[Freesurfer] installation problem

[Xue Zhang]

dear freesurfer experts,
 I tried to install freesurfer in a remote linux cluster, when I completed the 
installation, and began to run the freesurfer gui use my own windows PC, the 
command line showed erro belowing information :


[wanglhlab@node01 freesurfer]$ tkmedit bert orig.mgz
GLUT: Fatal Error in tkmedit.bin: OpenGL GLX extension not supported by 
display: localhost:11.0


could anyone tell me the reason why my installation failed?  The video card on 
cluster is Matrox Graphics, Inc. MGA G200eW WPCM450 (rev 0a), my own PC video 
card is AMD Radeon HD 7800 Series.




regards


Xue Zhang___
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Re: [Freesurfer] Brainsuite --> FreeSurfer

[Valtina Pouegue]

Hi bruce, 
I want cortical thickness, total surface area, instrinsec curvature index and 
folfing index. 
VP

Date: Wed, 20 Mar 2013 13:09:54 -0400
From: fis...@nmr.mgh.harvard.edu
To: pval...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Brainsuite --> FreeSurfer

it depends on what measures you want
Bruce
On Wed, 20 Mar 2013, Valtina Pouegue 
wrote:
 
> Hi Bruces, 
> It's because i'm doing a comparison between brainsuite and freesrufer. So , I 
> would like to export results of
> segmentation with Brainsuite and make measurements with FreeSurfer. In Fact, 
> with freesurfer I can have more parameters
> than with freesurfer. 
> Does it exist another way for get measurements with surfaces ( not generated 
> by Freesurfer)? 
> Thx . 
> 
> VP
> Date: Wed, 20 Mar 2013 08:38:26 -0400
> From: fis...@nmr.mgh.harvard.edu
> To: pval...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Brainsuite --> FreeSurfer
> 
> Hi Valtina
> 
> you can try opening it with freeview if all you want is visualization. If 
> you are trying to produce anatomical stats you will need a lot more than 
> just the pial surface, as mris_anatomical_stats computes many things from 
> an array of inputs (such as the wm.mgz, the aseg.mgz, etc). Why not 
> just run recon-all and generate them?
> Bruce
>
> 
> On Tue, 19 Mar 2013, Valtina Pouegue wrote:
> 
> > I could  see the  created surface in MAtlab ( 'read_surf,) but I could't 
> > open the file in Freesurfer with tksurfer 
> > 
> > VP
> > 
> > ___
> __
> > From: pval...@hotmail.com
> > To: freesurfer@nmr.mgh.harvard.edu
> > Subject: Brainsuite --> FreeSurfer
> > Date: Tue, 19 Mar 2013 22:34:39 -0400
> > 
> > Hi, 
> > 
> > I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like 
> > to get measurements with FreeSurfer. SO, I
> > convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be 
> > usable with Freesurfer. Then, I tried to get
> > measurements with the command .'mris_anatomical_stats' .  with the file 
> > created previously in Matlab (I called it
> >  'rh.pial'). But I got this error like the system is not able to read 
> > wm.mgz.
> > That's why I thought I could juste replace th 'rh.pial' of the segmentation 
> > with Freesurfey by the 'rh.pial' created wi
> th
> > Matalb and then run mris_anatomical_Stats. IS this a good approximation. 
> > Could you recommand another way.
> > 
> > 
> > VP
> > 
> >
> 
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>

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[Freesurfer] fs-fast processing questions

[preciado]

Hello all,
I am starting to run some analysis using fs-fast and I had a few basic
questions that I couldn't find answers on the wiki/tutorial.

1) Format of files for mkanalysis-sess -tpexclude tpexclude.dat
What is the format of the input file for -tpexclude? Is it simply a single
column of integers representing the seconds that need to be excluded? My
example, my TR is 3 and I know I want to remove acquisitions 134 and 140
because of motion. Do I simply need to have a file that has the following
content?
402
403
404
420
421
422


2) bold data - Resampling to "common space"
In the preprocessing step, the bold data is resampled to 76x76x93. My data
is 96x96x50. Does starting with data that is larger than the "common
space" cause a problem in the analysis?

3) Viewing analysis for individual bold data runs
When the First level analysis is completed, the resulting files are a
combination of all of the bold data runs of the session. Is there a way to
make it so that I can also see the different activity for individual runs
within the session or does the analysis only do it by combining data for
all runs within a session?

