[Freesurfer] can I run Monte Carlo simulation without calling mri_glmfit

[Wang, Xin]

Hello,
I repeated same mri_glmfit at multiple depth of cortical thickness and merged 
the maximal values of the sig.mghs for all depths to a merged_sig.mgh (as in 
Wang X, et al. Neuroimage. 49(4):3075-85; 2010). I need to run Monte Carlo 
simulation
 on the merged_sig.mgh. I have the .fsgd and .mtx files for this glm design  
but I don't have a smoothed input image as fs.8.mgh for this merged sig.mgh. 
Can I modify the mri_glmfit-sim to run the correction without calling fs.8.mgh?

Thank you.

Xin
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[Freesurfer] Fwd: can I run Monte Carlo simulation without calling mri_glmfit

[Wang, Xin]

Subject: can I run Monte Carlo simulation without calling mri_glmfit

Hello,
I repeated same mri_glmfit at multiple depth of cortical thickness and merged 
the maximal values of the sig.mghs for all depths to a merged_sig.mgh (as in 
Wang X, et al. Neuroimage. 49(4):3075-85; 2010). I need to run Monte Carlo 
simulation
 on the merged_sig.mgh. I have the .fsgd and .mtx files for this glm design  
but I don’t have a smoothed input image as fs.8.mgh for this merged sig.mgh. 
Can I modify the mri_glmfit-sim to run the correction without calling fs.8.mgh?

Thank you.

Xin
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[Freesurfer] group analysis of large data sets

[Wang, Xin]

Hello, FreeSurfer Group,

What is the maximal matrix size for glm_fit process?
How to use FreeSurfer for group analyses of more than 2000 subjects, 128 
variables, and 128 Classes?

Thank you.

Xin
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Re: [Freesurfer] group analysis of large data sets

[Wang, Xin]

Thank you, Dr. Greve.
when I ran >2000 subjects in Version 5.3, I received this error message 
"##ERROR: gdfReadV1: the number of inputs in FSGD file exceeds the maximum 
allowed 2000##"
In your previous post about mri_glmfit, 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-September/033151.html,
 I found
#define FSGDF_NCLASSES_MAX  128 
#define FSGDF_NVARS_MAX 128 
#define FSGDF_NINPUTS_MAX  2000 
Are these the maximum? The mri_glmfit is written in C. Could you send me a 
version of mri_glmfit code without limits?
Thank you very much.

Xin

-Original Message-
From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] 
Sent: Monday, March 27, 2017 1:47 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] group analysis of large data sets

I don't think there is a maximum size. You would do the big analysis the same 
way as the small.


On 03/26/2017 07:54 PM, Wang, Xin wrote:
>
> Hello, FreeSurfer Group,
>
> What is the maximal matrix size for glm_fit process?
>
> How to use FreeSurfer for group analyses of more than 2000 subjects, 
> 128 variables, and 128 Classes?
>
> Thank you.
>
> Xin
>
>
>
> ___
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> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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[Freesurfer] glmfit: matrix error

[Wang, Xin]

Hello, FreeSurfer group,

When I ran glmfit I got the following error massage. I standardize ages but the 
problem remains. Any other suggestions? Alternatively, is there any way to 
by-pass this design checking step?

Thank you very much.

Xin


ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08

Possible problem with experimental design:
Check for duplicate entries and/or lack of range of
continuous variables within a class.
If you seek help with this problem, make sure to send:
  1. Your command line:
mri_glmfit.bin --y 
RESULT/group_currPTSD_AgeGenderSiteFACT_adult/lh_group_currPTSD_AgeGenderSiteFACT_adult.fwhm10.fsaverage.mgh
 --fsgd group_currPTSD_AgeGenderSiteFACT_adult.fsgd dods --glmdir 
RESULT/group_currPTSD_AgeGenderSiteFACT_adult/lh --surf fsaverage/ lh --C 
group_currPTSD_AgeGenderSiteFACT_adult.mtx
  2. The FSGD file (if using one)
  3. And the design matrix above
Attempting to diagnose further
SumSq: Min=0.33 (col 38), Max=18.703472 (col 62)
The scale is much different between columns 38 and 62, you may want to
 normalize by subtracting the mean and dividing by the standard deviation.
ERROR: cannot find RESULT/group_currPTSD_AgeGenderSiteFACT_adult/lh/fwhm.dat

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[Freesurfer] questions about longitudinal analysis

[Wang, Xin]

Hi, groups,

I noticed the updates of longitudinal analysis in the new version of 
Freesurfer. However, I still have a couple of questions about the goal of 
longitudinal analysis.

1. The goal of longitudinal analysis is to detect the atrophy (thinning), but 
the transformation in the registration step will minimize any atrophy. An 
example of outcomes of FLIRT and FNIRT on FSL website exactly demonstrates that 
the atrophy disappears in the 'best' transformation (FNIRT) 
http://www.fmrib.ox.ac.uk/fsl/fnirt/index.html. In our experience, the number 
of vertex of post-transformed tp2 is very close to tp1. It is not clear to me 
how the difference in the original thickness between tp2 and tp1 is preserved 
in this transformation. 

One may argue that processing tp1 and tp2 independently does not solve this 
problem because the registration is also used in the routine recon. Is it true? 
 

2. The new longitudinal process is still using volume-based registration if I 
read it correctly. Why not switch to surface-based since people have argued the 
advantage of surface-based over volume-based?

 

Thank you for any clarification,

 

Wang

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RE: [Freesurfer] tksurfer display problems

[Wang, Xin]

We did for one node, and going to up-grade the rest. A simple answer to your 
question is to up-grade any node you want to run tksurfer. Help it helps.
 
Xin



From: Siddharth Srivastava [mailto:[EMAIL PROTECTED]
Sent: Wed 11/19/2008 6:37 PM
To: Wang, Xin
Subject: Re: [Freesurfer] tksurfer display problems


Hi Xin,
  Thanks for the reply. I am contacting you since you mentioned that you
are running freesurfer on a cluster. I contacted my sysad regarding this 
problem,
and they want to know if this upgrade has to be dome on every node of the 
cluster.
can you recommend something regarding this?
best regards,
sid.


On Wed, Nov 19, 2008 at 11:46 AM, Wang, Xin <[EMAIL PROTECTED]> wrote:


We just solved the same problem by upgrading the driver of video card 
on the cluster.  An early massage in the freesurfer archive gives more details.
 
Xin 



From: Siddharth Srivastava [mailto:[EMAIL PROTECTED]
Sent: Wed 11/19/2008 1:21 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] tksurfer display problems


Hi mjp,
   Thanks for an account of a working solution to the problem. 
I just wanted to
know if this intervention has to done on the client machine (from where 
i am 
viewing the results), or on the server side (on which i am processing 
the data)? Further,
in case of a 64 bit machine, would the source and the destination 
directories change
accordingly? 
best regards,
sid.


On Wed, Nov 19, 2008 at 8:50 AM, Mark J. Pearrow <[EMAIL PROTECTED]> 
wrote:


Hi all,

This is a bug that has baffled me for almost a year now, so 
today I decided to just attend to it exclusively. I have never understood why, 
exactly, the anecdotal and illogical fix for the sliver-of-the-brain issue 
seems to be to install an NVidia graphics card in the afflicted server.

I found this posting:

https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2008-April/007558.html

Which seemed to indicate that it was not the card itself that 
made the difference, but rather some software component that made things work. 
There is an extension to X11, called GLX, which allows the remote side (the 
"client", in X11 speak) to bypass the processing of OpenGL commands and to send 
them to the server.

So, following the advice in the posting above, I downloaded the 
latest NVidia.run package and unpacked it by using the "-x" flag - then I 
copied all of the usr/lib/ and usr/lib32/ difrectories in the (freshly 
unpacked) NVIDIA-linux directory into /usr/lib and /usr/lib32, respectively. 
Then I ran "ldconfig -v" to update the ld cache.

And voila, I can run tksurfer over X11, VNC and NX now on a 
server that has no NVidia card, without any problems.

