Re: [Freesurfer] FTP server error

[Bruce Fischl]

We are experiencing center-wide hardware problems, and it's likely to be down 
for a while

> On Sep 15, 2016, at 11:07 PM, Chris Filo Gorgolewski 
>  wrote:
> 
> FYI - there is something wrong with the FTP server:
> 
> $ wget 
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP.tar.gz
> --2016-09-15 20:04:51--  
> ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP.tar.gz
>=> 'freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP.tar.gz'
> Resolving surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)... 
> 132.183.202.158
> Connecting to surfer.nmr.mgh.harvard.edu 
> (surfer.nmr.mgh.harvard.edu)|132.183.202.158|:21... connected.
> Error in server response. Closing.
> Retrying.
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[Freesurfer] FTP server error

[Chris Filo Gorgolewski]

FYI - there is something wrong with the FTP server:

$ wget
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP.tar.gz
--2016-09-15 20:04:51--
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-HCP/freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP.tar.gz
   => 'freesurfer-Linux-centos4_x86_64-stable-pub-v5.3.0-HCP.tar.gz'
Resolving surfer.nmr.mgh.harvard.edu (surfer.nmr.mgh.harvard.edu)...
132.183.202.158
Connecting to surfer.nmr.mgh.harvard.edu
(surfer.nmr.mgh.harvard.edu)|132.183.202.158|:21...
connected.
Error in server response. Closing.
Retrying.
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[Freesurfer] Cortical thickness to AAL template

[neuroimage analyst]

Hello, freesurfer users.

Reposting the previous question again here. I would appreciate any response.

I tried searching for this question on the mailing list but couldn't get an
answer. Hence, I am posting this here again.

I ran the freesurfer analysis and got cortical thickness map for my group.
I want to build an adjacency matrix by finding the correlation between the
cortical thickness of various ROIs on an atlas (Either the
default freesurfer atlas or AAL atlas).
1) How can I map the cortical thickness map to freesurfer template volume
so that I can average the cortical thickness in the ROI to build the
connectivity matrix?
2) Instead of mapping to freesurfer template, if I have to use AAL atlas
can I simply map the cortical thickness map to MNI template and use AAL
atlas in MNI template to carry out step (1). If yes, how should I go about
doing that?

I would appreciate any response.

Thanks

Regards!
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[Freesurfer] area and smoothing

[Seung Gul Kang]

Dear Freesurfer experts,

1. I want to compare the area and/or areapial between two groups in qdec
menu.
I think that the eTIV or total surface area should be used as a covariate.
Which is more appropriate between eTIV and total surface area?

2. Is there any guideline or rule for the smoothing in the thickness, area,
and volume comparison?
How about the smoothing=5?

Thank you.

Best,
Seung-Gul

---
*Seung Gul Kang, M.D., Ph.D. *

*Psychiatrist, Associate Professor*; Department of Psychiatry, Gil Medical
Center, Gachon University, School of Medicine, 21, Namdong-daero 774
beon-gil, Namdong-gu, Incheon, 21565, South Korea
*Research scholar*; Sleep Disorders Clinical Research Program, Department
of Psychiatry, Massachusetts General Hospital, Harvard Medical School, 1
Bowdoin Square, 9th floor, Boston, MA 02114, USA
*Collaboration researcher*; Division of Sleep & Circadian Disorders,
Brigham & Women's Hospital, Harvard Medical School, 221 Longwood Ave,
Boston MA 02115
ᐧ
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[Freesurfer] FS V6.0 gtmseg unsegmented WM

[Pradeep]

Dear Freesurfers,

I am interested us using  centrum semiovale as reference region while
calculation SUVR values. Is there a way to save the unsegmented white
matter [5001& 5002] during the gtmseg step ?

in other words looking for an option like this
--keep-unsegmented-WM :do not relabel unsegmented_WM as WM

Thanks,
Pradeep
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[Freesurfer] Display FSL PALM(permutation) stats in freeview

[Ajay Kurani]

Hello Freesurfer Experts,
   I was running permutation simulations on cortical thickness data and I
had an issue with non-orthogonal covariates with mri_glmfit-sim -perm.  I
then tried FSL's PALM which is an extension of randomize to calculate
threshold free stats.  I saved the output as logp(which is similar to qdec
I believe), however I have not been able to load the stats files
correctly.  The output of palm is lh.thickness_tfce.mgz for my various
contrasts.

