[Freesurfer] 答复: Questions about surface coordanates

[Dongnandi]

Thanks a lot!

Just want to make sure that the “RAS”(FS cords?) and “MNI Talairach” is the 
MNI305 coords.



 

发件人: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] 代表 Douglas Greve
发送时间: 2016年8月30日 21:21
收件人: freesurfer@nmr.mgh.harvard.edu
主题: Re: [Freesurfer] Questions about surface coordanates

 

tksurfer always uses the ?h.orig coordinates. Also keep in mind that the vertex 
index is 0-based whereas matlab is 1-based. When you click on a point, you 
should see something like the following print out

selected vertex 123491 out of 163842
current  -39.11  15.65  11.26
orig -55.67 -10.37  19.95
pial   0.00   0.00   0.00
white-55.76 -10.29  19.93




On 8/30/16 5:12 AM, Dongnandi wrote:

Dear Experts,

I tried to extract vertex coordinates information from ‘fsaverage/surf/lh.pial’ 
file using matlab function ‘read_surf’, but I found that the coordinates 
returned by the function are different from what I saw in tksurfer, here are 
the screenshots:



The vertex index starts from 0 in tksurfer, so I select the second elements in 
matlab. Why is the result different from what has been shown in tksurfer(also 
different in freeview)? Which one should I report?

Is there any way to transform the surface coordinates to the MNI152 space?

 

Thank you very much!

Dong

 






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Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Bruce Fischl]

Hi Matt

I don't think that counts as a methods paper for the T2-based 
deformation. There is no validation or comparison with other methods in 
it, and really not enough detail to replicate what we did.


cheers
Bruce
On Tue, 30 Aug 
2016, Matt Glasser wrote:



Sure there¹s a publication.  See Figure 14:

http://www.sciencedirect.com/science/article/pii/S1053811913005053

Peace,

Matt.

On 8/30/16, 10:21 AM, "Bruce Fischl"
 wrote:


Hi Don

the T2 or FLAIR helps us avoid dura. It is still a beta version though as
we don't have a ton of experience with it, and no, there is no reference
for it yet (or maybe ever) :)
Bruce


On Tue, 30 Aug 2016, Krieger, Donald N. wrote:



Dear list:



What are the advantages of including a T2 scan when running recon-all
­all
 ?

Which results can it effect and to what extent?

And how sensitive is freesurfer to artifacts in the T2 scan?

Is there a good reference for this/



Thanks and best - Don




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Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Matt Glasser]

Sure there¹s a publication.  See Figure 14:

http://www.sciencedirect.com/science/article/pii/S1053811913005053

Peace,

Matt.

On 8/30/16, 10:21 AM, "Bruce Fischl"
 wrote:

>Hi Don
>
>the T2 or FLAIR helps us avoid dura. It is still a beta version though as
>we don't have a ton of experience with it, and no, there is no reference
>for it yet (or maybe ever) :)
>Bruce
>
>
>On Tue, 30 Aug 2016, Krieger, Donald N. wrote:
>
>> 
>> Dear list:
>> 
>>  
>> 
>> What are the advantages of including a T2 scan when running recon-all
>>­all
>>  ?
>> 
>> Which results can it effect and to what extent?
>> 
>> And how sensitive is freesurfer to artifacts in the T2 scan?
>> 
>> Is there a good reference for this/
>> 
>>  
>> 
>> Thanks and best - Don
>> 
>>  
>> 
>> 
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[Freesurfer] About TRACULA results

[Kang, XJ]

Hi,

I am trying to computer the changes of cortical parcellations and fiber 
pathways using FreeSurfer v5.3 and Tracula (2014/05/26 update) . I 
copied the anatomical and DWI images from the same scan session into 
five directories. Run recon-all and trac-all on the 5 same data sets, in 
order to check thereproducibility of the analysis.


Here are what I got: the /Desikan/-Killiany parcellations in both GM and 
WM, and the subcortical structures, repeat well. No difference found in 
volume or size of those structures. However, the volume and averaged DTI 
parameters of the fiber pathways, which found in the file 
~/sub/dpath/*_PP_avg33_mni_flt/pathstats.overall.txt, varies for the 5 
sets.   tracula.conf files were copied from ~/freesurfer/bin/dmrirc.example.


The changes are calculated in percentage by (S1-S0)/((S1+S0)/2)*100%. 
For example, the changes of averaged FA  between the 5 data sets are :

S1-S0, S2-S0, S3-S0, S4-S0
Corpus Callosum - Forceps Major ,   -1.1   ,6.0   ,0.5   
,1.3   ,
Corpus Callosum - Forceps Minor  ,0.1   ,0.0   ,   
-1.6   ,0.0   ,
Right Anterior Thalamic Radiations  ,0.1   ,   -1.0   ,
0.5   ,0.9   ,
Right Cingulum - Angular Bundle   ,   -4.8   ,   -2.0   ,   
-1.5   ,3.8   ,
Right Cingulum - Cingulate Gyrus Endings,
0.5   ,   -0.9   , 0.4   ,   -2.3   ,

Right Corticospinal Tract ,1.9   ,0.6   ,   -2.2   ,1.4   ,
Right Inferior Longitudinal 
Fasciculus ,   -2.2   , -0.8   ,   
-1.3   ,3.0   ,
Right Superior Longitudinal Fasciculus - Parietal Endings , 0.8   ,   
-0.4   ,   -1.2   ,0.2   ,
Right Superior Longitudinal Fasciculus - Temporal Endings , -4.9   ,   
-0.6   ,   -2.6   ,   -1.3   ,