Thanks in advance!
-Ronny
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Re: [Freesurfer] R: R: Re: Problem with tracula: incomplete or lacking tracts

[Anastasia Yendiki]

There are chunks of the brain missing from the brain mask. This may cause 
some tracts to be incomplete or missing.


But you should still check that the gradient directions are correct, so 
you know if you have multiple problems or just one. The FA map can't tell 
you if the gradient table was correct, you have to check the eigenvectors 
in dtifit_V1 for that.



On Wed, 20 Mar 2013, std...@virgilio.it wrote:


File attacked

Messaggio originale
Da: std...@virgilio.it
Data: 20-mar-2013 22.34
A: 
Cc: 
Ogg: [Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts

Thank you Anastasia. I'm checking gradient table but I would like underline 
that I'm noting some holes in
dti_FA.nii.gz  and not in dwi.nii.gz (I have attacked the relative images).

Stefano

Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 20-mar-2013 16.40
A: 
Cc: 
Ogg: Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts


Hi Stefano - Have you checked that your gradient table is correct by
looking at the output of the tensor fit?

a.y

On Wed, 20 Mar 2013, std...@virgilio.it wrote:

> Hi list and Anastasia,
> if you remember the last week I had same problems with tracula output: the  
final tract are lacking or
> incomplete for same subjects. Some of these are less wrong (only forceps 
major), other have more evident
> error (you can see this in picture that I have attacked). 
>
> To resolve this issue I have:
>
> 1-checked the correct overlap of dwi and dwi_mask
> 2-rerun data with new version 5.2
> 3-rerun new registration using bbregister (fsl/spm option): for example, in 
the subject of the picture
> attacked, the .mincost file now contains as first value 0.87 (previous it was 
1.1)
>
> Please, give me an advise
>
> Thanks
>
>
> Stefano
>
>
>
>
> Messaggio originale
> Da: std...@virgilio.it
> Data: 12-mar-2013 17.47
> A: 
> Cc: 
> Ogg: [Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlap
>
> I got it from mri directory but I'm understanding that this directory isn't 
ok.I'm attacking the image
> from dlabel/diff/aparc+aseg.bbr.nii
>
>
> Stefano
>
>
>
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 12-mar-2013 17.19
> A: 
> Cc: 
> Ogg: Re: [Freesurfer] R: Re:  Question on tracula and dwi-T1 overlap
>
>
> Can you please answer my question? I can't really tell if the issue is due 
> poor dwi-aseg overlap unless you tell me where you got that aseg volume 
> from.
>
> On Tue, 12 Mar 2013, std...@virgilio.it wrote:
>
> > Thank you Anastasia. What do you think about the issue in the file attacked
> > (I'm noting that same subjects are lacking of same
> >  tracts or same tracts are incomplete)
> > 
> > 
> > Stefano
> > 
> > 
> > Messaggio originale
> > Da: ayend...@nmr.mgh.harvard.edu
> > Data: 12-mar-2013 17.02
> > A: 
> > Cc: 
> > Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap
> > 
> > 
> > Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's in
> > the dlabel/diff/ directory has been mapped to the same space as the DWI,
> > so those are the volumes that can be compared directly to dwi.nii.gz.
> > 
> > a.y
> > 
> > On Tue, 12 Mar 2013, std...@virgilio.it wrote:
> > 
> > > Hi list,
> > >
> > > I have two questions, please.
> > >
> > > I'm using version 5.1 to complete my analysis.
> > >
> > > 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of the same
> > > subject (figure 1 and 3). You can note the dwi do not overlap to the aseg.
> > > How can I resolve this issue? 
> > >
> > > 2-After TRACULA analysis, I'm noting that same subjects are lacking of
> > same
> > > tracts or same tracts are incomplete (figure 3).
> > >
> > > Could it depends from the issue in question 1? I'm thinking to rerun all
> > > using version 5.2 but before starting new analyses, I'd like to ask you
> > > which is the possible error.
> > >
> > >
> > > Stefano
> > >
> > >___
> > Freesurfer mailing list
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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > 
> > The information in this e-mail is intended only for the person to whom it is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you in
> > error
> > but does not contain patient information, please contact the sender and
> > properly
> > dispose of the e-mail.
> > 
> > 
> > 
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>
>
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> 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 Help

