[Freesurfer] Request for 7z VM passcode

2022-06-23 Thread Chuang, Tzu-Chao 
External Email - Use Caution

Hello,

 

I need the passcode to expand the VM file (FS_7_2_0_Ubuntu_18_04_06.ova.7z).


Thank you!

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Re: [Freesurfer] [External] Re: aseg.stats - eTIV volume space

2022-06-23 Thread Katie Rose Jobson 
External Email - Use Caution

Paul,

Ah, this makes sense!

If I wanted to get it into native anatomical space, is it acceptable to 
transform the aseg.mgz file to native anatomical space (using 
mri_vol2vol)
 and then using '
mri_segstats --subject subjid --etiv-only' to extract eTIV in this space? I 
know the calculations are dependent on the talairach.xfm file (as noted in your 
link), so I was unsure if this was an acceptable thing to do. Unfortunately, I 
have data that needs to be analyzed in either native anatomical space or MNI 
standard space, so if it is not possible to get eTIV in either of these spaces, 
please let me know.

Apologies for such basic questions, I am new to FreeSurfer and its 
functionality! Thank you again for your help.

Best Wishes,
Katie

--
Katie Jobson, M.S.
PhD Student | Cognitive Neuroscience 
Lab
Department of Psychology and Neuroscience | Temple University
[cid:cbb9c020-8c58-4942-981b-bbe8abe2a3d3]

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Wighton, Paul 

Sent: Thursday, June 23, 2022 6:36 PM
To: Freesurfer support list 
Subject: [External] Re: [Freesurfer] aseg.stats - eTIV volume space

Hi Katie,

FreeSurfer operates mostly in "FreeSurfer Space", which is voxel resolution of 
1mm^3 and sagittal orientation.

You can compare orig.mgz to the original input to see what the difference 
between native space and FreeSurfer Space would be.

eTIV is computed using the transformation matrix from FreeSurfer Space to 
MNI305 space.  There is more information here about it here:
https://secure-web.cisco.com/1fAv8VSclMi1E00qLOqqHaJALwYSkesj51WLpVUNlr2wiCIeYq5J1t91ML88xLki3fmV6_OWVz1rZrgZGO0OkMGlkzsqSxwdSmG4cOf1Wx3tzvQTtiNQgrgc3qnyRSHDvXuq5AYXcEAgviz7GSFjdiH6HEO99S9oid17BKSSsgjZ32ap4CJxHY0COFsakYnx0NYqLj661uhvUCLFRnjzVR3dZbRYCKEYhTWn-njP695SNIBH9E5zdPdYs-Al7FdksZbAhcBSxMcl2SvZt3ST5aVwveCiLn9sj4Zpnw0wqLFSz7aCTNydbx6wlS34VtuCkRZJ0bHraZJvUuqxDIqLvd7ArVtE_iLu499_X2oRwj_E/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FeTIV

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Katie Rose Jobson 

Sent: Thursday, June 23, 2022 6:08 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] aseg.stats - eTIV volume space


External Email - Use Caution

Hi FreeSurfer experts,

I apologize if this question has been addressed, but I was unable to find a 
definitive answer elsewhere.

I am using the aseg.stats file to extract the estimated Total Intracranial 
Volume (eTIV) value to be used as a correction to my anatomical data. I just 
want to confirm what space this data is in. I had previously assumed this data 
was in native anatomical space. But I read on the wiki that this statistic is 
calculated using the Talairach transform file (talairach.xfm), which is the 
conversion from MNI305 to Talairach. I just want to ensure I am correct in the 
assumption that this data is represented in native anatomical space.

Thank you so much for your help in this matter.

Best Wishes,
Katie

--
Katie Jobson, M.S.
PhD Student | Cognitive Neuroscience

Re: [Freesurfer] aseg.stats - eTIV volume space

2022-06-23 Thread Wighton, Paul 
Hi Katie,

FreeSurfer operates mostly in "FreeSurfer Space", which is voxel resolution of 
1mm^3 and sagittal orientation.

You can compare orig.mgz to the original input to see what the difference 
between native space and FreeSurfer Space would be.

eTIV is computed using the transformation matrix from FreeSurfer Space to 
MNI305 space.  There is more information here about it here:
https://surfer.nmr.mgh.harvard.edu/fswiki/eTIV

-Paul


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Katie Rose Jobson 

Sent: Thursday, June 23, 2022 6:08 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] aseg.stats - eTIV volume space


External Email - Use Caution

Hi FreeSurfer experts,

I apologize if this question has been addressed, but I was unable to find a 
definitive answer elsewhere.

I am using the aseg.stats file to extract the estimated Total Intracranial 
Volume (eTIV) value to be used as a correction to my anatomical data. I just 
want to confirm what space this data is in. I had previously assumed this data 
was in native anatomical space. But I read on the wiki that this statistic is 
calculated using the Talairach transform file (talairach.xfm), which is the 
conversion from MNI305 to Talairach. I just want to ensure I am correct in the 
assumption that this data is represented in native anatomical space.

Thank you so much for your help in this matter.

