[Freesurfer] tkmedit background color

[Righart, Ruthger Dr.]

Dear Freesurfer experts,

I am trying to find out how to change the background color of tkmedit.

Is there a possibility to change the background color from black to white, just 
for display purposes? (to avoid laborious photoshop work).

Best Regards,

Ruthger Righart
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Re: [Freesurfer] mergecontrasts-sess group map

[Alexandra Tanner]

Hi Doug,

So if I run a group analysis with each contrast separately, would I then
be running mri_concat to do a conjunction of the group sig maps? Also, can
I merge more than 2 contrasts at once when using mri_concat? Thanks!

Alex

>
> Hi Alex, unfortunately, you cannot compute a conjunction with the CES.
That's the problem with trying to do group-wise multi-variate analysis.
Another thing you can do is to do a group analysis with each contrast
separately, then do a conjunction of the group sig maps.
> doug
>
> On 11/29/2012 03:39 PM, Alexandra Tanner wrote:
>> Thanks for the clarification! So I will rerun mergecontrasts-sess using
the ces image on my subjects and then run mri_vol2surf and mri_concat
to
>> get the group map. Thanks for your help!
>> Best,
>> Alex
>>> Usually the contrast effects size (ces) (in SPM this is the CON image,
in FSL it is the COPE image). Univariate maps are usually passed up to
the group level (the conjunction done with mergecontrasts is
>>> multivariate).
>>> doug
>>> On 11/29/2012 01:05 PM, Alexandra Tanner wrote:
 Hi Doug,
 Thanks for the response! Just out of curiosity, what map is typically
used
 for group analyses? Should I have used a map other than sig on the
individual subject level as well?
 Thanks!
 Alex
> You'll have to run mri_vol2surf on each one separately to bring it into
> the fsaverage space, then mri_concat to stack all of the maps into one
> file. At that point you can compute a mean (also with mri_concat).
Generally, one does not do group analysis on sig maps though. doug
> On 11/27/2012 05:08 PM, Alexandra Tanner wrote:
>> Hi Doug and Freesurfers,
>> I recently used mergecontrasts-sess to merge two contrasts of an
analysis
>> in 50 different subjects. The command ran on each subject
>> individually
>> and
>> created a sig.nii and sig.ovpl file within a merged contrast folder
for
>> each subject. I'd now like to look at an average map of the merged
contrasts across all 50 subjects.
>> Does anyone know how to go about getting this average map for my group
>> of
>> 50 subjects?
>> Command I ran to get the sig.nii/sig.ovpl file for each subject:
mergecontrasts-sess -mergedcontrast Merge_7vFix_1vFix -conjunction
andor
>> -analysis SIRP_Stable5 -contrast Cond7vFix 3 pos 0 -contrast Cond1vFix
>> 3
>> pos 0 -map sig -sf
>> /cluster/roffman/users/Stable5_PerRun/Subject_Files/50_MTH_Subjects
-df
>> /cluster/roffman/users/Stable5_PerRun
>> Any help would be greatly appreciated!
>> Thanks,
>> Alex
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>> --
>>> Douglas N. Greve, Ph.D.
>>> MGH-NMR Center
>>> gr...@nmr.mgh.harvard.edu
>>> Phone Number: 617-724-2358
>>> Fax: 617-726-7422
>>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
>>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>



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Re: [Freesurfer] FW: TRACULA some fiber volumes being too small

[Anastasia Yendiki]

Fantastic, thanks!

On Fri, 30 Nov 2012, Fernando Ventrice wrote:


Dear Anastasia, now it worked perfectly well changing the Z gradient with 
*(-1)! Here I send you a screenshot.
Best,
Fernando

-Mensaje original-
De: Fernando Ventrice
Enviado el: 29 November 2012 11:39
Para: Anastasia Yendiki
Asunto: RE: [Freesurfer] FW: TRACULA some fiber volumes being too small

Hi Anastasia,
I'll rerun all steps changing the Z gradient with *(-1). Thanks and I'll write 
with the results. Best,
Fernando

-Mensaje original-
De: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] En nombre de Anastasia Yendiki
Enviado el: 28 November 2012 15:30
Para: Fernando Ventrice
CC: freesurfer@nmr.mgh.harvard.edu
Asunto: Re: [Freesurfer] FW: TRACULA some fiber volumes being too small


Hi Fernando - I looked at your data and changing the sign of the z
coordinate in your gradient table gave me eigenvectors that looked fine in
both fslview and freeview. Why you would get eigenvectors that look
different in freeview and fslview before flipping z but not after is still
a mystery to me, but at this point I'd just try starting clean, changing
the sign in the 3rd column of your gradient table, and testing the whole
pipeline on a test subject to see if that fixes things. Let me know how it
goes!

a.y


Dear Anastasia,
When I open the dtifit_V1 and dtifit_FA with Freeview the vector directions 
actually are OK, but when I open them with FSLview they are similar to your 
screen-shot. Here I also send a screen-shot with the comparison between the two 
softwares in each monitor.
Best,
Fernando