Re: [Freesurfer] y values from glmfit-sim

[Douglas N Greve]

They are the input (mri_glmfit --y y.mgh) averaged over the clusters. 
They are raw input, no detrending.
doug
On 03/20/2013 05:16 PM, Laura M. Tully wrote:
> Hello experts,
>
> could someone clarify for me what the y values in the xxx.ocn.y.dat 
> files represent following glmfit-sim? are they the residualized y 
> values of avg cortical thickness in that specific cluster after 
> regressing out the effect of any predictor variables in the glm?
>
> Thanks!
>
> Laura.
> -- 
> --
> Laura M. Tully, MA
> Social Neuroscience & Psychopathology, Harvard University
> Center for the Assessment and Prevention of Prodromal States, UCLA 
> Semel Institute of Neuroscience
> ltu...@mednet.ucla.edu 
> ltu...@fas.harvard.edu 
> 310-267-0170
> -- 
> My musings as a young clinical scientist: 
> http://theclinicalbrain.blogspot.com/
> Follow me on Twitter: @tully_laura
>
>
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-- 
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MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

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

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[Freesurfer] R: Re: Problem with tracula: incomplete or lacking tracts

[stdp82]

Thank you Anastasia. I'm checking gradient table but I would like underline 
that I'm noting some holes in dti_FA.nii.gz  and not in dwi.nii.gz (I have 
attacked the relative images).

Stefano



Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 20-mar-2013 16.40
A: 
Cc: 
Ogg: Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts


Hi Stefano - Have you checked that your gradient table is correct by 
looking at the output of the tensor fit?

a.y

On Wed, 20 Mar 2013, std...@virgilio.it wrote:

> Hi list and Anastasia,
> if you remember the last week I had same problems with tracula output: the  
> final tract are lacking or
> incomplete for same subjects. Some of these are less wrong (only forceps 
> major), other have more evident
> error (you can see this in picture that I have attacked). 
> 
> To resolve this issue I have:
> 
> 1-checked the correct overlap of dwi and dwi_mask
> 2-rerun data with new version 5.2
> 3-rerun new registration using bbregister (fsl/spm option): for example, in 
> the subject of the picture
> attacked, the .mincost file now contains as first value 0.87 (previous it was 
> 1.1)
> 
> Please, give me an advise
> 
> Thanks
> 
> 
> Stefano
> 
> 
> 
> 
> Messaggio originale
> Da: std...@virgilio.it
> Data: 12-mar-2013 17.47
> A: 
> Cc: 
> Ogg: [Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlap
> 
> I got it from mri directory but I'm understanding that this directory isn't 
> ok.I'm attacking the image
> from dlabel/diff/aparc+aseg.bbr.nii
> 
> 
> Stefano
> 
> 
> 
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 12-mar-2013 17.19
> A: 
> Cc: 
> Ogg: Re: [Freesurfer] R: Re:  Question on tracula and dwi-T1 overlap
> 
> 
> Can you please answer my question? I can't really tell if the issue is due 
> poor dwi-aseg overlap unless you tell me where you got that aseg volume 
> from.
> 
> On Tue, 12 Mar 2013, std...@virgilio.it wrote:
> 
> > Thank you Anastasia. What do you think about the issue in the file attacked
> > (I'm noting that same subjects are lacking of same
> >  tracts or same tracts are incomplete)
> > 
> > 
> > Stefano
> > 
> > 
> > Messaggio originale
> > Da: ayend...@nmr.mgh.harvard.edu
> > Data: 12-mar-2013 17.02
> > A: 
> > Cc: 
> > Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap
> > 
> > 
> > Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's in
> > the dlabel/diff/ directory has been mapped to the same space as the DWI,
> > so those are the volumes that can be compared directly to dwi.nii.gz.
> > 
> > a.y
> > 
> > On Tue, 12 Mar 2013, std...@virgilio.it wrote:
> > 
> > > Hi list,
> > >
> > > I have two questions, please.
> > >
> > > I'm using version 5.1 to complete my analysis.
> > >
> > > 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of the same
> > > subject (figure 1 and 3). You can note the dwi do not overlap to the aseg.
> > > How can I resolve this issue? 
> > >
> > > 2-After TRACULA analysis, I'm noting that same subjects are lacking of
> > same
> > > tracts or same tracts are incomplete (figure 3).
> > >
> > > Could it depends from the issue in question 1? I'm thinking to rerun all
> > > using version 5.2 but before starting new analyses, I'd like to ask you
> > > which is the possible error.
> > >
> > >
> > > Stefano
> > >
> > >___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > 
> > 
> > The information in this e-mail is intended only for the person to whom it is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you in
> > error
> > but does not contain patient information, please contact the sender and
> > properly
> > dispose of the e-mail.
> > 
> > 
> > 
> >___
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> 
> 
> The information in this e-mail is intended only for the person to whom it is
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> contains patient information, please contact the Partners Compliance HelpLine 
> at
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> error
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> properly
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> 
> 
> 
> 
> 
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Re: [Freesurfer] mri_info crashing (bits stored vs bits allocated?)