Right Uncinate Fasciculus ,0.5   ,1.6   ,   -0.9   ,3.5   ,


Even larger changes for the volume of the pathways:
S1-S0, S2-S0, S3-S0, S4-S0
Corpus Callosum - Forceps Major  
  ,2.2   , -33.7   ,  -12.3   ,1.1   ,
Corpus Callosum - Forceps 
Minor,   11.9   , 4.8   ,
0.6   ,7.2   ,
Right Anterior Thalamic Radiations   
   ,   -8.9 ,2.2   ,  -12.5   ,7.5   ,
Right Cingulum - Angular 
Bundle   ,  -38.1 ,   41.6   
,   34.8   ,8.6   ,
Right Cingulum - Cingulate Gyrus Endings  
,   24.4   ,   33.1   , 21.3   ,   17.5   ,

Right Corticospinal Tract ,9.8   ,   -3.0   ,2.2   ,   19.5   ,
Right Inferior Longitudinal 
Fasciculus  ,7.2   , 24.1   ,   
-7.3   ,   23.8   ,
Right Superior Longitudinal Fasciculus - Parietal Endings  , 17.2   ,   
10.2   ,   25.1   ,9.9   ,
Right Superior Longitudinal Fasciculus - Temporal Endings , 15.4   ,
3.4   ,   -3.1   ,  -11.5   ,
Right Uncinate Fasciculus ,   13.3   ,   -1.2   
,   16.4   , -3.4   ,


Any expert has the experience on these? Thank you for your help.

XJ Kang

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Re: [Freesurfer] hippo sf segmentation 6.0 dev

[Iglesias, Eugenio]

Hi Renata,
In general, mixing’n’matching is not a good idea, since different sequences 
bias the volumes in different directions. Now, if the differences in sequences 
were independent of whether subjects are patients or controls, it wouldn’t be 
*that* bad. But, if patients have different sequences than controls, the 
results are catastrophic because you cannot tell whether detected differences 
are due to anatomy or to the differences in sequences …
- For the T1s, rather than having two groups, you could possibly resample the 
higher-res (0.8) images to 1mm isotropic. But I wonder if this is introducing a 
bias (I’d expect it to be small, but…).
- T2 vs FLAIR: I’d need to see examples to decide. In principle, the one with 
higher contrast and resolution is better ;-)
Cheers,
/Eugenio


Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 30 Aug 2016, at 17:28, Vaz pandolfo, Renata 
> wrote:

Dear Eugenio,

I have a couple of questions regarding the hippocampus subfields segmentation 
on the dev FS 6.0 which I hope you could help me with.

We are comparing the volumes of hippocampal subregions of patients and 
controls, and we would like to be as consistent as possible with the input so 
that the output reflects only the differences we expect to see.

The problem is that we have a large number of controls but not all of them have 
the same sequences (T1, T2 or FLAIR) as the patients. So our questions are:

If the T1s from some subjects have a 1x1x1 resolution and others have 
0.8x0.8x0.8 isotropic resolution, do we have to create two groups of controls 
and patients for each sequence? In other words, does the resolution of the T1 
affect the freesurfer segmentation in a way that we can't compare 1x1x1 with 
0.8 x 0.8 x 0.8?

Also, we would like to use T2s or FLAIRs as additional inputs to improve the 
results. Which sequence is preferably recommended? In our case, most controls 
and patients have the same FLAIR sequence, so to keep it consistent we would 
probably use FLAIR if that's worth it.

Finally, we also have different T2s: some isotropic, some anisotropic and 
partial cooverage of the brain, and some anisotropic that are aligned to the 
hippocampus (resolution: 1x1x3, best resolution on coronal slices). Considering 
that they are just additional inputs, do they have to be consistent as well? In 
other words, should we only compare patients and controls that had the same T2 
sequence as additional input and same T1 sequence as main input, or can we "mix 
and match" the additional inputs?

Thank you in advance for your help,

Renata
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Re: [Freesurfer] Brainstem nucleus

[Iglesias, Eugenio]

Hi Mohamad,
For now, our brainstem module separates this structure into midbrain, pons, 
medulla and SCP - please see this link:
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures
If you want to segment more specific nuclei, we don’t have a tool capable of 
doing that yet.
Cheers,
/Eugenio


Juan Eugenio Iglesias
Translational Imaging Group
University College London
http://www.jeiglesias.com
http://cmictig.cs.ucl.ac.uk/


On 30 Aug 2016, at 17:34, Alshikho, Mohamad J. 
> wrote:

Hi Iglesias,
Kindly, we would like to know if there are any methods in Freesurfer that can 
help to segment thatbrain stem nucleus. I mean output the nucleus automatically 
as a small masks, so these small masks can be used in other analyses (e.g. fMRI)

I am thinking of creating masks for these nucleus depending on an atlas. I open 
the T1 image in Fslview and I create the mask for the nucleus of interest. But 
this is so hard, not accurate and time consuming. The reason for my question.
We highly appreciate any suggestion!

Best,
Mohamad






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[Freesurfer] Brainstem nucleus

[Alshikho, Mohamad J.]

Hi Iglesias,
Kindly, we would like to know if there are any methods in Freesurfer that can 
help to segment that brain stem nucleus. I mean output the nucleus 
automatically as a small masks, so these small masks can be used in other 
analyses (e.g. fMRI)

I am thinking of creating masks for these nucleus depending on an atlas. I open 
the T1 image in Fslview and I create the mask for the nucleus of interest. But 
this is so hard, not accurate and time consuming. The reason for my question.
We highly appreciate any suggestion!