El contenido del presente mensaje y el de sus adjuntos, es confidencial, 
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revisión, divulgación, publicación, modificación, copia, distribución o acción 
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tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son 
exclusivas de su autor, y no representa necesariamente, la opinión de FLENI.
http://www.fleni.org.ar



El contenido del presente mensaje y el de sus adjuntos, es confidencial, 
privado y de uso exclusivo de los destinatarios a los cuales está dirigido, 
pudiendo contener información legalmente protegida. Queda prohibida la 
revisión, divulgación, publicación, modificación, copia, distribución o acción 
en relación con esta información, por personas o entidades distintas al 
destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor 
tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son 
exclusivas de su autor, y no representa necesariamente, la opinión de FLENI.
http://www.fleni.org.ar

El contenido del presente mensaje y el de sus adjuntos, es confidencial, 
privado y de uso exclusivo de los destinatarios a los cuales está dirigido, 
pudiendo contener información legalmente protegida. Queda prohibida la 
revisión, divulgación, publicación, modificación, copia, distribución o acción 
en relación con esta información, por personas o entidades distintas al 
destinatario. Si usted, por alguna razón, lo ha recibido por error, por favor 
tenga la amabilidad de eliminarlo de su sistema. Las opiniones contenidas, son 
exclusivas de su autor, y no representa necesariamente, la opinión de FLENI.
http://www.fleni.org.ar
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Re: [Freesurfer] p-value too small?

[Caspar M. Schwiedrzik]

Hi Doug and Sebastian,
thanks for your input. I think I can confirm that it is the problem
that Sebastian described. FS 5.1 uses betainc, which returns 0, even
in Matlab R2011b.
The workaround that Sebastian suggested works, with a slight modification.
In line 888 in fast_selxavg3.m currently reads
ind = find(pmat == 0); pmat(ind) = 1;
That seems wrong to me, as -log10(1) gives 1.
I replaced line 888 with
ind = find(pmat == 0); pmat(ind) = eps(0);
-log10(eps(0)) gives 323.3062.
Sebastian's solution of pmat(ind) = eps underestimates the
significance because eps is by default eps(1).
Does that make sense?

I confirmed that the time courses indicate a highly significant
difference; I have 27 runs of block design; the problem happens both
for contrasts against baseline and for contrasts between conditions; I
currently have this problem only in one subject.

Thanks, Caspar




2012/11/29 Sebastian Moeller :
> Hi Doug, hi Caspar,
>
> which matlab version are you using? We had some issues in the past that some 
> matlab 2007 and 2009 statistics toolbox versions returned p values of 0, 
> which obviously will not work as overlay, since those typically assume a 
> volume of:
> -log10(p_value)
> and on matlab 2007b (maci):
>>> -log10(0.0)
> ans =
>Inf
>>> -log10(eps)
> ans =
>15.6536
> So you should
>
> So test your input stat volumes for 0.0 and try to replace those with eps in 
> matlab and see how the overlay look then. Then try to teach fs-fast to do 
> this automagically :)
> For saity checking have a look at the time course at those voxels (I assume 
> NHP block design data here), and remember if you can see the modulation in 
> the time courses with your bare eyes it will most likely be significant. So 
> at those voxels where the contrasts return zero I would expect really great 
> time courses with strong differences in modulation hiught between the members 
> of the -a and -c collections of contrast blocks.
>
> best
> Sebastian
>
>
> On Nov 29, 2012, at 09:55 , Douglas N Greve wrote:
>
>>
>> Oh, I did not realize this was an fsfast issue, I thought you were using
>> mri_glmfit. In that case, I'm not sure what could be causing the problem
>> since the p-values are being computed by matlab. How many runs do you
>> have? Is is a contrast that has a huge amount of power(eg, something vs
>> fixation)? Does it happen in other subjects? One path to debugging is to
>> run selxavg3-sess with -run-wise. This will create an analysis for each
>> run separately. You can then see whether one run in particular is
>> causing the problem.
>> doug
>>
>> On 11/27/2012 08:34 PM, Caspar M. Schwiedrzik wrote:
>>> Hi Doug,
>>> I am afraid the p values are still too small in Free Surfer
>>> Linux-centos4_x86_64-stable-pub-v5.1.0-full.
>>> I redid
>>> mkanalysis-sess
>>> mkcontrast-sess
>>> selxavg3-sess
>>> in 5.1., it looks verz similar as in 4.5., including a whole of 0.0 in
>>> the center of the cluster.
>>> Any further advice?
>>> Thanks,
>>> Caspar
>>>
>>>
>>>
>>> 2012/11/26 Douglas Greve :
 No, it does not. With version 5 I went to a simple AR1 model instead.
 doug