Best Wishes,
Katie

--
Katie Jobson, M.S.
PhD Student | Cognitive Neuroscience 
Lab
Department of Psychology and Neuroscience | Temple University
[cid:dcfe96a7-bf68-4d92-8c1e-61f5814893fa]
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 .
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[Freesurfer] aseg.stats - eTIV volume space

2022-06-23 Thread Katie Rose Jobson 
External Email - Use Caution

Hi FreeSurfer experts,

I apologize if this question has been addressed, but I was unable to find a 
definitive answer elsewhere.

I am using the aseg.stats file to extract the estimated Total Intracranial 
Volume (eTIV) value to be used as a correction to my anatomical data. I just 
want to confirm what space this data is in. I had previously assumed this data 
was in native anatomical space. But I read on the wiki that this statistic is 
calculated using the Talairach transform file (talairach.xfm), which is the 
conversion from MNI305 to Talairach. I just want to ensure I am correct in the 
assumption that this data is represented in native anatomical space.

Thank you so much for your help in this matter.

Best Wishes,
Katie

--
Katie Jobson, M.S.
PhD Student | Cognitive Neuroscience 
Lab
Department of Psychology and Neuroscience | Temple University
[cid:dcfe96a7-bf68-4d92-8c1e-61f5814893fa]
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 .
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Re: [Freesurfer] selxavg3-sess out of memory error

2022-06-23 Thread Caspar M. Schwiedrzik 
External Email - Use Caution

Hi!
Any advice on this issue?
The error message is:

Starting contrasts
UrInv J=1 -
Out of memory. Type "help memory" for your options.

Error in fast_glm_pcc (line 39)
yhatd = Rd*(X*beta);

Error in fast_fratiow (line 136)
  if(nargout == 6) pccbin = fast_glm_pcc(beta(:,indbin),Xbin,C,rvarbin);
  end

Error in fast_selxavg3b (line 1148)
 fast_fratiow(betamat,X,rvarmat,C,acfsegmn,acfseg.vol(:));

>> --
ERROR: fast_selxavg3() failed\n

Thank you,
Caspar


Am Mo., 20. Juni 2022 um 10:17 Uhr schrieb Caspar M. Schwiedrzik <
cschwie...@rockefeller.edu>:

> Hi!
> I am running large single subject GLMs with selxavg3-sess and I run into a
> Matlab "out of memory" error. I was wondering whether you had any advice on
> how to get around that.
>
> I have 40-50 runs per subject, and the analyses are whole brain.
> The GLM per subject runs through fine, but the error occurs once
> selxavg3-sess starts computing contrasts.
> The problem occurs with v5.3 and v7.2.
>
> This is a Centos 7 system with 320 GB of memory, and 7 GB of swap memory.
>
> Any advice would be appreciated!
> Caspar
>
>
>
>
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[Freesurfer] freeview and dmri_trk2trk

2022-06-23 Thread Juan 
   External Email - Use Caution


Hello freesurfer experts,

I have been using TRACULA to analyze my group of images and I have 
noticed a bug or not.

But I would like to comment it so that you can help me to solve it.
I embed the two files with the dmri_trk2trk function.
- perm.th20.pos.sig.voxel.mgh

- z.mgh

I visualize them with the freeview image viewer and when I try to 
exchange the files to see them, only one of the two is reflected, that 
is to say, they don't change, the same map is maintained at all times. 
This is an error of my computer, or maybe my freesurfer could be wrongly 
installed.

Thank you very much for the clarification.

Juan___
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contains patient information, please contact the Mass General Brigham 
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Re: [Freesurfer] VirtualBox appliance 7z pass code

2022-06-23 Thread Ryan Johnson 
External Email - Use Caution

Hello, any chance I could get the pass code? I'm really hoping to start my
project soon, and I haven't been able to get Freesurfer running from
scratch.

On Fri, Jun 17, 2022 at 2:05 PM Ryan Johnson  wrote:

> Good afternoon!
>
> I would like the pass code to unzip the FreeSurfer 7 VirtualBox VM.
>
>
> Thank you,
>
> Ryan Johnson
>
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[Freesurfer] Visualizing and interpreting vertex-wise GLM analysis

2022-06-23 Thread Julian Macoveanu 
External Email - Use Caution



Dear Freesurfers,

I have a simple design with patients and controls and would like to
find regions showing group differences in cortical volume and
thickness. I also remove the effect of age, sex and ICV. Running the
GLM group analysis by the book I get a few clusters showing
significant differences in intercept.

1. I interpret this like patients have smaller “predicted” regional
volume at age 0, or at mean age of the group (if demeaned age
covariate) compared to controls. How can this finding be described in
a more clinically meaningful way?

2. Related to the above, how do I visualize what is going on in the
significant clusters? The extracted values from these clusters
(ocn.dat) show no group differences in volume when displaying the
group means in SPSS (using either age/sex/ICV adjusted or non-adjusted
values). Maybe I am misunderstanding something, how can there be
differences in intercept but no differences between group means?
(slopes not significantly different). How do I best describe and
visualize this group difference in a paper?

Going through the studies I found on Pubmed that used Freesurfer with
vertex-wise GLM, so far, I only found e.g. the “lower thickness”
interpretation in one group vs the other and not “lower intercept”. In
my case at least, I cannot say this since the extracted values between
groups show no group difference.

Julian

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