proceesing. The follows are the details. Could anyone give me an idea?
> 
> Thanks a lot in advance!
> 
> p.s. nu_correct seems fine while typing nuc_correct, it returns vesion info 
> (1.04).
> 
> [EMAIL PROTECTED] ~/freesurfer]$ recon-all -autorecon1 -subjid Sub05
> INFO: SUBJECTS_DIR is /home/riobravo/freesurfer/subjects
> Actual FREESURFER_HOME /home/riobravo/freesurfer
> Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 
> i686 i686 i386 GNU/Linux
> 
> program versions used
> $Id: recon-all-nmr,v 1.104 2005/09/07 15:59:46 greve Exp $
> $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $
> mri_convert --version
>  $
> $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 
> 1999/10/19 14:45:31 neelin Exp $
> minctracc.c
> $Header: 
> /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 
> 2000/03/15 08:42:41 stever Exp $
> $Header: 
> /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 
> 1999/10/19 14:45:27 neelin Exp $
> $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 
> 6.1 1999/10/19 14:45:18 neelin Exp $
> $Id: talairach2,v 1.8 2005/09/06 13:54:17 nicks Exp $
> mri_convert --version
>  $
> # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $
> Program nu_correct, built from:
> Package MNI N3, version 1.04, compiled by [EMAIL PROTECTED] 
> (i686-pc-linux-gnu) on 2001-08-09 at 10:52:16
> ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: 
>  $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_normalize.c,v 1.36 
> 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain 
> Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC 
> CompilerVersion: 30200
> ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: 
>  $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_watershed.cpp,v 1.34 
> 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain 
> Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC 
> CompilerVersion: 30200
> ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name:  
> $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 
> 19:48:08 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
> Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
> ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name:  $ 
> TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_fill.c,v 1.95 2005/09/05 
> 20:49:50 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
> Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
> ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: 
> $Name:  $ TimeStamp: 05/09/21-14:13:44-GMT CVS: $Id: mri_tessellate.c,v 1.24 
> 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain 
> Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC 
> CompilerVersion

RE: [Freesurfer] A problem occurred while running recon-all in the new dev version

[Nick Schmansky]