 On 11/26/12 10:34 PM, Caspar M. Schwiedrzik wrote:
> Hi Doug,
> thanks for the input. What I meant is that in version 5.1,
> mkanalysis-sess does not seem to recognize the -taumax flag to set the
> maximum delay for the autocorrelation function.
> Caspar
>
>
> 2012/11/26 Douglas N Greve :
>>
>> On 11/26/2012 02:12 PM, Caspar M. Schwiedrzik wrote:
>>> Hi Doug,
>>> I'll do that.
>>> Two quick follow-up questions regarding 5.1:
>>> - it seems that I cannot specify taumax anymore in mkanalysis-sess. Is
>>> there another argument that would allow me to set the autocorrelation?
>> What do you mean by "set the autocorrelation"? You can turn it off with
>> -no-whiten.
>>
>>> - in a block design, would refeventduration be the block length or the
>>> length of the individual events within a block?
>> The block length. This will not change the p-values, only percent signal
>> change values (often not even looked at).
>> doug
>>
>>> Thanks,
>>> Caspar
>>>
>>> 2012/11/26 Douglas N Greve:
 Hi Caspar, I think I fixed this in later versions. If you upgrade, you
 can run the stats from 5.1 with recons from 4.5 (just don't mix recons
 from different versions).
 doug

 On 11/26/2012 01:15 PM, Caspar M. Schwiedrzik wrote:
> Hi!
> I ran into a funny problem when calculating contrasts in Freesurfer
> 4.5.0.
> Namely, the center of my cluster of significant voxels has a p-value
> of -0.0, resulting in a funny whole where you would otherwise expect
> to find the most significant voxel(s).
> It seems that the p-value is too small. Is there a workaround
> available?
> Thank you very much,
> Caspar
> __

Re: [Freesurfer] p-value too small?

[Caspar M. Schwiedrzik]

sorry, -log10(1) gives 0 of course.
caspar

2012/11/30 Caspar M. Schwiedrzik :
> Hi Doug and Sebastian,
> thanks for your input. I think I can confirm that it is the problem
> that Sebastian described. FS 5.1 uses betainc, which returns 0, even
> in Matlab R2011b.
> The workaround that Sebastian suggested works, with a slight modification.
> In line 888 in fast_selxavg3.m currently reads
> ind = find(pmat == 0); pmat(ind) = 1;
> That seems wrong to me, as -log10(1) gives 1.
> I replaced line 888 with
> ind = find(pmat == 0); pmat(ind) = eps(0);
> -log10(eps(0)) gives 323.3062.
> Sebastian's solution of pmat(ind) = eps underestimates the
> significance because eps is by default eps(1).
> Does that make sense?
>
> I confirmed that the time courses indicate a highly significant
> difference; I have 27 runs of block design; the problem happens both
> for contrasts against baseline and for contrasts between conditions; I
> currently have this problem only in one subject.
>
> Thanks, Caspar
>
>
>
>
> 2012/11/29 Sebastian Moeller :
>> Hi Doug, hi Caspar,
>>
>> which matlab version are you using? We had some issues in the past that some 
>> matlab 2007 and 2009 statistics toolbox versions returned p values of 0, 
>> which obviously will not work as overlay, since those typically assume a 
>> volume of:
>> -log10(p_value)
>> and on matlab 2007b (maci):
 -log10(0.0)
>> ans =
>>Inf
 -log10(eps)
>> ans =
>>15.6536
>> So you should
>>
>> So test your input stat volumes for 0.0 and try to replace those with eps in 
>> matlab and see how the overlay look then. Then try to teach fs-fast to do 
>> this automagically :)
>> For saity checking have a look at the time course at those voxels (I assume 
>> NHP block design data here), and remember if you can see the modulation in 
>> the time courses with your bare eyes it will most likely be significant. So 
>> at those voxels where the contrasts return zero I would expect really great 
>> time courses with strong differences in modulation hiught between the 
>> members of the -a and -c collections of contrast blocks.
>>
>> best
>> Sebastian
>>
>>
>> On Nov 29, 2012, at 09:55 , Douglas N Greve wrote:
>>
>>>
>>> Oh, I did not realize this was an fsfast issue, I thought you were using
>>> mri_glmfit. In that case, I'm not sure what could be causing the problem
>>> since the p-values are being computed by matlab. How many runs do you
>>> have? Is is a contrast that has a huge amount of power(eg, something vs
>>> fixation)? Does it happen in other subjects? One path to debugging is to
>>> run selxavg3-sess with -run-wise. This will create an analysis for each
>>> run separately. You can then see whether one run in particular is
>>> causing the problem.
>>> doug
>>>
>>> On 11/27/2012 08:34 PM, Caspar M. Schwiedrzik wrote:
 Hi Doug,
 I am afraid the p values are still too small in Free Surfer
 Linux-centos4_x86_64-stable-pub-v5.1.0-full.
 I redid
 mkanalysis-sess
 mkcontrast-sess
 selxavg3-sess
 in 5.1., it looks verz similar as in 4.5., including a whole of 0.0 in
 the center of the cluster.
 Any further advice?
 Thanks,
 Caspar