Best,
Mohamad




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[Freesurfer] hippo sf segmentation 6.0 dev

[Vaz pandolfo, Renata]

Dear Eugenio,

I have a couple of questions regarding the hippocampus subfields
segmentation on the dev FS 6.0 which I hope you could help me with.

We are comparing the volumes of hippocampal subregions of patients and
controls, and we would like to be as consistent as possible with the input
so that the output reflects only the differences we expect to see.

The problem is that we have a large number of controls but not all of them
have the same sequences (T1, T2 or FLAIR) as the patients. So our questions
are:

If the T1s from some subjects have a 1x1x1 resolution and others have
0.8x0.8x0.8 isotropic resolution, do we have to create two groups of
controls and patients for each sequence? In other words, does the
resolution of the T1 affect the freesurfer segmentation in a way that we
can't compare 1x1x1 with 0.8 x 0.8 x 0.8?

Also, we would like to use T2s or FLAIRs as additional inputs to improve
the results. Which sequence is preferably recommended? In our case, most
controls and patients have the same FLAIR sequence, so to keep it
consistent we would probably use FLAIR if that's worth it.

Finally, we also have different T2s: some isotropic, some anisotropic and
partial cooverage of the brain, and some anisotropic that are aligned to
the hippocampus (resolution: 1x1x3, best resolution on coronal slices).
Considering that they are just additional inputs, do they have to be
consistent as well? In other words, should we *only* compare patients and
controls that had the same T2 sequence as additional input and same T1
sequence as main input, or can we "mix and match" the additional inputs?

Thank you in advance for your help,

Renata
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Re: [Freesurfer] Pial refinement with FLAIR

[Bruce Fischl]

Hi Eelco

we've made a bunch of improvements in the T2/FLAIR stream since 5.3 so you 
might check them out. Unfortunately I don't think they  will be officially 
supported in 6.0 as we just don't have the resources to include it in our 
unit/system/regression test cycle.


cheers
Bruce


On Tue, 30 Aug 2016, Eelco van Duinkerken wrote:


Dear all,

Sorry for spamming, as I have posted this message about 2 weeks ago, but
didn't receive an answer just yet.
I probably did something wrong :).

I've been preprocessing, in FS5.3, 3T GE data in controls, obese and
diabetes patients and adding the available flair to do the pial refinement
as follows:

recon-all -i t1 -s participant -all -FLAIR flair -FLAIRpial

This works excellent for most of the scans. Unfortunately, for some scans
adding the flair leads to some interesting refinements, either extending
outside of the brain.mgz or going deep into the white matter.

I didn't notice any misregistrations of the flair to the T1 scan when
checking the bb-registration. I have added some screenshots and the
recon-all.log files. The red lines represent the pial with the flair
refinement, and the blue lines the pial without the refinement. As you can
see, these interesting segmentations are not there when the flair is no
used.

Does anyone know what is going on?

Thanks a lot,

Eelco

--
Eelco van Duinkerken, PhD
Pontifícia Universidade Católica | Department of Psychology | 
R. Marquês de São Vicente 225 | Gávea, Rio de Janeiro - RJ | CEP 22451-900 |
Brasil |
E-mail: e.vanduinker...@vumc.nl | Phone: +55-21-35271855 |
http://lattes.cnpq.br/7180895567820901
&
VU University Medical Center | Department of Medical Psychology | 
De Boelelaan 1117 | 1081 HV | Amsterdam | The Netherlands

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Re: [Freesurfer] rfMRI and T2w image

[Bruce Fischl]

Hi Vasudev

probably not. What resolution are they? They are likely to be too low 
resolution to be useful and also quite significantly distorted w.r.t. the 
T1s. You can try it if you like, but my guess is it will hurt more than it 
helps


sorry
Bruce

On Tue, 30 Aug 2016, Dev vasu wrote:



Dear sir,

I was checking for your reply about my question in Freesurfer Forum but
unfortunately i could not your answer although ":Freesurfer Digest, Vol 150,
Issue 43 " Today's topics section indicates that you have replied to my
question.

Following is my question :

In order to  run my structural analysis pipeline , i require T2w images, 
but unfortunately we have not performed T2w scans , my colleague suggests we
can use rfMRI instead T2w images Could you please let me know if i can use
rfMRI image instead of T2w image?.


Thanks
Vasudev


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Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Bruce Fischl]

Hi Don

the T2 or FLAIR helps us avoid dura. It is still a beta version though as 
we don't have a ton of experience with it, and no, there is no reference 
for it yet (or maybe ever) :)

Bruce


On Tue, 30 Aug 2016, Krieger, Donald N. wrote:



Dear list:

 

What are the advantages of including a T2 scan when running recon-all –all
 ?

Which results can it effect and to what extent?

And how sensitive is freesurfer to artifacts in the T2 scan?

Is there a good reference for this/

 

Thanks and best - Don

 


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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] rfMRI and T2w image

[Dev vasu]

Dear sir,

I was checking for your reply about my question in Freesurfer Forum but
unfortunately i could not your answer although ":Freesurfer Digest, Vol
150, Issue 43 " Today's topics section indicates that you have replied to
my question.

Following is my question :

In order to  run my structural analysis pipeline , i require T2w images,
but unfortunately we have not performed T2w scans , my colleague suggests
we can use rfMRI instead T2w images Could you please let me know if i can
use rfMRI image instead of T2w image?.