1) Is .mgz the proper format for the stats files or do I need to convert
this to another type like .mgh etc?

2) Can I display this in freeview or is another program needed?  I also
tried tksurfer but when I loaded the stats file as an overlay nothing
displayed.  I want to make sure that the stats is loaded as an overlay in
freeview/tksurfer and if so, do I need to select anything special so that
it scales the logp values correctly?

Thanks,
Ajay
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Re: [Freesurfer] group by age-squared interaction on thickness

[Douglas N Greve]

I don't think you are modeling gender and scanner appropriately. It 
looks like you have them as continuous covariates? The right way is to 
create classes. In your case, you'd have 8 classes, Group1MaleScanner1, 
Group1FemaleScanner2, etc.


On 09/15/2016 10:48 AM, Eryilmaz, H. Hamdi wrote:
> Dear Doug/FreeSurfers,
>
> We are looking at effects of age-squared on cortical thickness in two 
> different groups.  We are interested in age-squared by group 
> interactions on cortical thickness across the surface.  Nuisance 
> covariates include age, sex, scanner, and total brain volume.
>
> The sig map for the interaction shows numerous highly significant 
> regions. When we extract cortical thickness from individual subjects 
> for these regions, and then plot the relationship between age-squared 
> and cortical thickness (after adjusting for the covariates) in group 1 
> versus group 2, the interaction is very clear.
>
> However, using linear regression in SPSS, we are not able to reproduce 
> these results.  I suspect we are not using the same model in SPSS that 
> FreeSurfer is using to do the interaction analysis.
>
> This is how our fsgd file looks like:
>
> GroupDescriptorFile 1
> Title GroupAgesqInteraction
> Class Group1
> Class Group2
> Variables Agesq Age Gender Scanner TBV
>
> Input3662291Group10.6070.654 -1.0611.0410.706
> Input3665043Group11.2941.237 -1.0611.041-0.747
> .
> .
>
> This is the contrast we used:
>
> [0 0 1 -1 0 0 0 0 0 0 0 0]
>
> What would be the translation of this contrast to a linear model, 
> where we are interested in the age -squared by group interaction on 
> cortical thickness after controlling for the four nuisance covariates?
>
> Thanks very much!
>
> Hamdi and Josh
>
>
>
>
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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] group by age-squared interaction on thickness

[Eryilmaz, H. Hamdi]

Dear Doug/FreeSurfers,

We are looking at effects of age-squared on cortical thickness in two different 
groups.  We are interested in age-squared by group interactions on cortical 
thickness across the surface.  Nuisance covariates include age, sex, scanner, 
and total brain volume.

The sig map for the interaction shows numerous highly significant regions. When 
we extract cortical thickness from individual subjects for these regions, and 
then plot the relationship between age-squared and cortical thickness (after 
adjusting for the covariates) in group 1 versus group 2, the interaction is 
very clear.

However, using linear regression in SPSS, we are not able to reproduce these 
results.  I suspect we are not using the same model in SPSS that FreeSurfer is 
using to do the interaction analysis.

This is how our fsgd file looks like:

GroupDescriptorFile 1
Title GroupAgesqInteraction
Class Group1
Class Group2
Variables Agesq Age Gender Scanner TBV

Input3662291Group10.6070.654-1.0611.0410.706
Input3665043Group11.2941.237-1.0611.041-0.747
.
.

This is the contrast we used:

[0 0 1 -1 0 0 0 0 0 0 0 0]

What would be the translation of this contrast to a linear model, where we are 
interested in the age -squared by group interaction on cortical thickness after 
controlling for the four nuisance covariates?

Thanks very much!

Hamdi and Josh


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