I still don't understand what exactly is being provided by 
NVidia's version of the libraries, but I suspect it has to do with "TLS" (in 
the context of OpenGL, not in the crypto sense). This appeared in the output of 
`ldd tksurfer.bin` on my systems with nvidia cards, and on my previously-broken 
system after I installed those files:

libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1

mjp 






On Nov 18, 2008, at 9:35 PM, Bruce Fischl wrote:



Hi Sid,

this is a known problem. It actually used to work and 
we broke it. The current workaround is to use VNC.

cheers,
Bruce


On Tue, 18 Nov 2008, Siddharth Srivastava wrote:



Hi !
  I am a relatively new user of freesurfer, and 
currently i have 2
instances
of the same -stable 64bit Linux versions 
installed, one on my local machine,
and the
other on a cluster, accessible over the 
network. I have been able to get
freesurfer
running without any problems on my local 
machine, but after i installed the
same version on the remote machine, the 
tksurfer window did not display
what i expectd to see, but only a small part of 
the

RE: [Freesurfer] reg-feat2anat failed

[Wang, Xin]

Thank you very much for your quick reply, Dr. Greve. I asked our institutional 
MRI center for correct information on qform and sform since the header of nifti 
files are created by their scripts. But I do not know what they can do to fix 
this problem. I will appreciate if you have any further suggestion on how to do 
the registration without the information on qform and sform in case I can not 
get them. Does convert to ANALYZE format or manually correct in tkregister2 
work?

Thank you again,

Xin  


-Original Message-
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Mon 12/15/2008 1:09 PM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] reg-feat2anat failed
 
Hi Xin, the problem is that neither the sform nor the qform are valid. 
Did the message below not appear when you ran tkmedit?

WARNING: neither NIfTI-1 qform or sform are valid
WARNING: your volume will probably be incorrectly oriented

Fix that, and everything will work fine.

doug


Wang, Xin wrote:

> Hello, Freesurfer group,
> I am registering the fMRI results to surface using reg-feat2anat (v 
> 1.26.2.1 2007/08/15) and tkregister2. The automatic registration 
> catastrophically failed in the subject space, but worked fine in the 
> standard space. The orientations of example_func.nii.gz in the subject 
> space are flipped in any view. I use the tkmedit to view the 
> example_func, and found the orientation is wrong. It seems Freesurfer 
> can not read nifti header correctly. I attach the reg-feat2anat log 
> file and an example_func.nii.gz.  
> I found the following message from Freesurfer email list.
> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html
> Does Freesurfer have a solution for this type of problems by now?
>
> Thank you in advance,
>
> Xin
>
>
>
>___
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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

In order to help us help you, please follow the steps in:
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RE: [Freesurfer] reg-feat2anat failed

[Wang, Xin]

hello, Freesurfer group,

I try to use registration.mat files of FSL/FEAT routines, instead of 
anat2example_func.bat, to register the orig.mgz and example_func.nii.gz with 
the thinking that using initial_highres in FEAT may improve the reg. However, 
tkregister2 catastrophically failed to register two brains when I use --fsl 
flag. Modifying header of example_func with mri_convert does not solve the 
problem. I will appreciate any suggestion on using .mat file for registration. 

second question: what is the best registration of example_func and orig.mgz? In 
another word, what should I check besides things in the FS tutorial when I 
check/modify the registration in tkregister2? Is there golden reference points 
I can use?

Thank you in advance for any suggestion.

Xin wang 


-Original Message-
From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Mon 12/15/2008 1:26 PM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] reg-feat2anat failed
 
There is a flag in the nifti header saying whether the qform or sform 
are valid, and it looks like your scripts do not set this flag. You can 
use mri_convert (the freesurfer program). This will create valid files 
that can be read into any program.

doug

Wang, Xin wrote:

> Thank you very much for your quick reply, Dr. Greve. I asked our 
> institutional MRI center for correct information on qform and sform 
> since the header of nifti files are created by their scripts. But I do 
> not know what they can do to fix this problem. I will appreciate if 
> you have any further suggestion on how to do the registration without 
> the information on qform and sform in case I can not get them. Does 
> convert to ANALYZE format or manually correct in tkregister2 work?
>
> Thank you again,
>
> Xin 
>
>
> -Original Message-
> From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
> Sent: Mon 12/15/2008 1:09 PM
> To: Wang, Xin
> Cc: freesurfer
> Subject: Re: [Freesurfer] reg-feat2anat failed
>
> Hi Xin, the problem is that neither the sform nor the qform are valid.
> Did the message below not appear when you ran tkmedit?
>
> WARNING: neither NIfTI-1 qform or sform are valid
> WARNING: your volume will probably be incorrectly oriented
>
> Fix that, and everything will work fine.
>
> doug
>
>
> Wang, Xin wrote:
>
> > Hello, Freesurfer group,
> > I am registering the fMRI results to surface using reg-feat2anat (v
> > 1.26.2.1 2007/08/15) and tkregister2. The automatic registration
> > catastrophically failed in the subject space, but worked fine in the
> > standard space. The orientations of example_func.nii.gz in the subject
> > space are flipped in any view. I use the tkmedit to view the
> > example_func, and found the orientation is wrong. It seems Freesurfer
> > can not read nifti header correctly. I attach the reg-feat2anat log
> > file and an example_func.nii.gz. 
> > I found the following message from Freesurfer email list.
> > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg05573.html
> > Does Freesurfer have a solution for this type of problems by now?
> >
> > Thank you in advance,
> >
> > Xin
> >
> >
> >
> >___
> >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
>
> In order to help us help you, please follow the steps in:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
>
>

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

In order to help us help you, please follow the steps in:
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RE: [Freesurfer] Problem with post-spm registered data

[Wang, Xin]

Sorry for asking same question here again. I asked Dung before holiday about 
the criteria of good registration of fMRI and thickness map. 
http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg08913.html 
 
I paste my question again: what is the best registration of example_func and 
orig.mgz? In another word, what should I check besides things in the FS 
tutorial when I check/modify the registration in tkregister2? Is there golden 
reference points I can use?

 
I will appreciate if Dave could give more explanation or references of 
"beautiful match between functional and structural images".  

Thank you in advance.

Xin Wang 




From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Mon 1/5/2009 2:03 PM
To: Dave Brohawn
Cc: jroff...@partners.org; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Problem with post-spm registered data



Hi Dave, I'm not sure where to begin with this. Can you give more info?
In particular, you might look at
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting for ways to report issues
efficiently.

doug

Dave Brohawn wrote:

>Hello,
>
>Josh Roffman and I recently ran an fMRI scan. Our subject's data viewed in
>tkmedit seemed to be shifted inferiorly in the coronal view by a wide
>margin (an inch or so), leaving no functional activation in the top of the
>cortex, even when set at an extremely low threshold.
>
>When running the fMRI scan, we checked our slice prescription and ensured
>the area of view covered the entire cortex. We also checked the raw data
>output during the scan in the viewing window, and functional activity was
>present.
>
>After running the unpacking and recon-all processes, I ran the pre-proc
>command and spm-register, and viewed the output using tkregister2. The
>registered functional data matched up beautifully with the underlying
>anatomy, and went right to the top of the cortex in the coronal view.
>
>We ran our analysis using the appropriate paradigm files (has worked
>without fail for our previous subjects) and there is no functional
>activity in the top inch or so of the cortex whatsoever.
>
>Please let me know if you have an answer to how this could have happened.
>
>Dave Brohawn
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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

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting





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RE: [Freesurfer] questions about region-wise analysis data

[Wang, Xin]

I want to ask a related question: We study group differences between patients 
and controls, and correlations of symptoms and thickness in patients only. We 
would like to display (and extract) the common regions between two analyses in 
ONE figure. Which template can we use?
We created two sets of ROIs in Qdec: one set is defined using an averge from 
all subjects; the other set is defined using an average of patients only. The 
ROI.labels from one set can not be loaded correctly on the average tamplate of 
the other set. The problem remains even if we convert both sets of ROI.labels 
to individual spaces.   can we use fsaverage for both analyses? 
 
thanks,
 
Xin Wang



From: Doug Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Mon 1/5/2009 2:23 PM
To: Siddharth Srivastava
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] questions about region-wise analysis data




Siddharth Srivastava wrote: 

Hi all,
 I am trying to understand the --surf flag in the mri_glmfit
command, and the 2 parameters that follow it. The tutorial mentions
--surf average lh . 
1) what should "average" contain? should it point to the average of
the population, of fsaverage, or is it just a flag?


This is the name of the average subject as created by make_average_subject. If 
you did not make an average subject, then use fsaverage.


2) lh: is this just the specification of the hemisphere to be processed
or should it point to a valid set of files. 


Just the hemisphere



If i am doing a group analysis of a measure (say, thickness), and i have
smoothed thickness maps registered to a population specific template in
a subdir, how should i specify --surf and subsequebt parameters? 


The input is specified with with --y. The --surf just tells glmfit that it is a 
surface so that it can compute the FWHM appropriately.