Thanks
Vasudev
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Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Harms, Michael]

FWIW, we’ve had good success with including the T2w scan as part of the FS 5.3-HCP release.


cheers,
-MH




-- 
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. 
Tel: 314-747-6173
St. Louis, MO  63110 
Email: mha...@wustl.edu






From:  on behalf of "Krieger, Donald N." 
Reply-To: 'Freesurfer support list' 
Date: Tuesday, August 30, 2016 at 9:25 AM
To: 'Freesurfer support list' 
Subject: Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run








Thank you – very helpful.
 

Best – Don

 



From:
freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu]
On Behalf Of Douglas Greve
Sent: Tuesday, August 30, 2016 10:23 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run


 
ps. The 5.3 version is pretty buggy, so I'd wait until 6.0 to test it out
 

On 8/30/16 10:12 AM, Krieger, Donald N. wrote:


Dear list:
 
What are the advantages of including a T2 scan when running recon-all –all  ?
Which results can it effect and to what extent?
And how sensitive is freesurfer to artifacts in the T2 scan?
Is there a good reference for this/
 
Thanks and best - Don
 




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Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

[Harms, Michael]

Sure, any simulation can’t be exhaustive, but my understanding, chatting
with Anderson, is that their 2014 paper simulated a quite large space of
designs and Freedman-Lane is appropriate for the vast majority of the GLMs
that we would encounter in neuroimaging.

Also, again per Anderson, I believe that method implemented in
mri_glmfit-sim is that of Manly for those interested in linking what
mri_glmfit-sim is doing to the results in Winkler (e.g., Table 7).

cheers,
-MH

--
Michael Harms, Ph.D.

---
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave.Tel: 314-747-6173
St. Louis, MO  63110Email: mha...@wustl.edu




On 8/30/16, 8:33 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
Douglas Greve"  wrote:

By "wrong" I meant that permutation no longer  gives exact p-values in
expectation with non-orthogonal designs. There is no theory to
characterize the accuracy of  Freeman-Lane of the other methods. In this
sense, they are not approximations but ad hoc methods that people hope
do a better job than parametric methods. Anderson tested them on a wide
range of designs, but it was, of course, not exhaustive. The accuracy of
his results may not extend to other designs, so it is a buyer-beware
situation (as with all neuroimaging).


On 8/29/16 10:16 PM, Harms, Michael wrote:
> Hi,
> I wouldn’t say that non-orthogonal designs are “wrong” to use with
> permutation.  Rather, there are different approaches to handling that
> situation and produce approximate p-values.  See Table 2 in Winkler’s
>2014
> paper, and the results therein comparing the various approaches:
>
> http://www.ncbi.nlm.nih.gov/pubmed/24530839
>
>
> PALM actually gives you control over the method used, with the default
> (and recommended) approach being that of “Freedman-Lane", which is the
> same approach used by FSL’s ‘randomise’ tool to handle correlated
> covariates.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
> On 8/29/16, 7:49 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> Matt Glasser"  m...@ma-tea.com> wrote:
>
> PALM handles GIFTI and CIFTI data.
>
> Peace,
>
> Matt.
>
> On 8/29/16, 6:21 PM, "Douglas N Greve"
>  gr...@nmr.mgh.harvard.edu> wrote:
>
>> Does PALM do surface-based? Also, there is no way to appropriately
>> handle this. For permutation, non-orthogonal designs are wrong. There
>> are ways to try to compensate for it, which is what PALM is doing. Sorry
>> to be nit-picky!
>>
>>
>> On 08/29/2016 06:12 PM, Harms, Michael wrote:
>>> Hi Maaike,
>>> Why not just use PALM?  Then you don¹t have to worry about this (since
>>> PALM appropriately handles the situation of correlated covariates).
>>>
>>> cheers,
>>> -MH
>>>
>>> --
>>> Michael Harms, Ph.D.
>>>
>>> ---
>>> Conte Center for the Neuroscience of Mental Disorders
>>> Washington University School of Medicine
>>> Department of Psychiatry, Box 8134
>>> 660 South Euclid Ave.Tel: 314-747-6173
>>> St. Louis, MO  63110Email: mha...@wustl.edu
>>>
>>>
>>>
>>>
>>> On 8/29/16, 4:45 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>> of
>>> Douglas N Greve" >> gr...@nmr.mgh.harvard.edu> wrote:
>>>
>>> It is hard to say. Since the subjects are not exchangeable, the
>>> permutation is technically not appropriate. Check the winkler paper,  I
>>> think he talks about what happens if you just don't do anything.
>>>
>>>
>>> On 08/29/2016 11:07 AM, maaike rive wrote:
 Hi all,


 Is using forced permutation for non-orthogonal design matrices wrong
 or is it allowed to do this instead of using tools like palm (what
 happens eg with the covariates when using forced permutation)? I
 used forced permutation  and it seemed to work, results were (partly)
 comparable to what I found with monte carlo simulations.


 Thanks, Maaike



---
-
 *Van:* freesurfer-boun...@nmr.mgh.harvard.edu
  namens Harms, Michael
 
 *Verzonden:* vrijdag 26 augustus 2016 01:00:13
 *Aan:* Freesurfer support list
 *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing
 running after 3 days!