 2012/11/26 Douglas Greve :
> No, it does not. With version 5 I went to a simple AR1 model instead.
> doug
>
>
>
> On 11/26/12 10:34 PM, Caspar M. Schwiedrzik wrote:
>> Hi Doug,
>> thanks for the input. What I meant is that in version 5.1,
>> mkanalysis-sess does not seem to recognize the -taumax flag to set the
>> maximum delay for the autocorrelation function.
>> Caspar
>>
>>
>> 2012/11/26 Douglas N Greve :
>>>
>>> On 11/26/2012 02:12 PM, Caspar M. Schwiedrzik wrote:
 Hi Doug,
 I'll do that.
 Two quick follow-up questions regarding 5.1:
 - it seems that I cannot specify taumax anymore in mkanalysis-sess. Is
 there another argument that would allow me to set the autocorrelation?
>>> What do you mean by "set the autocorrelation"? You can turn it off with
>>> -no-whiten.
>>>
 - in a block design, would refeventduration be the block length or the
 length of the individual events within a block?
>>> The block length. This will not change the p-values, only percent signal
>>> change values (often not even looked at).
>>> doug
>>>
 Thanks,
 Caspar

 2012/11/26 Douglas N Greve:
> Hi Caspar, I think I fixed this in later versions. If you upgrade, you
> can run the stats from 5.1 with recons from 4.5 (just don't mix recons
> from different versions).
> doug
>
> On 11/26/2012 01:15 PM, Caspar M. Schwiedrzik wrote:
>> Hi!
>> I ran into a funny problem when calculating contrasts in Freesurfer
>> 4.5.0.
>> Namely, the center of my cluster of significant voxels has a p-value
>> of -0.0, resulting in a funny whole where

Re: [Freesurfer] TRACULA tract path failure

[Anastasia Yendiki]

Hi Arman - Yes, this looks like a tough one. This subject has 
mega-ventricles and a pretty thin, oddly shaped forceps minor. I can't 
actually test if this'll work b/c the bedpost directory is missing from 
the uploaded data, but can you please try changing the 2nd control point 
in this text file:

dlabel/diff/fminor_PP_avg33_mni_flt_cpts_5.txt
to this:
81   87   25
and rerun the path reconstruction step only for fminor?

Let me know if it works. If it doesn't, send over the bedpostx directory 
too and I can try some more things. Thanks!


a.y

On Fri, 30 Nov 2012, Arman Eshaghi wrote:


Dear Anastasia,
Thanks for your response. I have sent a subject that the problem in forceps 
minor persists. 
What I have done so far was to re-run the pipeline with "reinit=1", check the 
eigenvectors, increase control
points, switch off brain anatomical mask in dmric. It made the tracts look 
better for many subjects but this one
still has problems in forceps minor.

Thanks,
Arman


On Fri, Nov 30, 2012 at 11:08 AM, Arman Eshaghi  wrote:
  Dear Anastasia,
  Thanks for your response. I have sent a subject that the problem in 
forceps minor persists. 
What I have done so far was to re-run the pipeline with "reinit=1", check the 
eigenvectors, increase control
points, switch off brain anatomical mask in dmric. It made the tracts look 
better for many subjects but this
one still has problems in forceps minor.

Thanks,
Arman


On Wed, Nov 28, 2012 at 7:34 PM, Anastasia Yendiki 
 wrote:

  Hi Arman - Have you ruled out any issues with the gradient directions? In 
situations where the
  problem is wide-spread, this seems to be the usual suspect. If you've 
checked the eigenvectors
  and they're ok, can you send an example case where the problem persists? 
You can use this page to
  upload a tar ball of all the tracula-related directories of the subject:
          https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

  Thanks!
  a.y

  On Mon, 26 Nov 2012, Arman Eshaghi wrote:

Dear all,
I have difficulty sorting out the problem with some tracts in 
several subjects,
tracts are incomplete or
missing. As it has come up quite a few times on the list, for this 
sort of problem I
have first set
"reinit=1" and then increased control points to 7, and re-ran trac-all with 
"-prior"
flag. This has worked
for some tracts in several subjects, however there are a few 
subjects that still have
this problem. 

It would be great if someone could let me know what else I might be 
able to do in
order to correct
missing/faulty tracts in my subjects. (The problem is not limited 
to a specific
tract, it varies in
different subjects)

All the best,
-Arman




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Re: [Freesurfer] mergecontrasts-sess group map

[Douglas N Greve]