rfer/subjects/Sub05/mri/rawavg.mgz 
> /home/riobravo/freesurfer/subjects/Sub05/mri/orig.mgz --conform
> mri_convert /home/riobravo/freesurfer/subjects/Sub05/mri/rawavg.mgz 
> /home/riobravo/freesurfer/subjects/Sub05/mri/orig.mgz --conform
> reading from /home/riobravo/freesurfer/subjects/Sub05/mri/rawavg.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (0, -1, 0)
> j_ras = (0, 0, -1)
> k_ras = (-1, 0, 0)
> Original Data has (1, 1, 1) mm size and (256, 256, 160) voxels.
> Data is conformed to 1 mm size and 256 voxels for all directions
> changing data type from 4 to 0 (noscale = 0)...
> MRIchangeType: Building histogram
> Reslicing using trilinear interpolation
> writing to /home/riobravo/freesurfer/subjects/Sub05/mri/orig.mgz...
> -
> Nu Intensity Correction Wed Sep 21 10:14:06 EDT 2005
> mri_convert orig.mgz nu0.mnc
> mri_convert orig.mgz nu0.mnc
> reading from orig.mgz...
> TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0, -1)
> k_ras = (0, 1, 0)
> writing to nu0.mnc...
> nu_correct -clobber nu0.mnc nu1.mnc
> nu_estimate_np_and_em: data directory for package "N3" not found in 
> /home/riobravo/freesurfer/lib/mni/data
> [EMAIL PROTECTED]:/home/riobravo/freesurfer/subjects/Sub05/mri/] [2005-09-21 
> 10:14:18] running:
>   /usr/pubsw/packages/mni/current/bin/nu_estimate_np_and_em -parzen -log 
> -sharpen 0.15 0.01 -iterations 50 -stop 0.001 -shrink 4 -auto_mask -nonotify 
> -b_spline 1 -distance 200 -quiet -execute -clobber -nokeeptmp -tmpdir 
> /usr/tmp/nu_correct_7260/ nu0.mnc nu1.imp
> 
> nu_correct: crashed while running nu_estimate_np_and_em (termination 
> status=512)
> ERROR: nu_correct
> Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 
> i686 i686 i386 GNU/Linux
> recon-all exited with errors at Wed Sep 21 10:14:18 EDT 2005
> 
> 
> 
> -Original Message-
> From: Brian T. Quinn [mailto:[EMAIL PROTECTED]
> Sent: Wed 9/21/2005 10:01 AM
> To: Hsu, Shen-Mou
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] A problem occurred while running recon-all in the 
> new   dev version
>  
> try renaming the .mgz volume (Sub05.mgz) in orig with a 3 digit zero 
> padded number such as 001.mgz
> 
> thanks,
> brian
> 
> On Wed, 21 Sep 2005, Hsu, Shen-Mou wrote:
> 
> > Hi!
> >
> > I am running the freesurfer on redhat 9 with the latest release 
> > (freesurfer-Linux-rh9-dev20050915-full.tar.gz.) Unfortunately, while 
> > running recon-all -autorecon1, it returns that no data is found, but the 
> > data exists indeed. Could anyone help me this out?
> >
> > Many thanks!
> >
> > Shen-Mou Hsu
> >
> > Here are the details.
> >
> > [EMAIL PROTECTED] freesurfer]$ tcsh
> > Setting up environment for FreeSurfer/FS-FAST (and FSL)
> > FREESURFER_HOME /home/riobravo/freesurfer
> > FSFAST_HOME /home/riobravo/freesurfer/fsfast
> > SUBJECTS_DIR/home/riobravo/freesurfer/subjects
> > FUNCTIONALS_DIR /home/riobravo/freesurfer/sessions
> > MINC_BIN_DIR/usr/pubsw/packages/mni/current/bin
> > MINC_LIB_DIR/usr/pubsw/packages/mni/current/lib
> > PERL5LIB
> > GSL_DIR /home/riobravo/freesurfer/lib/gsl
> > QTDIR   /home/riobravo/freesurfer/lib/qt
> > TCLLIBPATH  /home/riobravo/freesurfer/lib/tcltktixblt/lib
> > FSL_DIR /home/riobravo/fsl
> >
> > [EMAIL PROTECTED] orig]$ mri_convert 
> > /home/riobravo/Exp3/prefreesurfer/Sub05MP_ave+orig.BRIK Sub05.mgz
> > [EMAIL PROTECTED] orig]$ ls
> > Sub05.mgz
> >
> > [EMAIL PROTECTED] ~/freesurfer]$ recon-all -autorecon1 -subjid Sub05
> > INFO: SUBJECTS_DIR is /home/riobravo/freesurfer/subjects
> > Actual FREESURFER_HOME /home/riobravo/freesurfer
> > Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 
> > i686 i686 i386 GNU/Linux
> > 
> > program versions used
> > $Id: recon-all-nmr,v 1.104 2005/09/07 15:59:46 greve Exp $
> > $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $
> > mri_convert --version
> > $
> > $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 
> > 6.3 1999/10/19 14:45:31 neelin Exp $
> > minctracc.c
> > $Header: 
> > /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 
> > 2000/03/15 08:42:41 stever Exp $
> > $Header: 
> > /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 
> > 1999/10/19 14:45:27 neelin Exp $
> > $Header: 
> > /software/sourc

RE: [Freesurfer] A problem occurred while running recon-all in the new dev version

[Hsu, Shen-Mou]

: crashed while running nu_estimate_np_and_em (termination status=512)
ERROR: nu_correct
Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 
i686 i686 i386 GNU/Linux
recon-all exited with errors at Wed Sep 21 10:14:18 EDT 2005



-Original Message-
From: Brian T. Quinn [mailto:[EMAIL PROTECTED]
Sent: Wed 9/21/2005 10:01 AM
To: Hsu, Shen-Mou
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] A problem occurred while running recon-all in the new 
dev version
 
try renaming the .mgz volume (Sub05.mgz) in orig with a 3 digit zero 
padded number such as 001.mgz

thanks,
brian

On Wed, 21 Sep 2005, Hsu, Shen-Mou wrote:

> Hi!
>
> I am running the freesurfer on redhat 9 with the latest release 
> (freesurfer-Linux-rh9-dev20050915-full.tar.gz.) Unfortunately, while running 
> recon-all -autorecon1, it returns that no data is found, but the data exists 
> indeed. Could anyone help me this out?
>
> Many thanks!
>
> Shen-Mou Hsu
>
> Here are the details.
>
> [EMAIL PROTECTED] freesurfer]$ tcsh
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME /home/riobravo/freesurfer
> FSFAST_HOME /home/riobravo/freesurfer/fsfast
> SUBJECTS_DIR/home/riobravo/freesurfer/subjects
> FUNCTIONALS_DIR /home/riobravo/freesurfer/sessions
> MINC_BIN_DIR/usr/pubsw/packages/mni/current/bin
> MINC_LIB_DIR/usr/pubsw/packages/mni/current/lib
> PERL5LIB
> GSL_DIR /home/riobravo/freesurfer/lib/gsl
> QTDIR   /home/riobravo/freesurfer/lib/qt
> TCLLIBPATH  /home/riobravo/freesurfer/lib/tcltktixblt/lib
> FSL_DIR /home/riobravo/fsl
>
> [EMAIL PROTECTED] orig]$ mri_convert 
> /home/riobravo/Exp3/prefreesurfer/Sub05MP_ave+orig.BRIK Sub05.mgz
> [EMAIL PROTECTED] orig]$ ls
> Sub05.mgz
>
> [EMAIL PROTECTED] ~/freesurfer]$ recon-all -autorecon1 -subjid Sub05
> INFO: SUBJECTS_DIR is /home/riobravo/freesurfer/subjects
> Actual FREESURFER_HOME /home/riobravo/freesurfer
> Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 
> i686 i686 i386 GNU/Linux
> 
> program versions used
> $Id: recon-all-nmr,v 1.104 2005/09/07 15:59:46 greve Exp $
> $Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $
> mri_convert --version
> $
> $Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 
> 1999/10/19 14:45:31 neelin Exp $
> minctracc.c
> $Header: 
> /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 96.3 
> 2000/03/15 08:42:41 stever Exp $
> $Header: 
> /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 6.2 
> 1999/10/19 14:45:27 neelin Exp $
> $Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 
> 6.1 1999/10/19 14:45:18 neelin Exp $
> $Id: talairach2,v 1.8 2005/09/06 13:54:17 nicks Exp $
> mri_convert --version
> $
> # $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $
> Program nu_correct, built from:
> Package MNI N3, version 1.04, compiled by [EMAIL PROTECTED] 
> (i686-pc-linux-gnu) on 2001-08-09 at 10:52:16
> ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name: 
>  $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_normalize.c,v 1.36 
> 2005/08/15 14:05:49 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain 
> Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC 
> CompilerVersion: 30200
> ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name: 
>  $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_watershed.cpp,v 1.34 
> 2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain 
> Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC 
> CompilerVersion: 30200
> ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name:  
> $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 
> 19:48:08 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
> Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
> ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name:  $ 
> TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_fill.c,v 1.95 2005/09/05 
> 20:49:50 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
> Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
> ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: 
> $Name:  $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_tessellate.c,v 1.24 
> 2005/08/18 16:19:10 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain 
> Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC 
> CompilerVersion: 30200
> ProgramName: mris_smooth ProgramArguments: -all-info Progra

Re: [Freesurfer] A problem occurred while running recon-all in the new dev version

[Brian T. Quinn]

try renaming the .mgz volume (Sub05.mgz) in orig with a 3 digit zero 
padded number such as 001.mgz


thanks,
brian

On Wed, 21 Sep 2005, Hsu, Shen-Mou wrote:


Hi!