 Hi,
 You might want to check out FSL¹s 

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

[Anderson M. Winkler]

Hi all,

In the presence of nuisance (orthogonal or not) the permutation test is
only approximate, whatever is the method used. Regressing out the nuisance
introduces dependencies between the residuals that render them strictly not
exchangeable. However, in practice this is not an issue, and the FL method
has been assessed extensively by us and also by others (e.g., Anderson &
Legendre 1999; Anderson & Robinson, 2001; Anderson & ter Braak, 2003; among
others) and does lead to error rates that approach the test level.

In the Winkler et al 2014 paper, Table 7 gives a sense of how good or bad
some of the regression and permutation methods can be, and even the FL
method, that we advocate, can lead to error rates below or above the 95%
CI, although the chances of invalid results are very small. This is for a
single test. When we consider the thousands of voxels/vertices, this gets
further diluted in the distribution of the maximum, such that the FWER is
even closer to perfectly exact (this information isn't in the paper,
though).

In the presence of non-orthogonality between regressors of interest and
nuisance, the result remains approximately exact, only the power to detect
a true effect is reduced, as it cannot be disambiguated from the nuisance.

Cheers,

Anderson


On 30 August 2016 at 09:33, Douglas Greve  wrote:

> By "wrong" I meant that permutation no longer  gives exact p-values in
> expectation with non-orthogonal designs. There is no theory to
> characterize the accuracy of  Freeman-Lane of the other methods. In this
> sense, they are not approximations but ad hoc methods that people hope
> do a better job than parametric methods. Anderson tested them on a wide
> range of designs, but it was, of course, not exhaustive. The accuracy of
> his results may not extend to other designs, so it is a buyer-beware
> situation (as with all neuroimaging).
>
>
> On 8/29/16 10:16 PM, Harms, Michael wrote:
> > Hi,
> > I wouldn’t say that non-orthogonal designs are “wrong” to use with
> > permutation.  Rather, there are different approaches to handling that
> > situation and produce approximate p-values.  See Table 2 in Winkler’s
> 2014
> > paper, and the results therein comparing the various approaches:
> >
> > http://www.ncbi.nlm.nih.gov/pubmed/24530839
> >
> >
> > PALM actually gives you control over the method used, with the default
> > (and recommended) approach being that of “Freedman-Lane", which is the
> > same approach used by FSL’s ‘randomise’ tool to handle correlated
> > covariates.
> >
> > cheers,
> > -MH
> >
> > --
> > Michael Harms, Ph.D.
> >
> > ---
> > Conte Center for the Neuroscience of Mental Disorders
> > Washington University School of Medicine
> > Department of Psychiatry, Box 8134
> > 660 South Euclid Ave.Tel: 314-747-6173
> > St. Louis, MO  63110Email: mha...@wustl.edu
> >
> >
> >
> >
> > On 8/29/16, 7:49 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
> of
> > Matt Glasser"  > m...@ma-tea.com> wrote:
> >
> > PALM handles GIFTI and CIFTI data.
> >
> > Peace,
> >
> > Matt.
> >
> > On 8/29/16, 6:21 PM, "Douglas N Greve"
> >  > gr...@nmr.mgh.harvard.edu> wrote:
> >
> >> Does PALM do surface-based? Also, there is no way to appropriately
> >> handle this. For permutation, non-orthogonal designs are wrong. There
> >> are ways to try to compensate for it, which is what PALM is doing. Sorry
> >> to be nit-picky!
> >>
> >>
> >> On 08/29/2016 06:12 PM, Harms, Michael wrote:
> >>> Hi Maaike,
> >>> Why not just use PALM?  Then you don¹t have to worry about this (since
> >>> PALM appropriately handles the situation of correlated covariates).
> >>>
> >>> cheers,
> >>> -MH
> >>>
> >>> --
> >>> Michael Harms, Ph.D.
> >>>
> >>> ---
> >>> Conte Center for the Neuroscience of Mental Disorders
> >>> Washington University School of Medicine
> >>> Department of Psychiatry, Box 8134
> >>> 660 South Euclid Ave.Tel: 314-747-6173
> >>> St. Louis, MO  63110Email: mha...@wustl.edu
> >>>
> >>>
> >>>
> >>>
> >>> On 8/29/16, 4:45 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
> >>> of
> >>> Douglas N Greve"  >>> gr...@nmr.mgh.harvard.edu> wrote:
> >>>
> >>> It is hard to say. Since the subjects are not exchangeable, the
> >>> permutation is technically not appropriate. Check the winkler paper,  I
> >>> think he talks about what happens if you just don't do anything.
> >>>
> >>>
> >>> On 08/29/2016 11:07 AM, maaike rive wrote:
>  Hi all,
> 
> 
>  Is using forced permutation for non-orthogonal design matrices wrong
>  or is it allowed to do this instead of using tools like palm (what
>  happens eg with the covariates when using forced permutation)? I
>  used forced permutation  and it 

Re: [Freesurfer] Questions about surface coordanates

[Douglas Greve]

What is paraview? I would contact the developers.


On 8/30/16 10:24 AM, Islem Rekik wrote:

Hi all,

I have a similar problem using Paraview:
When I visualize the surface lh.pial and the anatomical image 
brainmask.mgz using FreeView they nicely overlap; however, after I 
convert lh.pial to lh.pial.vtk and brainmask*.mgz* to brainmask*.mha* 
and visualize them using Paraview, they are in different spaces.


Do I need to apply a transformation matrix to lh.pial using the 
command line mri_surf2surf so the VTK surface will overlap with the 
image when using Paraview?


I find this quite confusing.