yesand yes
doug

On 11/30/2012 10:53 AM, Alexandra Tanner wrote:
> Hi Doug,
>
> So if I run a group analysis with each contrast separately, would I then
> be running mri_concat to do a conjunction of the group sig maps? Also, can
> I merge more than 2 contrasts at once when using mri_concat? Thanks!
>
> Alex
>
>> Hi Alex, unfortunately, you cannot compute a conjunction with the CES.
> That's the problem with trying to do group-wise multi-variate analysis.
> Another thing you can do is to do a group analysis with each contrast
> separately, then do a conjunction of the group sig maps.
>> doug
>>
>> On 11/29/2012 03:39 PM, Alexandra Tanner wrote:
>>> Thanks for the clarification! So I will rerun mergecontrasts-sess using
> the ces image on my subjects and then run mri_vol2surf and mri_concat
> to
>>> get the group map. Thanks for your help!
>>> Best,
>>> Alex
 Usually the contrast effects size (ces) (in SPM this is the CON image,
> in FSL it is the COPE image). Univariate maps are usually passed up to
> the group level (the conjunction done with mergecontrasts is
 multivariate).
 doug
 On 11/29/2012 01:05 PM, Alexandra Tanner wrote:
> Hi Doug,
> Thanks for the response! Just out of curiosity, what map is typically
> used
> for group analyses? Should I have used a map other than sig on the
> individual subject level as well?
> Thanks!
> Alex
>> You'll have to run mri_vol2surf on each one separately to bring it into
>> the fsaverage space, then mri_concat to stack all of the maps into one
>> file. At that point you can compute a mean (also with mri_concat).
> Generally, one does not do group analysis on sig maps though. doug
>> On 11/27/2012 05:08 PM, Alexandra Tanner wrote:
>>> Hi Doug and Freesurfers,
>>> I recently used mergecontrasts-sess to merge two contrasts of an
> analysis
>>> in 50 different subjects. The command ran on each subject
>>> individually
>>> and
>>> created a sig.nii and sig.ovpl file within a merged contrast folder
> for
>>> each subject. I'd now like to look at an average map of the merged
> contrasts across all 50 subjects.
>>> Does anyone know how to go about getting this average map for my group
>>> of
>>> 50 subjects?
>>> Command I ran to get the sig.nii/sig.ovpl file for each subject:
> mergecontrasts-sess -mergedcontrast Merge_7vFix_1vFix -conjunction
> andor
>>> -analysis SIRP_Stable5 -contrast Cond7vFix 3 pos 0 -contrast Cond1vFix
>>> 3
>>> pos 0 -map sig -sf
>>> /cluster/roffman/users/Stable5_PerRun/Subject_Files/50_MTH_Subjects
> -df
>>> /cluster/roffman/users/Stable5_PerRun
>>> Any help would be greatly appreciated!
>>> Thanks,
>>> Alex
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing:
>> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
 --
 Douglas N. Greve, Ph.D.
 MGH-NMR Center
 gr...@nmr.mgh.harvard.edu
 Phone Number: 617-724-2358
 Fax: 617-726-7422
 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
 FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing:
 ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>>
>>
>
>
>

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] tkmedit background color

[Douglas N Greve]

No, sorry, black is the only choice.
doug


On 11/30/2012 07:13 AM, Righart, Ruthger Dr. wrote:
> Dear Freesurfer experts,
>
> I am trying to find out how to change the background color of tkmedit.
>
> Is there a possibility to change the background color from black to white, 
> just for display purposes? (to avoid laborious photoshop work).
>
> Best Regards,
>
> Ruthger Righart
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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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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Re: [Freesurfer] p-value too small?

[Sebastian Moeller]

Hi Caspar,


On Nov 30, 2012, at 08:25 , Caspar M. Schwiedrzik wrote:

> Hi Doug and Sebastian,
> thanks for your input. I think I can confirm that it is the problem
> that Sebastian described. FS 5.1 uses betainc, which returns 0, even
> in Matlab R2011b.
> The workaround that Sebastian suggested works, with a slight modification.
> In line 888 in fast_selxavg3.m currently reads
> ind = find(pmat == 0); pmat(ind) = 1;
> That seems wrong to me, as -log10(1) gives 1.
> I replaced line 888 with
> ind = find(pmat == 0); pmat(ind) = eps(0);
> -log10(eps(0)) gives 323.3062.
> Sebastian's solution of pmat(ind) = eps underestimates the
> significance because eps is by default eps(1).

Oh, I did not make a precise proposal for change, just a quick thing to 
test, and it seems quite okay to underestimate the P value, at least more 
conservative than overestimating it :) 


> Does that make sense?
> 
> I confirmed that the time courses indicate a highly significant
> difference; I have 27 runs of block design; the problem happens both
> for contrasts against baseline and for contrasts between conditions; I
> currently have this problem only in one subject.

Well, then you have it, only in one subject significance was large 
enough to cause this rounding artifact. Probamly the most conservative thing to 
do would be to set the value of those voxels to the highest "real" P value 
(unless you can deduce the real P value for thiose voxels) as otherwise FDR 
might not work as expected any more. But I am not looking at the code so I am 
basically just rambling here...