Further, i also get an error saying --C command not found (for the 
contrast vector).
why is this happenning?


Can't say without the cmd line, but I'm guessing you have a rouge space in your 
script



best regards,
sid.


On Sun, Dec 28, 2008 at 12:24 PM, Nick Schmansky 
 wrote:


Sid,

A group analysis can be performed from the command-line using 
mri_glmfit
directly.  See this tutorial:


http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

You can use a different average subject, other than fsaverage, 
although
it doesnt improve an analysis to use a subject from your group. 
 Also,
you can create a symlink from 
$FREESURFER_HOME/subjects/fsaverage to
your SUBJECTS_DIRS, to spare having to copy the data.

Nick



On Sun, 2008-12-28 at 12:01 -0800, Siddharth Srivastava wrote:
> Hi Nick,
>  Thanks, It was my mistake. It works exactly as 
you say.
> I still have to look at qdec documentation, but could i ask 
if it is
> possible to perform the group analysis in a batch mode, 
without
> the GUI, i.e ?
>
> regarding the movement of data, the first time i did it, i 
got a
> screen full
> of memory addresses and corresponding routines, followed by a 
crash (
> exit from wish, back to shell). I am not able to replicate 
it, seems
> to work
> now.
>
> Also, is it possible to register everything to a different 
surface,
> other
> that fsaverage.. for example to one of the subjects? Can this 
be
> located
> outside the relative paths reachable via $SUBJECTS_DIR ? In 
fact, can
> fsaverage be located outside? For the processing i did, i had 
to copy
> the fsaverage as one of the subjects, so that it can be 
located
> within
> the current context of $SUBJECTS_DIR .
>
> Thanks again, for the timely help.
> sid.
>
>
> On Sun, Dec 28, 2008 at 9:17 AM, Nick Schmansky
>  wrote:
> Sid,
>
> The .mgh files, in the case of the commands you ran, 
store
> surface data
> corresponding to the 'fsaverage' subject.  So you 
would first
> load the
> inflated surface for fsaverage (tksurfer fsaverage lh
> inflated), then
 

[Freesurfer] smoothing size

[Wang, Xin]

Hello, Freesurfer group,
Could you tell me the default size of smoothing extents (kernel?) of smooth1 
and smooth2 in the auto-recon-all? How can I change the size with mris_smooth 
in the auto-recon-all flow? And why does the smoothing not affect the thickness 
measure?
 
Thank you in advance,
 
Xin Wang
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RE: [Freesurfer] reg-feat2anat failed

[Wang, Xin]

Sorry for the confusion. Let me rephase my questions.
 
question 1: I want to use the example_func2highres.mat created by fsl/FEAT 
registration to register example_func and orig.mgz. Can the flag --fslregout or 
--fsl do it?
 
Question 2: These numbers appear in the terminal whenever I click a point in 
tkregister2? What do these numbers mean?  
Screen:  256 257 (113,113,113), inorm = 1, mov_frame = 0
 Anat:(128 126 127)   (   0.0   -1.02.0)   25.  32.7
 Func:( 31  32  21)   (   4.23.11.4)  756.  112.5
 
question 3: I can only see the middle portion of the brain in tkregister2 when 
I zoomed in. How can I see other parts of the target and movable pictures?
 
Thank you,
 
Xin Wang
  


 


From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Tue 1/13/2009 4:19 PM
To: Wang, Xin
Subject: Re: [Freesurfer] reg-feat2anat failed




1) I don't know what you mean. The fslmatout is for creating an fsl mat
file from a freesurfer register.dat

2. I don't know what you mean.

3. What do you mean by "moving the two images together"?


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RE: [Freesurfer] reg-feat2anat failed

[Wang, Xin]

Hello, Dr. Greve,
I followed the steps in the tkregister2 --help: converted both example_func and 
orig.mgz to .img of ANALYZE format and ran the tkregister2 use -- fsl 
example_func2highres.mat of fsl/FEAT. The two brains are in the different views 
(i.e., axial view of example_func overlay on the coronal view of orig). I am 
still struggle with same questions as before. I appreciate any suggestion.
 
Thank you,
 
Xin Wang  



From: Wang, Xin
Sent: Tue 1/13/2009 4:36 PM
To: Douglas N Greve
Cc: freesurfer
Subject: RE: [Freesurfer] reg-feat2anat failed


Sorry for the confusion. Let me rephase my questions.
 
question 1: I want to use the example_func2highres.mat created by fsl/FEAT 
registration to register example_func and orig.mgz. Can the flag --fslregout or 
--fsl do it?
 
Question 2: These numbers appear in the terminal whenever I click a point in 
tkregister2? What do these numbers mean?  
Screen:  256 257 (113,113,113), inorm = 1, mov_frame = 0
 Anat:(128 126 127)   (   0.0   -1.02.0)   25.  32.7
 Func:( 31  32  21)   (   4.23.11.4)  756.  112.5
 
question 3: I can only see the middle portion of the brain in tkregister2 when 
I zoomed in. How can I see other parts of the target and movable pictures?
 
Thank you,
 
Xin Wang
  


 


From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Tue 1/13/2009 4:19 PM
To: Wang, Xin
Subject: Re: [Freesurfer] reg-feat2anat failed




1) I don't know what you mean. The fslmatout is for creating an fsl mat
file from a freesurfer register.dat

2. I don't know what you mean.

3. What do you mean by "moving the two images together"?


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[Freesurfer] more info about bbregister

[Wang, Xin]

Hello, Dr. Greve,
 
I am using bbregister to register the BOLD to T1. The --help does not provide 
any imformation about how it works. What are the difference from bbregister to 
flirt (fslregister)? more information about --intvol also needed. For example, 
the format of intvol.reg (.mat or .bat?) Can I reference to the help of same 
flag in the tkregister2? 
 
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[Freesurfer] questions about SPM surfrend

[Wang, Xin]

Dear Dr. Kahn,
 
I have a few question about your surfrend. I attended Freesurfer workshop a 
month ago, but I did not know your SPM surfrend tool at that time. So I send 
you this email to seek your help.
 
1) could you give some details about the surfrend? I am interested in the 
procedures and commands used in this tool.
 
2) I compared surfrend registration and the registration using bbregister 
SPM_fixedscapled_T1.img to my average. Some active ROIs are splited onto 
adjecent gyri after using .bat file produced by bbregister. In contrast, the 
active ROIs are continuous through sulcus using surfrend. Could you explain how 
did you correct for the cross sulcual spliting?
 
3) do you know anything like surfrend for FSL? 
 
I am looking forward to hearing from you.
 
Thank you in advance,
 
Xin Wang
 
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[Freesurfer] need T-values

[Wang, Xin]

Hello, Freesurfer group,
 
I need T values instead of F values for a one-sample T test GLM. How can I 
convert the values in F.mgh or sig.mgh (for 12 subjects one group no factor) to 
T values and overlay them on the surface? 
 
I found the similar questions in the following emails posted on freesurfer 
email list. I want to follow up these questions.
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2007-September/006199.html
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2007-September/006112.html
 
 
Thank you in advance,
 
Xin 
 
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[Freesurfer] How to project fMRI activity of entire depth of cortex on to surface

[Wang, Xin]

Hello, Freesurfer group,
 
The mri_vol2surf only register the fMRI activity at a certain depth of cortex, 
as specisfied by -projecfrac, to the cortical surface. mri_surf2surf does the 
same thing. I want to identify any cortical region have activation during the 
task, therefore, I need to project fMRI activity of entire depth of cortex onto 
surface. Some regions may have activity in different depth of cortex,  Ideally, 
the significent level of these regions reflect the peak of the activity cross 
entire depth or the sum of significense of entire depth. 
 
the --interp trilinear may do some toward my goal, but it elimit many 
activities compare to nearest. 
 
Thanks,
 
Xin Wang
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RE: [Freesurfer] How to project fMRI activity of entire depth of cortex on to surface

[Wang, Xin]

Thank you, Dr. Greve. 
 
Does -projfrac-max 0 1 register the maximal P value cross entire depth of 
cortex to the vertex on the surface?
 
Does -projfrac-avg 0 1 delta register the average P value cross entire depth of 
cortex to the vertex on the surface? 
 
Can I use these flags in mris_preproc or mris_surf2surf during the 
surface-based group analysis?   
 