I am running the freesurfer on redhat 9 with the latest release 
(freesurfer-Linux-rh9-dev20050915-full.tar.gz.) Unfortunately, while running 
recon-all -autorecon1, it returns that no data is found, but the data exists 
indeed. Could anyone help me this out?

Many thanks!

Shen-Mou Hsu

Here are the details.

[EMAIL PROTECTED] freesurfer]$ tcsh
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /home/riobravo/freesurfer
FSFAST_HOME /home/riobravo/freesurfer/fsfast
SUBJECTS_DIR/home/riobravo/freesurfer/subjects
FUNCTIONALS_DIR /home/riobravo/freesurfer/sessions
MINC_BIN_DIR/usr/pubsw/packages/mni/current/bin
MINC_LIB_DIR/usr/pubsw/packages/mni/current/lib
PERL5LIB
GSL_DIR /home/riobravo/freesurfer/lib/gsl
QTDIR   /home/riobravo/freesurfer/lib/qt
TCLLIBPATH  /home/riobravo/freesurfer/lib/tcltktixblt/lib
FSL_DIR /home/riobravo/fsl

[EMAIL PROTECTED] orig]$ mri_convert 
/home/riobravo/Exp3/prefreesurfer/Sub05MP_ave+orig.BRIK Sub05.mgz
[EMAIL PROTECTED] orig]$ ls
Sub05.mgz

[EMAIL PROTECTED] ~/freesurfer]$ recon-all -autorecon1 -subjid Sub05
INFO: SUBJECTS_DIR is /home/riobravo/freesurfer/subjects
Actual FREESURFER_HOME /home/riobravo/freesurfer
Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 
i686 i686 i386 GNU/Linux

program versions used
$Id: recon-all-nmr,v 1.104 2005/09/07 15:59:46 greve Exp $
$Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $
mri_convert --version
$
$Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 
1999/10/19 14:45:31 neelin Exp $
minctracc.c
$Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 
96.3 2000/03/15 08:42:41 stever Exp $
$Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 
6.2 1999/10/19 14:45:27 neelin Exp $
$Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 
6.1 1999/10/19 14:45:18 neelin Exp $
$Id: talairach2,v 1.8 2005/09/06 13:54:17 nicks Exp $
mri_convert --version
$
# $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $
Program nu_correct, built from:
Package MNI N3, version 1.04, compiled by [EMAIL PROTECTED] (i686-pc-linux-gnu) 
on 2001-08-09 at 10:52:16
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name:  
$ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_normalize.c,v 1.36 2005/08/15 
14:05:49 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name:  
$ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_watershed.cpp,v 1.34 
2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain 
Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 
30200
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name:  $ 
TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 
19:48:08 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name:  $ 
TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_fill.c,v 1.95 2005/09/05 
20:49:50 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name:  
$ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 
16:19:10 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name:  $ 
TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 
14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name:  $ 
TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 
14:23:37 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name:  $ 
TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 
14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
ProgramName: mris_fix_topology ProgramArguments: -al

[Freesurfer] A problem occurred while running recon-all in the new dev version

[Hsu, Shen-Mou]

Hi!

I am running the freesurfer on redhat 9 with the latest release 
(freesurfer-Linux-rh9-dev20050915-full.tar.gz.) Unfortunately, while running 
recon-all -autorecon1, it returns that no data is found, but the data exists 
indeed. Could anyone help me this out? 

Many thanks!

Shen-Mou Hsu

Here are the details.

[EMAIL PROTECTED] freesurfer]$ tcsh
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME /home/riobravo/freesurfer
FSFAST_HOME /home/riobravo/freesurfer/fsfast
SUBJECTS_DIR/home/riobravo/freesurfer/subjects
FUNCTIONALS_DIR /home/riobravo/freesurfer/sessions
MINC_BIN_DIR/usr/pubsw/packages/mni/current/bin
MINC_LIB_DIR/usr/pubsw/packages/mni/current/lib
PERL5LIB
GSL_DIR /home/riobravo/freesurfer/lib/gsl
QTDIR   /home/riobravo/freesurfer/lib/qt
TCLLIBPATH  /home/riobravo/freesurfer/lib/tcltktixblt/lib
FSL_DIR /home/riobravo/fsl