best
Sebastian

> 
> Thanks, Caspar
> 
> 
> 
> 
> 2012/11/29 Sebastian Moeller :
>> Hi Doug, hi Caspar,
>> 
>> which matlab version are you using? We had some issues in the past that some 
>> matlab 2007 and 2009 statistics toolbox versions returned p values of 0, 
>> which obviously will not work as overlay, since those typically assume a 
>> volume of:
>> -log10(p_value)
>> and on matlab 2007b (maci):
 -log10(0.0)
>> ans =
>>   Inf
 -log10(eps)
>> ans =
>>   15.6536
>> So you should
>> 
>> So test your input stat volumes for 0.0 and try to replace those with eps in 
>> matlab and see how the overlay look then. Then try to teach fs-fast to do 
>> this automagically :)
>> For saity checking have a look at the time course at those voxels (I assume 
>> NHP block design data here), and remember if you can see the modulation in 
>> the time courses with your bare eyes it will most likely be significant. So 
>> at those voxels where the contrasts return zero I would expect really great 
>> time courses with strong differences in modulation hiught between the 
>> members of the -a and -c collections of contrast blocks.
>> 
>> best
>>Sebastian
>> 
>> 
>> On Nov 29, 2012, at 09:55 , Douglas N Greve wrote:
>> 
>>> 
>>> Oh, I did not realize this was an fsfast issue, I thought you were using
>>> mri_glmfit. In that case, I'm not sure what could be causing the problem
>>> since the p-values are being computed by matlab. How many runs do you
>>> have? Is is a contrast that has a huge amount of power(eg, something vs
>>> fixation)? Does it happen in other subjects? One path to debugging is to
>>> run selxavg3-sess with -run-wise. This will create an analysis for each
>>> run separately. You can then see whether one run in particular is
>>> causing the problem.
>>> doug
>>> 
>>> On 11/27/2012 08:34 PM, Caspar M. Schwiedrzik wrote:
 Hi Doug,
 I am afraid the p values are still too small in Free Surfer
 Linux-centos4_x86_64-stable-pub-v5.1.0-full.
 I redid
 mkanalysis-sess
 mkcontrast-sess
 selxavg3-sess
 in 5.1., it looks verz similar as in 4.5., including a whole of 0.0 in
 the center of the cluster.
 Any further advice?
 Thanks,
 Caspar
 
 
 
 2012/11/26 Douglas Greve :
> No, it does not. With version 5 I went to a simple AR1 model instead.
> doug
> 
> 
> 
> On 11/26/12 10:34 PM, Caspar M. Schwiedrzik wrote:
>> Hi Doug,
>> thanks for the input. What I meant is that in version 5.1,
>> mkanalysis-sess does not seem to recognize the -taumax flag to set the
>> maximum delay for the autocorrelation function.
>> Caspar
>> 
>> 
>> 2012/11/26 Douglas N Greve :
>>> 
>>> On 11/26/2012 02:12 PM, Caspar M. Schwiedrzik wrote:
 Hi Doug,
 I'll do that.
 Two quick follow-up questions regarding 5.1:
 - it seems that I cannot specify taumax anymore in mkanalysis-sess. Is
 there another argument that would allow me to set the autocorrelation?
>>> What do you mean by "set the autocorrelation"? You can turn it off with
>>> -no-whiten.
>>> 
 - in a block design, would refeventduration be the block length or the
 length of the individual events within a block?
>>> The block length. This will not change the p-values, only percent signal
>>> change value

Re: [Freesurfer] p-value too small?

[Douglas N Greve]

That should work. I just made a slightly different modification to the 
code, which will be in 5.2

 pmat = FTest(dof1, dof2, Fmat);
 ind = find(rvarmat == 0); pmat(ind) = 1; % in case all time points 
are same value
 ind = find(pmat == 0);pmat(ind) = eps(0); % for REALLY sig voxels
 fsigmat = -log10(pmat);


On 11/30/2012 11:25 AM, Caspar M. Schwiedrzik wrote:
> Hi Doug and Sebastian,
> thanks for your input. I think I can confirm that it is the problem
> that Sebastian described. FS 5.1 uses betainc, which returns 0, even
> in Matlab R2011b.
> The workaround that Sebastian suggested works, with a slight modification.
> In line 888 in fast_selxavg3.m currently reads
> ind = find(pmat == 0); pmat(ind) = 1;
> That seems wrong to me, as -log10(1) gives 1.
> I replaced line 888 with
> ind = find(pmat == 0); pmat(ind) = eps(0);
> -log10(eps(0)) gives 323.3062.
> Sebastian's solution of pmat(ind) = eps underestimates the
> significance because eps is by default eps(1).
> Does that make sense?
>
> I confirmed that the time courses indicate a highly significant
> difference; I have 27 runs of block design; the problem happens both
> for contrasts against baseline and for contrasts between conditions; I
> currently have this problem only in one subject.
>
> Thanks, Caspar
>
>
>
>
> 2012/11/29 Sebastian Moeller :
>> Hi Doug, hi Caspar,
>>
>> which matlab version are you using? We had some issues in the past that some 
>> matlab 2007 and 2009 statistics toolbox versions returned p values of 0, 
>> which obviously will not work as overlay, since those typically assume a 
>> volume of:
>> -log10(p_value)
>> and on matlab 2007b (maci):
 -log10(0.0)
>> ans =
>> Inf
 -log10(eps)
>> ans =
>> 15.6536
>> So you should
>>
>> So test your input stat volumes for 0.0 and try to replace those with eps in 
>> matlab and see how the overlay look then. Then try to teach fs-fast to do 
>> this automagically :)
>> For saity checking have a look at the time course at those voxels (I assume 
>> NHP block design data here), and remember if you can see the modulation in 
>> the time courses with your bare eyes it will most likely be significant. So 
>> at those voxels where the contrasts return zero I would expect really great 
>> time courses with strong differences in modulation hiught between the 
>> members of the -a and -c collections of contrast blocks.
>>
>> best
>>  Sebastian
>>
>>
>> On Nov 29, 2012, at 09:55 , Douglas N Greve wrote:
>>
>>> Oh, I did not realize this was an fsfast issue, I thought you were using
>>> mri_glmfit. In that case, I'm not sure what could be causing the problem
>>> since the p-values are being computed by matlab. How many runs do you
>>> have? Is is a contrast that has a huge amount of power(eg, something vs
>>> fixation)? Does it happen in other subjects? One path to debugging is to
>>> run selxavg3-sess with -run-wise. This will create an analysis for each
>>> run separately. You can then see whether one run in particular is
>>> causing the problem.
>>> doug
>>>
>>> On 11/27/2012 08:34 PM, Caspar M. Schwiedrzik wrote:
 Hi Doug,
 I am afraid the p values are still too small in Free Surfer
 Linux-centos4_x86_64-stable-pub-v5.1.0-full.
 I redid
 mkanalysis-sess
 mkcontrast-sess
 selxavg3-sess
 in 5.1., it looks verz similar as in 4.5., including a whole of 0.0 in
 the center of the cluster.
 Any further advice?
 Thanks,
 Caspar