Xin



From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Thu 3/5/2009 11:25 AM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] How to project fMRI activity of entire depth of 
cortex on to surface



Do any of the other --proj flags do what you need? Eg,  --projfrac-max?
See the --help

doug

Wang, Xin wrote:
> Hello, Freesurfer group,
> 
> The mri_vol2surf only register the fMRI activity at a certain depth of
> cortex, as specisfied by -projecfrac, to the cortical
> surface. mri_surf2surf does the same thing. I want to identify any
> cortical region have activation during the task, therefore, I need to
> project fMRI activity of entire depth of cortex onto surface. Some
> regions may have activity in different depth of cortex,  Ideally, the
> significent level of these regions reflect the peak of the activity
> cross entire depth or the sum of significense of entire depth.
> 
> the --interp trilinear may do some toward my goal, but it elimit many
> activities compare to nearest.
> 
> Thanks,
> 
> Xin Wang
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


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RE: [Freesurfer] How to project fMRI activity of entire depth of cortex on to surface

[Wang, Xin]

Hello, Dr. Greve,
I am waiting for your new version of mris_preproc command that allows to 
project the max of activity within a column to the vertex on the surface. Could 
you kindly send me the command ASAP.
 
Thank you,
 
Xin



From: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
Sent: Thu 3/5/2009 1:01 PM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] How to project fMRI activity of entire depth of 
cortex on to surface





Wang, Xin wrote:
> Thank you, Dr. Greve.
> 
> Does _-projfrac-max 0 1_ register the maximal P value cross entire
> depth of cortex to the vertex on the surface?
yes
> 
> Does _-projfrac-avg 0 1 delta_ register the average P value cross
> entire depth of cortex to the vertex on the surface?
yes, but probably not what you want to do.
> 
> Can I use these flags in mris_preproc or mris_surf2surf during the
> surface-based group analysis? 
No, but I can add it.
> 
> Xin
> 
> *From:* Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
> *Sent:* Thu 3/5/2009 11:25 AM
> *To:* Wang, Xin
> *Cc:* freesurfer
> *Subject:* Re: [Freesurfer] How to project fMRI activity of entire
> depth of cortex on to surface
>
> Do any of the other --proj flags do what you need? Eg,  --projfrac-max?
> See the --help
>
> doug
>
> Wang, Xin wrote:
> > Hello, Freesurfer group,
> >
> > The mri_vol2surf only register the fMRI activity at a certain depth of
> > cortex, as specisfied by -projecfrac, to the cortical
> > surface. mri_surf2surf does the same thing. I want to identify any
> > cortical region have activation during the task, therefore, I need to
> > project fMRI activity of entire depth of cortex onto surface. Some
> > regions may have activity in different depth of cortex,  Ideally, the
> > significent level of these regions reflect the peak of the activity
> > cross entire depth or the sum of significense of entire depth.
> >
> > the --interp trilinear may do some toward my goal, but it elimit many
> > activities compare to nearest.
> >
> > Thanks,
> >
> > Xin Wang
> > 
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>


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[Freesurfer] active volume of surface-based analysis

[Wang, Xin]

Hello, Freesurfer group,
In the tutorial of surface-based fMRI analysis, the active volume are 
calculated from the entire depth of an given active vertex. I do not think it 
is the best way to measure it since no all activities occupy the entire depth 
of cortex. A logical way to get accurate active volume is measuring the active 
verities of multiple planes (e.g., at 0.1 mm distance) and then constructing 
the active volume from activity on these planes. A option (similar as 
--projfrac_max) can project the sum of all planes on the surface, and 3D active 
volume can be viewed in tkmedit. 
 
Does Freesurfer currently have commands to achieve something like this 
procedure?
 
I am looking forward to hearing from you ASAP.
 
Thanks,
 
Xin 
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[Freesurfer] the program for analysis of SI cortex

[Wang, Xin]

Hello, group
I need to compare thickness of left v.s. the right SI and MI cortices. I saw 
some matlab tools for comparsion of left and right hippocampus in 
Lundervold.pdf. I could not find similar tools in the matlab folder of 
Freesurfer stable release 3.0.5 that I just installed. Could anybody kindly 
tell me the tools I could use for my study?
Thank you in advance.
Xin Wang
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[Freesurfer] ROI of SI cortex

[Wang, Xin]

Hello, group
I need to compare thickness of left v.s. the right SI and MI cortices. I saw 
some matlab tools for comparsion of left and right hippocampus in 
Lundervold.pdf. I could not find similar tools in the matlab folder of 
Freesurfer stable release 3.0.5 that I just installed. Could anybody kindly 
tell me the tools I could use for my study?
Thank you in advance.
Xin Wang
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[Freesurfer] problem of group analysis

[Wang, Xin]

Hello, Group
I have a question about mri_glmfit. I can not run this commend on my data. 
An error 
"MatrixReadTxT: could not scan value [1] [2] 
file exists
ERROR: loading C age.mat" 
appeared. 
I do not know what is wrong. 
The only warning I saw is "ERROR: cound not find volume 
$SUBJECTS_DIR/average/surf/../mri/orig. Does it exist?" when I ran 
mri_surf2surf.  
 
I am doing group comparison of cortical thickness on 2X2 data. The following is 
my fsgd.txt 
 and *.mat.
 
GroupDescriptorFile 1

Title thick vs group

Class group1

Class group2

Variables age

Input APL02R700 group1 48

Input APN02G650 group1 35

Input APN02G700 group2 35 

Input APN03L700 group2 30

DefaultVariable age

age.mat: -1, 1, 0

If anyone know what is wrong in my analysis, please help.

Thank you in advance,

 

Xin 

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答复: [Freesurfer] ROI of SI cortex

[Wang, Xin]

Hello, Rahul
Two more questions. 1. How can I get the volumes of subcortical structures, 
like in the presentation of freesurfer & matlab? I did not find the matlab 
script to do so.
2. where are the thickness of every voxel saved? Can I access to it and copy 
data out?
Many thanks to you and Doug
 
XIn



From: Rahul Desikan [mailto:[EMAIL PROTECTED]
Sent: 2007-4-30 (星期一) 16:06
To: Wang, Xin
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] ROI of SI cortex



Hi Xin,

Within the *h.aparc.annot files for each subject, there should be
individual label files for *h.precentral.label and *h.postcentral.label.
If you take a look at your *h.aparc.stats, there should be a value for the
thickness and volume. You can, of course, take this *h.aparc.stats file
and upload it into matlab, spss or any other stats package and do
statistics on these values.

Best,

rahul

On Mon, 30 Apr 2007, Wang, Xin wrote:

> Dear Rahul
> The SI is primary somatosensory cortex (or postcentral gyrus) and MI is 
> primary motor cortex (or precentral gyrus). I want to compare the thickness 
> and volume of these two areas from left side to right side.
> Thank you,
>
> Xin
>
> 
>
> From: Rahul Desikan [mailto:[EMAIL PROTECTED]
> Sent: Mon 4/30/2007 3:52 PM
> To: Wang, Xin
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] ROI of SI cortex
>
>
>
> Hi Xin,
>
> What exactly do SI and MI cortices refer to?
>
> rahul
>
> On Mon, 30 Apr 2007, Wang, Xin wrote:
>
>> Hello, group
>> I need to compare thickness of left v.s. the right SI and MI cortices. I saw 
>> some matlab tools for comparsion of left and right hippocampus in 
>> Lundervold.pdf. I could not find similar tools in the matlab folder of 
>> Freesurfer stable release 3.0.5 that I just installed. Could anybody kindly 
>> tell me the tools I could use for my study?
>> Thank you in advance.
>> Xin Wang
>>
>
> --
>
>
>
>
>
>
>
>
>
>

--









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RE: [Freesurfer] problem of group analysis

[Wang, Xin]

Thank you, Doug. My problem is solved after I removed the commas.
Xin 



From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Thu 5/3/2007 8:38 PM
To: Wang, Xin
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] problem of group analysis


It's having problems reading the 2nd column of the 1st row (ie, [1][2]]). Does 
your age.mat file have commas in it? If so remove them and try again.

doug

Wang, Xin wrote: 

Hello, Group
I have a question about mri_glmfit. I can not run this commend on my 
data. 
An error 
"MatrixReadTxT: could not scan value [1] [2] 
file exists
ERROR: loading C age.mat" 
appeared. 
I do not know what is wrong. 
The only warning I saw is "ERROR: cound not find volume 
$SUBJECTS_DIR/average/surf/../mri/orig. Does it exist?" when I ran 
mri_surf2surf.  
 
I am doing group comparison of cortical thickness on 2X2 data. The 
following is my fsgd.txt 
 and *.mat.
 