Thanks!
Kindly,
Islem


On Tue, Aug 30, 2016 at 9:21 AM, Douglas Greve 
> wrote:


tksurfer always uses the ?h.orig coordinates. Also keep in mind
that the vertex index is 0-based whereas matlab is 1-based. When
you click on a point, you should see something like the following
print out

selected vertex 123491 out of 163842
current  -39.11  15.65  11.26
orig -55.67 -10.37  19.95
pial   0.00   0.00   0.00
white-55.76 -10.29  19.93




On 8/30/16 5:12 AM, Dongnandi wrote:


Dear Experts,

I tried to extract vertex coordinates information from
‘fsaverage/surf/lh.pial’ file using matlab function ‘read_surf’,
but I found that the coordinates returned by the function are
different from what I saw in tksurfer, here are the screenshots:

The vertex index starts from 0 in tksurfer, so I select the
second elements in matlab. Why is the result different from what
has been shown in tksurfer(also different in freeview)? Which one
should I report?

Is there any way to transform the surface coordinates to the
MNI152 space?

Thank you very much!

Dong



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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
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 . If the e-mail was sent
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--
Dr. Islem Rekik; MSc, PhD
IDEA Lab, UNC-Chapel Hill
Biomedical Research Imaging Center
Chapel Hill, NC 27599

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Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Krieger, Donald N.]

Thank you - very helpful.

Best - Don

From: freesurfer-boun...@nmr.mgh.harvard.edu 
[mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve
Sent: Tuesday, August 30, 2016 10:23 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run


ps. The 5.3 version is pretty buggy, so I'd wait until 6.0 to test it out

On 8/30/16 10:12 AM, Krieger, Donald N. wrote:
Dear list:

What are the advantages of including a T2 scan when running recon-all -all  ?
Which results can it effect and to what extent?
And how sensitive is freesurfer to artifacts in the T2 scan?
Is there a good reference for this/

Thanks and best - Don





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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
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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] Questions about surface coordanates

[Islem Rekik]

Hi all,

I have a similar problem using Paraview:
When I visualize the surface lh.pial and the anatomical image brainmask.mgz
using FreeView they nicely overlap; however, after I convert lh.pial to
lh.pial.vtk and brainmask*.mgz* to brainmask*.mha* and visualize them using
Paraview, they are in different spaces.

Do I need to apply a transformation matrix to lh.pial using the command
line mri_surf2surf so the VTK surface will overlap with the image when
using Paraview?

I find this quite confusing.

Thanks!
Kindly,
Islem


On Tue, Aug 30, 2016 at 9:21 AM, Douglas Greve 
wrote:

> tksurfer always uses the ?h.orig coordinates. Also keep in mind that the
> vertex index is 0-based whereas matlab is 1-based. When you click on a
> point, you should see something like the following print out
> selected vertex 123491 out of 163842
> current  -39.11  15.65  11.26
> orig -55.67 -10.37  19.95
> pial   0.00   0.00   0.00
> white-55.76 -10.29  19.93
>
>
>
>
> On 8/30/16 5:12 AM, Dongnandi wrote:
>
> Dear Experts,
>
> I tried to extract vertex coordinates information from
> ‘fsaverage/surf/lh.pial’ file using matlab function ‘read_surf’, but I
> found that the coordinates returned by the function are different from what
> I saw in tksurfer, here are the screenshots:
>
> The vertex index starts from 0 in tksurfer, so I select the second
> elements in matlab. Why is the result different from what has been shown in
> tksurfer(also different in freeview)? Which one should I report?
>
> Is there any way to transform the surface coordinates to the MNI152 space?
>
>
>
> Thank you very much!
>
> Dong
>
>
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> ___
> Freesurfer mailing list
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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
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>


-- 
Dr. Islem Rekik; MSc, PhD
IDEA Lab, UNC-Chapel Hill
Biomedical Research Imaging Center
Chapel Hill, NC 27599
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Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Douglas Greve]

ps. The 5.3 version is pretty buggy, so I'd wait until 6.0 to test it out


On 8/30/16 10:12 AM, Krieger, Donald N. wrote:


Dear list:

What are the advantages of including a T2 scan when running recon-all 
–all  ?


Which results can it effect and to what extent?

And how sensitive is freesurfer to artifacts in the T2 scan?

Is there a good reference for this/

Thanks and best - Don



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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Douglas Greve]

Hi Don,

the T2 stream is a work-in-progress, so we don't have a lot of these 
answers. In theory, a T2 will allow better placement of the pial surface 
allowing it to better exclude dura. No publication on this yet.


doug



On 8/30/16 10:12 AM, Krieger, Donald N. wrote:


Dear list:

What are the advantages of including a T2 scan when running recon-all 
–all  ?


Which results can it effect and to what extent?

And how sensitive is freesurfer to artifacts in the T2 scan?

Is there a good reference for this/

Thanks and best - Don



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but does not contain patient information, please contact the sender and properly
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[Freesurfer] inclusion of both T1 and T2 in a recon-all run

[Krieger, Donald N.]

Dear list:

What are the advantages of including a T2 scan when running recon-all -all  ?
Which results can it effect and to what extent?
And how sensitive is freesurfer to artifacts in the T2 scan?
Is there a good reference for this/

Thanks and best - Don

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Re: [Freesurfer] rfMRI and T2w image

[Douglas Greve]

You don't need T2w to run FreeSurfer/recon-all. There is an option to 
add a T2, but it is not necessary. In any event, you will not be able to 
use an fMRI scan for this purpose.