 2012/11/26 Douglas Greve :
> No, it does not. With version 5 I went to a simple AR1 model instead.
> doug
>
>
>
> On 11/26/12 10:34 PM, Caspar M. Schwiedrzik wrote:
>> Hi Doug,
>> thanks for the input. What I meant is that in version 5.1,
>> mkanalysis-sess does not seem to recognize the -taumax flag to set the
>> maximum delay for the autocorrelation function.
>> Caspar
>>
>>
>> 2012/11/26 Douglas N Greve :
>>> On 11/26/2012 02:12 PM, Caspar M. Schwiedrzik wrote:
 Hi Doug,
 I'll do that.
 Two quick follow-up questions regarding 5.1:
 - it seems that I cannot specify taumax anymore in mkanalysis-sess. Is
 there another argument that would allow me to set the autocorrelation?
>>> What do you mean by "set the autocorrelation"? You can turn it off with
>>> -no-whiten.
>>>
 - in a block design, would refeventduration be the block length or the
 length of the individual events within a block?
>>> The block length. This will not change the p-values, only percent signal
>>> change values (often not even looked at).
>>> doug
>>>
 Thanks,
 Caspar

 2012/11/26 Douglas N Greve:
> Hi Caspar, I think I fixed this in later versions. If you upgrade, you
> can run the stats from 5.1 with recons from 4.5 (just don't mix recons
> from different versions).
> doug
>
> O

[Freesurfer] Public Supercomputing service to process FreeSurfer data

[Pedro Paulo de Magalhães Oliveira Junior]

We are announcing today the release of the Public Beta of
CerebralVol.com,
a public cloud based supercomputer service to process FreeSurfer data.

CerebralVol.com users can process large amount of data using recon-all in a
single day without the hassle of dealing with Unix commands, scripts, etc.
Users can upload input data (NifTI and MGZ) through the web and download
the results of the recon-all from the web interface.

It's also possible to separate your cases in Groups and have Studies
associated with the Groups.

This week we are shipping the service with 20 CPUs and we are growing it to
1024 CPUs by the end of next week. The system will be fully operational by
January with 4096 nodes available to process more than 4000 recon-all per
day.

Those of you who want to know more about the technical details of the
project can find more information at
https://www.cerebralvol.com/about.html also
you can find information regarding HIPAA at
https://www.cerebralvol.com/hipaa.html

Signup for free at: https://www.cerebralvol.com

We strongly appreciate any suggestions and feedback.

Pedro Paulo Oliveira Jr.

-
Pedro Paulo de Magalhães Oliveira Junior
Netfilter & SpeedComm Telecom
-- www.netfilter.com.br
-- For mobile: http://itunes.apple.com/br/artist/netfilter/id365306441
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[Freesurfer] question on invoking partial volume calculations in freesurfer 4.3

[John Drozd]

Hello,

My freesurfer version is freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0

I noticed that the aparc+aseg.mgz label map is resampled to 1mm x 1mm
x 1mm voxels,
eventhough the .mgz grayscale mri image file remains as per the
original voxel size and is not 1x1x1.  mri_convert .nii to .mgz
translates the grayscale image down the y direction in the horizontal
plane transverse/axial slices.

I noticed that the aseg.stats files list the number of voxels and the
volume, and these numbers match because the voxel size is 1 x 1 x 1.

My question is whether freesurfer 4.3 can be invoked to perform
partial volume error corrections, and if so how do you invoke this
feature?

My interests lie in segmentations of the lateral ventricles including
their posterior and inferior horns.

thank you,
john
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Re: [Freesurfer] question on invoking partial volume calculations in freesurfer 4.3

[Douglas N Greve]

Hi John, it has been a long time since I looked at version 4.3, so I 
don't know if it can or not. One thing you can try is to use the version 
5.x mri_segstats (the program which computes the aseg.stats table). You 
could run this outside of recon-all and generate a file with a different 
name. That way you won't have to worry about mixing version.
doug