GroupDescriptorFile 1

Title thick vs group

Class group1

Class group2

Variables age

Input APL02R700 group1 48

Input APN02G650 group1 35

Input APN02G700 group2 35 

Input APN03L700 group2 30

DefaultVariable age

age.mat: -1, 1, 0

If anyone know what is wrong in my analysis, please help.

Thank you in advance,

 

Xin 





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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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[Freesurfer] problem to save images

[Wang, Xin]

Hello, group
I have problems to save the display in TKsurfer. I tried 'Save RGB as', but I 
could not open the file with photoshop in windows, and it was total black when 
I opened it with adobe illustrator in windows or GIMP in Linux. 
Please tell me how to save the images so that I can open them with photoshop. 
Thank you in advance,
 
XIn   
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[Freesurfer] mean thickness of whole cortex

[Wang, Xin]

Hello, Group
Could anybody please tell me how to get the mean thickness of whole cortex? I 
got only the average thickness of each hemisphere with mris_anatomical_stats -a 
subject/lable/lh.aparc.annot -b subject lh
 
Thank you in advance,
 
Xin Wang
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[Freesurfer] add the gray matter

[Wang, Xin]

Hello, Group
 
I need to edit the pial surface. I learned to remove points with tkmedit from 
the tutorial. But how to add gray matter in the pial surface?
 
Thank you in advance.
 
Xin 
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RE: [Freesurfer] add the gray matter

[Wang, Xin]

Dear, Dr. Fischl
Thank you for your suggestion. My problems are around hippocampus. The 
grey/white surface is OK now. but some grey matters are not included in the 
pial surface. How to change the Pial surface? 
Thank you again,
 
Xin  



From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Mon 7/9/2007 5:53 PM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] add the gray matter



it depends why it's not getting out far enough. Usually you need to add
control points in the nearby white matter that are <110 on the
brainmask.mgz volume.

On Mon, 9 Jul
2007, Wang, Xin wrote:

> Hello, Group
>
> I need to edit the pial surface. I learned to remove points with tkmedit from 
> the tutorial. But how to add gray matter in the pial surface?
>
> Thank you in advance.
>
> Xin
>


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[Freesurfer] statistical designs

[Wang, Xin]

Hello, group
I want to learn more about designs of the general linear models for different 
statistical tests, such as paired T, ANOVA, and correlation tests. Could 
anybody suggest some examples of the designs for each model? 
I am facing a few problems of correlation analysis. If I want to do the within 
group correlation analysis, how can I do it without groups (or classes) as a 
regressor (if I only have one class and assign a 0 for the group in the 
contrast, does it work)? How can I specify the pearson's or Spearman's 
correlation in the analysis? How to know I have enough subjects for this 
correlation analysis?
 
Thank you in advance,
 
XIn Wang   
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RE: [Freesurfer] statistical designs

[Wang, Xin]

 
Thank you, Doug. Do you have more examples of different designs? Could anyone 
answer the rest of my questions?
 
Thank you again,
 
Xin   



From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Fri 7/20/2007 2:45 PM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] statistical designs



Check out

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

for some answers. For paired-t, you can specify --paired-diff to mris_preproc


Wang, Xin wrote: 

Hello, group
I want to learn more about designs of the general linear models for 
different statistical tests, such as paired T, ANOVA, and correlation tests. 
Could anybody suggest some examples of the designs for each model? 
I am facing a few problems of correlation analysis. If I want to do the 
within group correlation analysis, how can I do it without groups (or classes) 
as a regressor (if I only have one class and assign a 0 for the group in the 
contrast, does it work)? How can I specify the pearson's or Spearman's 
correlation in the analysis? How to know I have enough subjects for this 
correlation analysis?
 
Thank you in advance,
 
XIn Wang   




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MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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[Freesurfer] left-right comparsion

[Wang, Xin]

Hello, Group
Could anyone kindly share the method to compare the thickness between left and 
right hemispheres (vertex-by-vertex)? Did David C. Van Essen use Freesurfer in 
his article (NeuroImage 28 (2005) 635 - 662) to do the left-right comparison? 
 
Thank you in advance,
 
Xin Wang
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[Freesurfer] images use different protocols

[Wang, Xin]

Hello, Group
 
I have two set of images acquired with different imaging protocols (e.g., TRs 
and bandwidth are different). Can I poll them together for the analysis? 
 
I saw in the email list that some groups reported problems in generating the 
average of images with different TR for the group analysis.  I do not seem have 
problem to make average include all the images. 
 
But is the result acceptable if the images acquired with multiple protocols?
 
Thank you 
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RE: [Freesurfer] images use different protocols

[Wang, Xin]

Hello, Dr. Fischl
Thank you very much for your quickly response.
 
flip angle

TI   TR  TE  # ImagesBand width 
  

9   700  7.796   2.984   164 244.141
9   700  7.482.984   164244.141

9   650  7.482.984   164 244.141
 
 
Three protocols are different in TR and TI. 
We are not interested in comparing the protocols. GE just updated patchs for 
the scanner we are using. We can not run the original protocol (the second 
one). The first line is what the scanner uses now when we load the original 
protocol. This update intereupts our data aqusition. we have subjects in two 
study groups has been scanned with the original protocol, but we may have to 
use the new protocol from now on for any new subjects in both groups. 
 
We may not be able to balance the number of subjects for each acqusition type 
between two groups, unless we throw away some data.
 
Can we use the new protocol to continue our study?
 
Thank you again,
 
Xin Wang 



From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Thu 8/16/2007 11:32 AM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] images use different protocols



can you give us the details of the protocols? And are  you talking about
2 different acquisitions on the same subject, or two groups of subjects
with different acquisitions? If the latter then your groups must be
balanced in terms of # of subjects for each acquisition type.

On Thu, 16 Aug 2007, Wang, Xin wrote:

> Hello, Group
>
> I have two set of images acquired with different imaging protocols (e.g., TRs 
> and bandwidth are different). Can I poll them together for the analysis?
>
> I saw in the email list that some groups reported problems in generating the 
> average of images with different TR for the group analysis.  I do not seem 
> have problem to make average include all the images.
>
> But is the result acceptable if the images acquired with multiple protocols?
>
> Thank you
>


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Re: [Freesurfer] Re: Freesurfer Digest, Vol 41, Issue 13-add gray matter

[Wang, Xin]

Thank great helps from the group. I have a related issue. In my images some 
gray matters at the top of medial wall is lass than 60, so that these small 
areas are not included in gray matter. This may be due to the shadow of RF 
coil. Can I fix it by either decrease the threshold of gray matter or manually 
include these small areas?
 
Thank you again,
 
Xin 
 
 
 
 
 
Bruce Fischl
Mon, 09 Jul 2007 15:08:20 -0700
usually it's because the bias field brings the gm too low, so if you find 
nearby white matter (that is *not* partial volumed) that is below 110, putting 
some control points there will also move the pial surface out a bit. Or the 
skull strip could have removed it. Or the topology fixer might have done 
something strange. This can be checked by looking at the ?h.orig.nofix surface 
and seeing if it is more accurate than the ?h.orig. If this is the case you'll 
need to identify and correct the topological defect in the wm.mgz volume. 
cheers,
Bruce

On Mon, 9 Jul 2007, Sebastian Moeller wrote:
Hi,
not being an expert, please take my rambling with a grain of salt. But I am 
somewhat curious to learn better ways ;) 

On Jul 9, 2007, at 11:03 PM, [EMAIL PROTECTED] wrote:
Message: 9
Date: Mon, 9 Jul 2007 17:01:42 -0400
From: "Wang, Xin" <[EMAIL PROTECTED]>
Subject: [Freesurfer] add the gray matter
To: "freesurfer" 
Message-ID:
<[EMAIL PROTECTED]>
Content-Type: text/plain; charset="iso-8859-1"
Hello, Group
I need to edit the pial surface. I learned to remove points with tkmedit from 
the tutorial. But how to add gray matter in the pial surface? 
1) If you have nothing where gray matter should be, then check brainmask.mgz, 
if this is missing gray matter, around where your problems occur edit the 
bainmask.mgz volume and pick up your reconstruction from there. (IIRC there is 
something in the tutorial about this) 2) If there is white matter where gray 
matter should be, be sure to to check nu.mgz and brainmask.mgz at the critical 
parts for too high intensity in the supposed gray matter. Either control points 
might helo (unlikely) or redoing the intensity correction (and then starting 
again from that point). At least for my data, acquired with surface coils, 
sub-optimal intensity correction is really annoying. 
ahoi & good luck
Sebastian

Thank you in advance.
Xin
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End of Freesurfer Digest, Vol 41, Issue 13
**

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[Freesurfer] parcellation problem

[Wang, Xin]

Hello, Group,
 
After I manually removed the skull around cerebellum in the brainmask.mgz, the 
parcellation of the final inflated brain is totally messed up. Manual 
corrections of talairach transform and white matter surface did not mess up the 
parcellation. Could anyone tell me what is wrong?
 