On 8/30/16 7:50 AM, Dev vasu wrote:

Dear Sir,

In order to  run my structural analysis pipeline , i require T2w 
images,  but unfortunately we have not performed T2w scans , my 
colleague suggests we can use rfMRI instead T2w images Could you 
please let me know if i can use rfMRI image instead of T2w image?.



Thanks
Vasudev


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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

Re: [Freesurfer] mri_glmfit-sim permutation testing running after 3 days!

[Douglas Greve]

By "wrong" I meant that permutation no longer  gives exact p-values in 
expectation with non-orthogonal designs. There is no theory to 
characterize the accuracy of  Freeman-Lane of the other methods. In this 
sense, they are not approximations but ad hoc methods that people hope 
do a better job than parametric methods. Anderson tested them on a wide 
range of designs, but it was, of course, not exhaustive. The accuracy of 
his results may not extend to other designs, so it is a buyer-beware 
situation (as with all neuroimaging).


On 8/29/16 10:16 PM, Harms, Michael wrote:
> Hi,
> I wouldn’t say that non-orthogonal designs are “wrong” to use with
> permutation.  Rather, there are different approaches to handling that
> situation and produce approximate p-values.  See Table 2 in Winkler’s 2014
> paper, and the results therein comparing the various approaches:
>
> http://www.ncbi.nlm.nih.gov/pubmed/24530839
>
>
> PALM actually gives you control over the method used, with the default
> (and recommended) approach being that of “Freedman-Lane", which is the
> same approach used by FSL’s ‘randomise’ tool to handle correlated
> covariates.
>
> cheers,
> -MH
>
> --
> Michael Harms, Ph.D.
>
> ---
> Conte Center for the Neuroscience of Mental Disorders
> Washington University School of Medicine
> Department of Psychiatry, Box 8134
> 660 South Euclid Ave.Tel: 314-747-6173
> St. Louis, MO  63110Email: mha...@wustl.edu
>
>
>
>
> On 8/29/16, 7:49 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of
> Matt Glasser"  m...@ma-tea.com> wrote:
>
> PALM handles GIFTI and CIFTI data.
>
> Peace,
>
> Matt.
>
> On 8/29/16, 6:21 PM, "Douglas N Greve"
>  gr...@nmr.mgh.harvard.edu> wrote:
>
>> Does PALM do surface-based? Also, there is no way to appropriately
>> handle this. For permutation, non-orthogonal designs are wrong. There
>> are ways to try to compensate for it, which is what PALM is doing. Sorry
>> to be nit-picky!
>>
>>
>> On 08/29/2016 06:12 PM, Harms, Michael wrote:
>>> Hi Maaike,
>>> Why not just use PALM?  Then you don¹t have to worry about this (since
>>> PALM appropriately handles the situation of correlated covariates).
>>>
>>> cheers,
>>> -MH
>>>
>>> --
>>> Michael Harms, Ph.D.
>>>
>>> ---
>>> Conte Center for the Neuroscience of Mental Disorders
>>> Washington University School of Medicine
>>> Department of Psychiatry, Box 8134
>>> 660 South Euclid Ave.Tel: 314-747-6173
>>> St. Louis, MO  63110Email: mha...@wustl.edu
>>>
>>>
>>>
>>>
>>> On 8/29/16, 4:45 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf
>>> of
>>> Douglas N Greve" >> gr...@nmr.mgh.harvard.edu> wrote:
>>>
>>> It is hard to say. Since the subjects are not exchangeable, the
>>> permutation is technically not appropriate. Check the winkler paper,  I
>>> think he talks about what happens if you just don't do anything.
>>>
>>>
>>> On 08/29/2016 11:07 AM, maaike rive wrote:
 Hi all,


 Is using forced permutation for non-orthogonal design matrices wrong
 or is it allowed to do this instead of using tools like palm (what
 happens eg with the covariates when using forced permutation)? I
 used forced permutation  and it seemed to work, results were (partly)
 comparable to what I found with monte carlo simulations.


 Thanks, Maaike


 
 *Van:* freesurfer-boun...@nmr.mgh.harvard.edu
  namens Harms, Michael
 
 *Verzonden:* vrijdag 26 augustus 2016 01:00:13
 *Aan:* Freesurfer support list
 *Onderwerp:* Re: [Freesurfer] mri_glmfit-sim permutation testing
 running after 3 days!

 Hi,
 You might want to check out FSL¹s PALM tool, which has a bit more
 sophisticated permutation framework, and allows for permutation in the
 context of non-orthogonal covariates.

 cheers,
 -MH

 --
 Michael Harms, Ph.D.
 ---
 Conte Center for the Neuroscience of Mental Disorders
 Washington University School of Medicine
 Department of Psychiatry, Box 8134
 660 South Euclid Ave.Tel: 314-747-6173
 St. Louis, MO  63110Email: mha...@wustl.edu

 From: > on behalf of Ajay
 Kurani >
 Reply-To: Freesurfer support list >
 Date: Thursday, August 25, 2016 at 4:13 PM
 To: Freesurfer support list 

Re: [Freesurfer] volume, surface area, and thickness

[Anderson M. Winkler]

Hi Woo-Suk

Just adding to Bruce's reply: area isn't a "technically more noisy and
usually thus less sensitive" as the reviewer suggests. Area isn't noisier
on its own right, and it's measured from the very same surfaces from which
thickness is measured. However, there is a much larger variability of area
across subjects than of thickness, even within the normal range, such that
the variance of volume, that can be explained by or associated with other
indices, is largely explained by the variance in area. The first paper that
(as far as I know) showed this is Voets et al. (Neuroimage, 2008), and we
keep observing this repeatedly in different datasets, published or not.