[EMAIL PROTECTED] orig]$ mri_convert 
/home/riobravo/Exp3/prefreesurfer/Sub05MP_ave+orig.BRIK Sub05.mgz
[EMAIL PROTECTED] orig]$ ls
Sub05.mgz

[EMAIL PROTECTED] ~/freesurfer]$ recon-all -autorecon1 -subjid Sub05
INFO: SUBJECTS_DIR is /home/riobravo/freesurfer/subjects
Actual FREESURFER_HOME /home/riobravo/freesurfer
Linux localhost.localdomain 2.4.20-6smp #1 SMP Thu Feb 27 09:59:40 EST 2003 
i686 i686 i386 GNU/Linux

program versions used
$Id: recon-all-nmr,v 1.104 2005/09/07 15:59:46 greve Exp $
$Id: mri_motion_correct2,v 1.9 2004/12/14 03:37:42 greve Exp $
mri_convert --version
 $
$Header: /software/source/minc/cvsroot/minc/progs/rawtominc/rawtominc.c,v 6.3 
1999/10/19 14:45:31 neelin Exp $
minctracc.c
$Header: /software/source/registration/mni_autoreg/minctracc/Main/minctracc.c,v 
96.3 2000/03/15 08:42:41 stever Exp $
$Header: /software/source/minc/cvsroot/minc/progs/mincresample/mincresample.c,v 
6.2 1999/10/19 14:45:27 neelin Exp $
$Header: /software/source/minc/cvsroot/minc/progs/mincaverage/mincaverage.c,v 
6.1 1999/10/19 14:45:18 neelin Exp $
$Id: talairach2,v 1.8 2005/09/06 13:54:17 nicks Exp $
mri_convert --version
 $
# $Id: mritotal.in,v 1.10 2000/06/14 12:55:01 louis Exp $
Program nu_correct, built from:
Package MNI N3, version 1.04, compiled by [EMAIL PROTECTED] (i686-pc-linux-gnu) 
on 2001-08-09 at 10:52:16
ProgramName: mri_normalize ProgramArguments: -all-info ProgramVersion: $Name:  
$ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_normalize.c,v 1.36 2005/08/15 
14:05:49 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
ProgramName: mri_watershed ProgramArguments: -all-info ProgramVersion: $Name:  
$ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_watershed.cpp,v 1.34 
2005/08/15 14:05:17 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain 
Platform: Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 
30200
ProgramName: mri_segment ProgramArguments: -all-info ProgramVersion: $Name:  $ 
TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_segment.c,v 1.27 2005/08/24 
19:48:08 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
ProgramName: mri_fill ProgramArguments: -all-info ProgramVersion: $Name:  $ 
TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_fill.c,v 1.95 2005/09/05 
20:49:50 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
ProgramName: mri_tessellate ProgramArguments: -all-info ProgramVersion: $Name:  
$ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mri_tessellate.c,v 1.24 2005/08/18 
16:19:10 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
ProgramName: mris_smooth ProgramArguments: -all-info ProgramVersion: $Name:  $ 
TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_smooth.c,v 1.13 2005/08/15 
14:22:53 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
ProgramName: mris_inflate ProgramArguments: -all-info ProgramVersion: $Name:  $ 
TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_inflate.c,v 1.28 2005/08/15 
14:23:37 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
ProgramName: mris_sphere ProgramArguments: -all-info ProgramVersion: $Name:  $ 
TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_sphere.c,v 1.31 2005/08/15 
14:24:12 fischl Exp $ User: UNKNOWN Machine: localhost.localdomain Platform: 
Linux PlatformVersion: 2.4.20-6smp CompilerName: GCC CompilerVersion: 30200
ProgramName: mris_fix_topology ProgramArguments: -all-info ProgramVersion: 
$Name:  $ TimeStamp: 05/09/21-13:51:01-GMT CVS: $Id: mris_fix_topology.c,v 1.31 
2005/08/15 14:28:43 fischl Exp $ User: UNKNOWN Machin