Thank you in advance,
 
Xin Wang  
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RE: [Freesurfer] parcellation problem

[Wang, Xin]

I did not run the autorecon3 before I checked the parcellation.
 
Thank you,
 
Xin



From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Tue 9/11/2007 11:33 AM
To: Wang, Xin
Cc: freesurfer
Subject: RE: [Freesurfer] parcellation problem



that type of pattern usually means you loaded the wrong hemisphere (e.g.
the lh.aparc.annot on the rh.inflated or visa versa)
On Mon, 10 Sep 2007,
Wang, Xin wrote:

> the following error is reported when I run the tksurfer and load annotation. 
> I attach a image of parcellation.
>
> Thank you.
>
> Xin
>
> Talairach transform 
> /home/xwang/bin/freesurfer/subjects/amputation/APN01R650/mri/transforms/talairach.xfm
>  does not exist ...
> Loading tal xfm file 
> /home/xwang/bin/freesurfer/subjects/APN01R650_f/mri/transforms/talairach.xfm
> surfer: Reading header info from 
> /home/xwang/bin/freesurfer/subjects/APN01R650_f/mri/T1.mgz
> surfer: vertices=130570, faces=261136
>  Talairach transform 
> /home/xwang/bin/freesurfer/subjects/amputation/APN01R650/mri/transforms/talairach.xfm
>  does not exist ...
> Loading tal xfm file 
> /home/xwang/bin/freesurfer/subjects/APN01R650_f/surf/../mri/transforms/talairach.xfm
>
>
> 
>
> From: Bruce Fischl [mailto:[EMAIL PROTECTED]
> Sent: Mon 9/10/2007 2:31 PM
> To: Wang, Xin
> Cc: freesurfer
> Subject: Re: [Freesurfer] parcellation problem
>
>
>
> can you send us an image to show what you mean by "completely messed up"?
> On
> Mon, 10 Sep 2007, Wang, Xin wrote:
>
>> Hello, Group,
>>
>> After I manually removed the skull around cerebellum in the brainmask.mgz, 
>> the parcellation of the final inflated brain is totally messed up. Manual 
>> corrections of talairach transform and white matter surface did not mess up 
>> the parcellation. Could anyone tell me what is wrong?
>>
>> Thank you in advance,
>>
>> Xin Wang
>>
>
>
>


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[Freesurfer] model for pair-T test

[Wang, Xin]

Hello, group,
Could anybody tell me how to do the pair T test and the repeat measurement F 
test? I will really appreciate if you can share the steps and GLM of the tests. 
I am using the old freesurfer group analysis.
 
Thank you, very much,
 
Xin Wang
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RE: [Freesurfer] model for pair-T test

[Wang, Xin]

Please give me more detailed explanations of how to run mris_preproc 
--paired-diff or (--paired-diff-norm)? and how to setup the GLM after run this 
commend? I could not find needed information on the website. 
Thank you very much.
 
Xin



From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Fri 10/5/2007 5:20 PM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] model for pair-T test


Can you use the --paired-diff to mris_preproc?

Wang, Xin wrote: 

Hello, group,
Could anybody tell me how to do the pair T test and the repeat 
measurement F test? I will really appreciate if you can share the steps and GLM 
of the tests. I am using the old freesurfer group analysis.
 
Thank you, very much,
 
Xin Wang




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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

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RE: [Freesurfer] model for pair-T test

[Wang, Xin]

Hello, Doug,
 
I ran into an error when I ran mri_glmfit after I finished mris_preproc 
--paired-diff. 
 
ERROR: dimension mismatch between y and x. y has 5 inputs, x has 10 inputs.
 
I think it is because the mris_preproc -paired-diff generated 5 inputs of 
difference within 5 pairs, but my FSGD file still has 10 images. In addition, I 
do not want to include age as regressor. but if I deleted the age column, there 
is no variable. I attach my FSGD file.  Please tell me how to modify the FSGD 
file. 
Thank you,

Xin Wang



From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Fri 10/12/2007 4:21 PM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] model for pair-T test


The --paired-diff options just take the difference between adjacently specfied 
inputs. You then set up your design matrix or FSGD file and then run 
mri_glmfit. The --help for mri_glmfit has a lot of info about the glm analysis. 
 If you just want to test whether the difference is 0, you can use the --osgm 
flag (one-sample group mean).

doug

Wang, Xin wrote: 

Please give me more detailed explanations of how to run mris_preproc 
--paired-diff or (--paired-diff-norm)? and how to setup the GLM after run this 
commend? I could not find needed information on the website. 
Thank you very much.
 
Xin



From: Doug Greve [mailto:[EMAIL PROTECTED]
Sent: Fri 10/5/2007 5:20 PM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] model for pair-T test


Can you use the --paired-diff to mris_preproc?

Wang, Xin wrote: 

Hello, group,
Could anybody tell me how to do the pair T test and the repeat 
measurement F test? I will really appreciate if you can share the steps and GLM 
of the tests. I am using the old freesurfer group analysis.
 
Thank you, very much,
 
Xin Wang




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-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

  


-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
[EMAIL PROTECTED]
Phone Number: 617-724-2358 
Fax: 617-726-7422

In order to help us help you, please follow the steps in:
surfer.nmr.mgh.harvard.edu/fswiki/BugReporting

  GroupDescriptorFile 1
  Title back to back no rp
  Class first
  Class second
  Variables age
  Input APN01R650_4  first   23
  Input APN01R650_5  second  23
  Input APN02G650_4  first   36
  Input APN02G650_5  second  36
  Input APN03L650_3  first   24
  Input APN03L650_4  second  24
  Input APN04E650_2  first   50
  Input APN04E650_3  second  50
  Input APN05T650_2  first   23
  Input APN05T650_3  second  23
  DefaultVariable age
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[Freesurfer] thickness difference map

[Wang, Xin]

Hello, Group,
 
We want to make a figure as Fig2 in Han X et al. 2006 reliability paper. Does 
anyone kindly share his/her way to make a map of difference in average 
thickness between two groups? 
 
Thank you in advance,
 
Xin Wang
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RE: [Freesurfer] thickness difference map

[Wang, Xin]

Thank you very much, Nick. I ran into a problem when I ran the step 3 of Han's 
note of thickness repeatability. The --tfmt of mri_surf2surf is curv. The step 
can not be completed. 
 
Please help me. 
 
Thank you again,
 
Xin



From: Nick Schmansky [mailto:[EMAIL PROTECTED]
Sent: Sat 10/20/2007 5:34 PM
To: Wang, Xin
Cc: Freesurfer Mailing List
Subject: Re: [Freesurfer] thickness difference map



Xin,

Have a look at this wiki page written by Xiao (the author of the paper):

  http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility

It describes the procedure for how Figure 2 was created.

Nick

On Fri, 2007-10-19 at 15:42 -0400, Wang, Xin wrote:
> Hello, Group,
> 
> We want to make a figure as Fig2 in Han X et al. 2006 reliability
> paper. Does anyone kindly share his/her way to make a map of
> difference in average thickness between two groups?
> 
> Thank you in advance,
> 
> Xin Wang
> ___
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[Freesurfer] the unknown zone in the average

[Wang, Xin]

Hello, Group,
 
We calculate the globe mean of thickness by using
  mris_convert -c lh.thickness lh.white lh.thickness.asc
  mris_convert -c rh.thickness rh.white rh.thickness.asc
and then
  merge two .asc files to calculate the average 
 
Does this procedure include the neocortex only, or also include some spots in 
the unknown zone that also have readings in the thickness map?
 
If the unknown zones are included how to exclude them? 
 
we processed the data with the version prior to 4.0.1.
 
Thank you in advance,
 
XIn Wang
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RE: [Freesurfer] the unknown zone in the average

[Wang, Xin]

Thank you very much very for your quickly reply, Dr. Fischl.
 
The commend you suggested only calculates the average for each hemisphere, but 
we need the average across both hemispheres (i.e., whole brain). 
Could you suggest how to do it without noncortical regions?
 