On 11/30/2012 03:00 PM, John Drozd wrote:
> Hello,
>
> My freesurfer version is freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0
>
> I noticed that the aparc+aseg.mgz label map is resampled to 1mm x 1mm
> x 1mm voxels,
> eventhough the .mgz grayscale mri image file remains as per the
> original voxel size and is not 1x1x1.  mri_convert .nii to .mgz
> translates the grayscale image down the y direction in the horizontal
> plane transverse/axial slices.
>
> I noticed that the aseg.stats files list the number of voxels and the
> volume, and these numbers match because the voxel size is 1 x 1 x 1.
>
> My question is whether freesurfer 4.3 can be invoked to perform
> partial volume error corrections, and if so how do you invoke this
> feature?
>
> My interests lie in segmentations of the lateral ventricles including
> their posterior and inferior horns.
>
> thank you,
> john
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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

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

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Re: [Freesurfer] recon-all unable to make pial and white surfaces

[Bruce Fischl]

Look like it is running out of memory. How much ram do you have on that machine?
Bruce



On Nov 30, 2012, at 9:29 PM, Negar Memarian  wrote:

> Hello,
>  
> I ran recon-all -all on my subject. The process ended after several minutes 
> with this message at the end:
> recon-all -s 350_FS exited with ERRORS at Fri Nov 30 17:57:59 PST 2012
>  
> I tried loading the pial and white surfaces for editing using this command:
> tkmedit 350_FS brainmask.mgz rh.white -aux-surface lh.white
>  
> but looks like these surfaces do not exist (since the recon-all exited 
> prematurely). When I check the recon-all.log file I do not see any errors 
> except a few MCSRCH errors. So I cannot understand what exactly went wrong in 
> the recon-all. I've attached the recon-all log file. Can someone please tell 
> me what the problem is and how I can fix it?
>  
> Many thanks,
> Negar
> p.s. I tried on more than one subject and I still face the same issue.
>  
>  
> Negar Memarian, MASc, PhD
> NSERC Postdoctoral Fellow
> Department of Neurology
> David Geffen School of Medicine at UCLA
>  
> 
> ___
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Re: [Freesurfer] question on invoking partial volume calculations in freesurfer 4.3

[John Drozd]

Thanks Doug. Do you know if the Freesurfer volumes in mm^3 that are posted on 
the ADNI website (particularly the longitudinal studies) include partial volume 
corrections? i.e., if they were run to include partial volume calculations?

Thank you,
John

On 2012-11-30, at 3:11 PM, Douglas N Greve  wrote:

> Hi John, it has been a long time since I looked at version 4.3, so I 
> don't know if it can or not. One thing you can try is to use the version 
> 5.x mri_segstats (the program which computes the aseg.stats table). You 
> could run this outside of recon-all and generate a file with a different 
> name. That way you won't have to worry about mixing version.
> doug
> 
> 
> On 11/30/2012 03:00 PM, John Drozd wrote:
>> Hello,
>> 
>> My freesurfer version is freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0
>> 
>> I noticed that the aparc+aseg.mgz label map is resampled to 1mm x 1mm
>> x 1mm voxels,
>> eventhough the .mgz grayscale mri image file remains as per the
>> original voxel size and is not 1x1x1.  mri_convert .nii to .mgz
>> translates the grayscale image down the y direction in the horizontal
>> plane transverse/axial slices.
>> 
>> I noticed that the aseg.stats files list the number of voxels and the
>> volume, and these numbers match because the voxel size is 1 x 1 x 1.
>> 
>> My question is whether freesurfer 4.3 can be invoked to perform
>> partial volume error corrections, and if so how do you invoke this
>> feature?
>> 
>> My interests lie in segmentations of the lateral ventricles including
>> their posterior and inferior horns.
>> 
>> thank you,
>> john
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
> 

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Re: [Freesurfer] recon-all unable to make pial and white surfaces

[Negar Memarian]

Hi Bruce,
I have 8 GB ram and have assigned 6GB of it to FreeSurfer. Shall I increase
it to 8? Would that be enough or still too low?

Thank you,
Negar


On Fri, Nov 30, 2012 at 7:31 PM, Bruce Fischl wrote:

> Look like it is running out of memory. How much ram do you have on that
> machine?
> Bruce
>
>
>
> On Nov 30, 2012, at 9:29 PM, Negar Memarian 
> wrote:
>
> > Hello,
> >
> > I ran recon-all -all on my subject. The process ended after several
> minutes with this message at the end:
> > recon-all -s 350_FS exited with ERRORS at Fri Nov 30 17:57:59 PST 2012
> >
> > I tried loading the pial and white surfaces for editing using this
> command:
> > tkmedit 350_FS brainmask.mgz rh.white -aux-surface lh.white
> >
> > but looks like these surfaces do not exist (since the recon-all exited
> prematurely). When I check the recon-all.log file I do not see any errors
> except a few MCSRCH errors. So I cannot understand what exactly went wrong
> in the recon-all. I've attached the recon-all log file. Can someone please
> tell me what the problem is and how I can fix it?
> >
> > Many thanks,
> > Negar
> > p.s. I tried on more than one subject and I still face the same issue.
> >
> >
> > Negar Memarian, MASc, PhD
> > NSERC Postdoctoral Fellow
> > Department of Neurology
> > David Geffen School of Medicine at UCLA
> >
> > 
> > ___
> > Freesurfer mailing list
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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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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
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