About the Schmaal et al. paper (Molecular Psychiatry, 2016): it is an
excellent paper in which the authors didn't spend time (or space)
discussing volume, going instead straight to the more interesting bits:
area and thickness.

All the best,

Anderson


On 29 August 2016 at 13:56, Bruce Fischl  wrote:

> Hi Woo-Suk
>
> why not just do the surface analysis that they are requesting? I'm not
> sure what you are asking, but certainly volume = surface area * thickness
> in general, and so a volumetric effect can be driven by one or both of
> surface area and thickness
>
> cheers
> Bruce
>
>
>
> On Sat, 27 Aug 2016, Woo-Suk Tae wrote:
>
> Dear FreeSurfer experts and developers
>>
>> I am confronted with some technical question of a reviewer.
>> I am not sure about "volume = thickness-by-surface area" and the review's
>> opinion (attached below) about volume, surface area, and thickness was
>> correct.
>> Any comments from FreeSurfer's experts would help me.
>>
>> Sincerely yours
>>
>> Woo-Suk Tae
>> Seoul, Korea
>>
>> I added the reviewer's comments.
>> -
>> 1. Volume/thickness: The authors cite many papers that show volume and
>> thickness differences in MDD. The unresolved part here, however, is the
>> RELATION between cortical thickness and cortical volume: There is no
>> doubt,
>> that both measures are found affected in MDD. This is, because cortical
>> thickess multiplied by the surface area of a gyrus results in its volume,
>> so
>> volumse = thickness-by-surface area. Surface area values themselves are
>> technically more noisy and usually thus less sensitive (due to the problem
>> of false attributions to an area).
>>
>> So, volume is influenced by thickness and surface and is the less specific
>> measure. If a volume effect is detected in a study, it is unclear, if it
>> is
>> driven by thickness, or surface area, or both. In this respect, the study
>> of
>> Schmaal et al. is telling, as it analyzed BOTH measures, finding only
>> thickness effects of MDD, and (practically) no surface area changes except
>> for adolescent MDD. In the adolescent MDD samples gross surface area
>> differences were detected.
>>
>> This means, that the question of "superiority" is rather a question of
>> "specificity": (Cortical) volume findings in adult MDD are mostly driven
>> by
>> thickness differences and are in on way independent from thickness
>> differences. In this respect, the authors should follow the basic
>> geometric
>> principles of morphometry and point out the relatedness of the two. They
>> can
>> simply check this in their FreeSurfer variables (e. g. for total grey
>> matter
>> volume). Not reporting surface area is leaving an interpretational gap as
>> surface area differences could in addition drive volume differences. The
>> authors may want to decide not to present surface area results, but then
>> they should discuss this as limitation to disentangle the origin of
>> volumetric (cortical) effects. This seems important as methylation effects
>> and FKBP5 interact with early life time stress, so effects on surface area
>> as seen in adolescent MDD highlight that surface area effects could play
>> in.
>>
>>
>>
>>
>>
>>
>>
>> 
>> ---
>> -
>> Woo-Suk, Tae  Ph.D.  Research Professor
>> Brain Convergence Research Center, Medical Research Center
>> Anam Hospital, Korea University Medical Center, Seoul, Korea
>> mobile: 82-10-9120-4629
>> office: 82-2-920-6831
>> email: woosuk@gmail.com, woos...@gmail.com
>> 
>> ---
>> -
>>
>>
>>
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> dispose of 

Re: [Freesurfer] Questions about surface coordanates

[Douglas Greve]

tksurfer always uses the ?h.orig coordinates. Also keep in mind that the 
vertex index is 0-based whereas matlab is 1-based. When you click on a 
point, you should see something like the following print out


selected vertex 123491 out of 163842
current  -39.11  15.65  11.26
orig -55.67 -10.37  19.95
pial   0.00   0.00   0.00
white-55.76 -10.29  19.93



On 8/30/16 5:12 AM, Dongnandi wrote:


Dear Experts,

I tried to extract vertex coordinates information from 
‘fsaverage/surf/lh.pial’ file using matlab function ‘read_surf’, but I 
found that the coordinates returned by the function are different from 
what I saw in tksurfer, here are the screenshots:


The vertex index starts from 0 in tksurfer, so I select the second 
elements in matlab. Why is the result different from what has been 
shown in tksurfer(also different in freeview)? Which one should I report?


Is there any way to transform the surface coordinates to the MNI152 space?

Thank you very much!

Dong



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[Freesurfer] rfMRI and T2w image

[Dev vasu]

Dear Sir,

In order to  run my structural analysis pipeline , i require T2w images,
but unfortunately we have not performed T2w scans , my colleague suggests
we can use rfMRI instead T2w images Could you please let me know if i can
use rfMRI image instead of T2w image?.


Thanks
Vasudev
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[Freesurfer] Questions about surface coordanates

[Dongnandi]

Dear Experts,

I tried to extract vertex coordinates information from
'fsaverage/surf/lh.pial' file using matlab function 'read_surf', but I found
that the coordinates returned by the function are different from what I saw
in tksurfer, here are the screenshots:



The vertex index starts from 0 in tksurfer, so I select the second elements
in matlab. Why is the result different from what has been shown in
tksurfer(also different in freeview)? Which one should I report?

Is there any way to transform the surface coordinates to the MNI152 space?

 

Thank you very much!

Dong

 

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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
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.