Thank you,
 
Xin
 



From: Bruce Fischl [mailto:[EMAIL PROTECTED]
Sent: Wed 12/19/2007 10:26 AM
To: Wang, Xin
Cc: freesurfer
Subject: Re: [Freesurfer] the unknown zone in the average



Hi Xin,

you can use mris_anatomical_stats with -l ?h.cortex.label, which should
be generated automatically, to avoid noncortical regions.

cheers,
Bruce
On Wed, 19 Dec
2007, Wang, Xin wrote:

> Hello, Group,
>
> We calculate the globe mean of thickness by using
>  mris_convert -c lh.thickness lh.white lh.thickness.asc
>  mris_convert -c rh.thickness rh.white rh.thickness.asc
> and then
>  merge two .asc files to calculate the average
>
> Does this procedure include the neocortex only, or also include some spots in 
> the unknown zone that also have readings in the thickness map?
>
> If the unknown zones are included how to exclude them?
>
> we processed the data with the version prior to 4.0.1.
>
> Thank you in advance,
>
> XIn Wang
>


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[Freesurfer] where is the patient information in the mgz files

[Wang, Xin]

Hello, Group,
 
I have a problem to read patient information in the .mgz files. this 
information was stored in the header files of dicom files. Could sb. tell me 
how to read this information from the .mgz files?
Thank you in advance,
 
Xin Wang 
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[Freesurfer] fsl ROIs become smaller after registered to freesurfer

[Wang, Xin]

Hello, Group,
 
I tried to registered the fsl average of one subject .gfeat to his freesurfer 
surface. After manual correction of register files, the ROIs of ,gfeat become 
much smaller on the freesufer surface (including less cortical areas). please 
help me with this problem.
 
Thank in advance,
 
Xin
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[Freesurfer] (no subject)

[Wang, Xin]

Hello, Group,
 
I have a hard time to register the functional ROIs to the exact location 
(x,y,z) on thickness map. I can't find articles that register the fsl result 
onto freesurfer thickness map and then do the ROI analysis. Could someone 
kindly list some references for me? I appreciate if anyone is willing to share 
his/her experience on registration of functional and thickness maps (especially 
ROIs).  
Thanks in advance,
 
Xin
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[Freesurfer] Job posting: SRA at UCSD

[Wang, Xin]

External Email - Use Caution

Hi there,

Could you help to post this job advertisement for our lab as below, please? 
Thank you so much.
Please let me know if you need more.

Best,
Xin Wang

Imaging Researcher

This position will work a hybrid schedule which includes a combination of 
working both onsite and remote.
DESCRIPTION
The research project will involve multiple neuroimaging studies examining 
biomarkers of brain aging and dementia. These studies will be partially 
conducted in collaboration with the UC San Diego Shiley-Marcos Alzheimer’s 
Disease Research Center. These studies will employ structural, diffusion and 
contrast MRI, amyloid and tau PET, neuropsychological testing, and blood and/or 
CSF biomarkers, among other tools, to better understand how brain 
microstructure, vascular integrity, and neuropathology, relate to disease risk 
and cognitive decline in Alzheimer’s disease or related dementias.
Under the supervision of the project PIs (Drs. Reas and Banks), the incumbent 
will serve as a research project associate for multiple research protocols 
assessing neuroimaging biomarkers of dementia. Incumbent is responsible for 
organizing and managing brain imaging research data. Incumbent will manage 
Linux based workstations for post processing/data manipulation, and data 
analysis as well as create, maintain and update research databases. Provide 
support in project administration and publication preparation of imaging 
research. May provide assistance and have direct communication with subjects 
and families involved in research projects.
MINIMUM QUALIFICATIONS
· Bachelor's degree (psychology, neuroscience, biology, cognitive 
science, statistics, computer science or related field preferred) or equivalent 
work experience.
· Proven knowledge of human subjects research policies and procedures. 
Knowledge of the human subject consent process, and federal government 
regulations pertaining to consenting of subjects. On-line training certificate 
(acquired on job). Knowledge of IRB, and sponsored research requirements.
· Experience in a clinical trials research environment including basic 
understanding of persons with dementia, preferred experience with MRI in order 
to recruit, schedule, and test patients for clinical study subjects.
· Thorough working knowledge of medical and scientific terminology.
· Knowledge of statistical analysis of quantitative brain imaging data 
measures using SPSS, Matlab, and other statistical programs and prefer skills 
in coding.
· Strong experienced with computers (Personal computer and Macintosh). 
Skill with personal computers, word processing, spreadsheet, e-mail software, 
databases, etc. Specifically Linux OS and the Microsoft office suite (excel, 
access, powerpoint, word, etc).
· Proven ability to determine sources of clinical data, analyze the 
data and information obtained, in order to create documents and to propose 
solutions to issues and to help in developing standardized operational 
procedures.
· Proven ability in researching clinical data in preparation for grant 
applications and technical manuals, staying abreast of new research 
developments. Ability to abstract information from protocol and investigator 
brochure, which requires summarizing large quantities of data.
· Skill in assembling written narrative information using word 
processing software for documenting image analysis procedures and tracking data.
· Excellent interpersonal skills with the ability to use tact and 
diplomacy with subjects (including patients with cognitive impairment), their 
families, faculty and institutional staff, as well as when representing the 
agency in the community.
· Ability to collaborate and communicate effectively and diplomatically 
at all organizational levels, both verbally and in writing. Ability to work 
professionally and effectively with a diverse population, including the 
business community, academicians, staff and students.
· Excellent record keeping, database management, detail oriented, 
logical, methodological approach to problem solving, strong process 
orientation, strong administrative and organizational skills with demonstrated 
ability to prioritize assignments, maintain workflow, and work productively in 
meeting critical deadlines and milestones.
PREFERRED QUALIFICATIONS
· Working knowledge of UCSD Human Research Protections Program policies 
and Procedures.
SPECIAL CONDITIONS
· Employment is subject to a criminal background check and 
pre-employment physical.

If anyone is interested in this position, you could contact Dr. Reas 
(er...@health.ucsd.edu ) and Dr. 
Banks(sba...@health.ucsd.edu ) for further 
detail.



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[Freesurfer] Job posting: SRA at UCSD

[Wang, Xin]

External Email - Use Caution

Imaging Researcher
University of California, San Diego.
Apply in Institution’s website 
(https://secure-web.cisco.com/1SDJQkDq6j9d8jlPgTY38dMqz5jAkszVSyrb5fr9lxdmTS2UQdtxkDv6psRu-rVLopDpJxd3C2OzndVaWjjBAWNWNoHwbdsmVrkmbosaIxM_ZWGCvQPe0IjSMG7l3jTtjO0NPUqeAiqOmPJiKHJO0taFX68-otfjv_RwThnZhIwnR36Toa9RcsKf-zc5HwogkJUJlaSIj6B02k3QfEwKgIOIa_qebnYe6MVMsWSFu6FUb8lhU9wEj6S-yjC1zYpc3orEqpmslq9hSPIUDgxJaEA6iSUOsQCc-O8NY36yhuzr3313cFFAOCTPB37o9a284/https%3A%2F%2Femployment.ucsd.edu%2Fimaging-researcher-hybrid-remote-115355%2Fjob%2F19041227)
This position will work a hybrid schedule which includes a combination of 
working both onsite and remote.
DESCRIPTION
The research project will involve multiple neuroimaging studies examining 
biomarkers of brain aging and dementia. These studies will be partially 
conducted in collaboration with the UC San Diego Shiley-Marcos Alzheimer’s 
Disease Research Center. These studies will employ structural, diffusion and 
contrast MRI, amyloid and tau PET, neuropsychological testing, and blood and/or 
CSF biomarkers, among other tools, to better understand how brain 
microstructure, vascular integrity, and neuropathology, relate to disease risk 
and cognitive decline in Alzheimer’s disease or related dementias.
Under the supervision of the project PIs (Drs. Reas and Banks), the incumbent 
will serve as a research project associate for multiple research protocols 
assessing neuroimaging biomarkers of dementia. Incumbent is responsible for 
organizing and managing brain imaging research data. Incumbent will manage 
Linux based workstations for post processing/data manipulation, and data 
analysis as well as create, maintain and update research databases. Provide 
support in project administration and publication preparation of imaging 
research. May provide assistance and have direct communication with subjects 
and families involved in research projects.
MINIMUM QUALIFICATIONS
· Bachelor's degree (psychology, neuroscience, biology, cognitive 
science, statistics, computer science or related field preferred) or equivalent 
work experience.
· Proven knowledge of human subjects research policies and procedures. 
Knowledge of the human subject consent process, and federal government 
regulations pertaining to consenting of subjects. On-line training certificate 
(acquired on job). Knowledge of IRB, and sponsored research requirements.
· Experience in a clinical trials research environment including basic 
understanding of persons with dementia, preferred experience with MRI in order 
to recruit, schedule, and test patients for clinical study subjects.
· Thorough working knowledge of medical and scientific terminology.
· Knowledge of statistical analysis of quantitative brain imaging data 
measures using SPSS, Matlab, and other statistical programs and prefer skills 
in coding.
· Strong experienced with computers (Personal computer and Macintosh). 
Skill with personal computers, word processing, spreadsheet, e-mail software, 
databases, etc. Specifically Linux OS and the Microsoft office suite (excel, 
access, powerpoint, word, etc).
· Proven ability to determine sources of clinical data, analyze the 
data and information obtained, in order to create documents and to propose 
solutions to issues and to help in developing standardized operational 
procedures.
· Proven ability in researching clinical data in preparation for grant 
applications and technical manuals, staying abreast of new research 
developments. Ability to abstract information from protocol and investigator 
brochure, which requires summarizing large quantities of data.
· Skill in assembling written narrative information using word 
processing software for documenting image analysis procedures and tracking data.
· Excellent interpersonal skills with the ability to use tact and 
diplomacy with subjects (including patients with cognitive impairment), their 
families, faculty and institutional staff, as well as when representing the 
agency in the community.
· Ability to collaborate and communicate effectively and diplomatically 
at all organizational levels, both verbally and in writing. Ability to work 
professionally and effectively with a diverse population, including the 
business community, academicians, staff and students.
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[Freesurfer] zero cortical thickness in the lingual and precuneus

[Wang, Xin]

 
Hello, Dr. Fischl,
 
I asked this quesion about zero thickness in the sulcus next to the lateral 
vertricle before, and corrected the wrong label of lateral vertricle in the 
aseg.mgz file and added white matter between lateral vertricle and this sulcus 
in the wm.mgz. But the problem is still exist in some slices after multiple 
times of correction. We have this problem in version 4.4.X to 4.5.0. 
My questions are
1) Do you have any additional suggestion to fix this bug?
2) If not, do you have a way to exclude this problematic sulcus? In another 
word, can we include this sulcus in the unknown zone? I don't like to exclude 
entire lingual, precunneus, and pericalcarine regions from mean thickness 
analysis and vertex-based analysis because these three labels occupy a large 
part of cortex. 
 
Thank you in advance,
 
Xin Wang 



From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
freesurfer-requ...@nmr.mgh.harvard.edu
Sent: Thu 10/7/2010 11:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 80, Issue 12



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Re: [Freesurfer] zero cortical thickness in the lingual and precuneus

[Wang, Xin]

one more question: I replace the mislabeled lateral ventricle with CSF because 
I can not find the "none" in the FreesurfercolorLUT.txt. How to change the  
mislabeled lateral ventricle to none?
 
Thank you,
 
Xin
 
____

From: Wang, Xin
Sent: Thu 10/7/2010 12:04 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: zero cortical thickness in the lingual and precuneus


 
Hello, Dr. Fischl,
 
I asked this quesion about zero thickness in the sulcus next to the lateral 
vertricle before, and corrected the wrong label of lateral vertricle in the 
aseg.mgz file and added white matter between lateral vertricle and this sulcus 
in the wm.mgz. But the problem is still exist in some slices after multiple 
times of correction. We have this problem in version 4.4.X to 4.5.0. 
My questions are
1) Do you have any additional suggestion to fix this bug?
2) If not, do you have a way to exclude this problematic sulcus? In another 
word, can we include this sulcus in the unknown zone? I don't like to exclude 
entire lingual, precunneus, and pericalcarine regions from mean thickness 
analysis and vertex-based analysis because these three labels occupy a large 
part of cortex. 
 
Thank you in advance,
 
Xin Wang 



From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
freesurfer-requ...@nmr.mgh.harvard.edu
Sent: Thu 10/7/2010 11:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Freesurfer Digest, Vol 80, Issue 12



Send Freesurfer mailing list submissions to
freesurfer@nmr.mgh.harvard.edu

To subscribe or unsubscribe via the World Wide Web, visit
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
or, via email, send a message with subject or body 'help' to
freesurfer-requ...@nmr.mgh.harvard.edu

You can reach the person managing the list at
freesurfer-ow...@nmr.mgh.harvard.edu

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."


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Re: [Freesurfer] zero cortical thickness in the lingual and precuneus

[Wang, Xin]

Thank you, Allison.
Is Unknown for the empty space between gyri? I did label the gray matter 
vertices as cortex. 
 
Xin  



From: Allison Stevens [mailto:astev...@nmr.mgh.harvard.edu]
Sent: Thu 10/7/2010 12:16 PM
To: Wang, Xin
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] zero cortical thickness in the lingual and precuneus



None should be the first label in the FreeSurferColorLUT.txt (it's labeled
as "Unknown" with an ID# of 0). But really you should be labeling it what
it truly is. Is this the gray matter you are labeling as CSF?

--

On Thu, 7 Oct 2010, Wang, Xin wrote:

> one more question: I replace the mislabeled lateral ventricle with CSF 
> because I can not find the "none" in the FreesurfercolorLUT.txt. How to 
> change the  mislabeled lateral ventricle to none?
>
> Thank you,
>
> Xin
>
> 
>
> From: Wang, Xin
> Sent: Thu 10/7/2010 12:04 PM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: zero cortical thickness in the lingual and precuneus
>
>
>
> Hello, Dr. Fischl,
>
> I asked this quesion about zero thickness in the sulcus next to the lateral 
> vertricle before, and corrected the wrong label of lateral vertricle in the 
> aseg.mgz file and added white matter between lateral vertricle and this 
> sulcus in the wm.mgz. But the problem is still exist in some slices after 
> multiple times of correction. We have this problem in version 4.4.X to 4.5.0.
> My questions are
> 1) Do you have any additional suggestion to fix this bug?
> 2) If not, do you have a way to exclude this problematic sulcus? In another 
> word, can we include this sulcus in the unknown zone? I don't like to exclude 
> entire lingual, precunneus, and pericalcarine regions from mean thickness 
> analysis and vertex-based analysis because these three labels occupy a large 
> part of cortex.
>
> Thank you in advance,
>
> Xin Wang
>
> 
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> freesurfer-requ...@nmr.mgh.harvard.edu
> Sent: Thu 10/7/2010 11:31 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Freesurfer Digest, Vol 80, Issue 12
>
>
>
> Send Freesurfer mailing list submissions to
>freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
>freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
>freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
>


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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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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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] zero cortical thickness in the lingual and precuneus

[Wang, Xin]

Thank you, Dr. Fischl.
 I will try another round of correction, and please instruct me how to upload a 
subject data to your workstation? so we can look into this problem at same time.
 
Xin



From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu]
Sent: Thu 10/7/2010 12:17 PM
To: Wang, Xin
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] zero cortical thickness in the lingual and precuneus



Hi Xin,

can you upload this dataset so we can take a look?

Bruce
On Thu, 7 Oct 2010, Wang,
Xin wrote:

>
> Hello, Dr. Fischl,
>
> I asked this quesion about zero thickness in the sulcus next to the
lateral vertricle before, and corrected the wrong label of lateral
vertricle in the aseg.mgz file and added white matter between lateral
vertricle and this sulcus in the wm.mgz. But the problem is still exist in
some slices after multiple times of correction. We have this problem in
version 4.4.X to 4.5.0.
> My questions are
> 1) Do you have any additional suggestion to fix this bug?
> 2) If not, do you have a way to exclude this problematic sulcus? In another 
> word, can we include this sulcus in the unknown zone? I don't like to exclude 
> entire lingual, precunneus, and pericalcarine regions from mean thickness 
> analysis and vertex-based analysis because these three labels occupy a large 
> part of cortex.
>
> Thank you in advance,
>
> Xin Wang
>
> 
>
> From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> freesurfer-requ...@nmr.mgh.harvard.edu
> Sent: Thu 10/7/2010 11:31 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Freesurfer Digest, Vol 80, Issue 12
>
>
>
> Send Freesurfer mailing list submissions to
>freesurfer@nmr.mgh.harvard.edu
>
> To subscribe or unsubscribe via the World Wide Web, visit
>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> or, via email, send a message with subject or body 'help' to
>freesurfer-requ...@nmr.mgh.harvard.edu
>
> You can reach the person managing the list at
>freesurfer-ow...@nmr.mgh.harvard.edu
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Freesurfer digest..."
>
>
>


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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