[Knut J Bjuland]

HI

I have similar problem and filled a bug report at.


Product: Fedorahttps://bugzilla.redhat.com/show_bug.cgi?id=905638  Patsy
Franklin  changed: What |Removed |Added

Flags|needinfo?(pfrankli@redhat.c  | |om) |
Flags|needinfo?(pfrankli@redhat.c  | |om) | --- Comment #27 from Patsy
Franklin  --- The most immediate solution is for
the application to be changed to use a compliant crypt salt value. After
further investigation, we found that the application is passing
unsupported, nonstandard salt to crypt(). This will result in crypt()
returning NULL and setting errno to EINVAL. It does not appear that the
application is checking for a NULL return value from crypt. It also
appears that the application is using this NULL return value in a
subsequent function call resulting in a segmentation fault. Previously
glibc would accept unsupported salt values, but newer versions of the
library have become stricter. We are currently reviewing the
implementation to see if the accepted salt values can be expanded while
still meeting our standards compliance requirements.
--

Knut J











On 03/20/2013 09:59 PM, Bruce Fischl wrote:
> Hi John
>
> if you email it to me I'll take a look
> Bruce
> On Wed, 20 Mar 2013, Ostuni, John
> (NIH/NINDS) [E] wrote:
>
>> We have a data set that mri_info cannot work with.
>>
>> We've tried multiple architectures and freesurfer versions, but mri_info 
>> either crashes with segmentation fault or generates errors such as
>> *** glibc detected *** mri_info: free(): invalid pointer: 0x006b 
>> ***
>>
>> One feature of the data set is that the bits stored(12) is different than 
>> the bits allocated(16).
>> Could this be the problem?
>>
>> I have an anonymized version of the data set I can upload if that helps.
>>
>> Thanks for any assistance,
>>John
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>>
>>
> ___
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>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
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> properly
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>
>
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[Freesurfer] y values from glmfit-sim

[Laura M. Tully]

Hello experts,

could someone clarify for me what the y values in the xxx.ocn.y.dat files
represent following glmfit-sim? are they the residualized y values of avg
cortical thickness in that specific cluster after regressing out the effect
of any predictor variables in the glm?

Thanks!

Laura.
-- 
--
Laura M. Tully, MA
Social Neuroscience & Psychopathology, Harvard University
Center for the Assessment and Prevention of Prodromal States, UCLA Semel
Institute of Neuroscience
ltu...@mednet.ucla.edu
ltu...@fas.harvard.edu
310-267-0170
--
My musings as a young clinical scientist:
http://theclinicalbrain.blogspot.com/
Follow me on Twitter: @tully_laura
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Re: [Freesurfer] libjpeg.so.62

[Ashley Shurick]

Hi all,

My RA's are having similar issues running Freeview on Ubuntu (I've read
others are having the same issue). They get the following error when trying
to call freeview:

"freeview.bin: error while loading shared libraries: libXss.so.1: cannot
open shared object file: No such file or directory"

We ran "apt-get install libjpeg62" to install missing libraries, and when
that didn't fix the issue we tried Nick's fix below just in case it might
work. Unfortunately we are still getting the error. Any ideas about what's
going on?

Thank you in advance for your assistance!


On Tue, Feb 26, 2013 at 7:47 AM, Nick Schmansky
wrote:

> Chikku,
>
> I am guessing that you are using Ubuntu.  To fix this problem:
>
> cd /usr/lib
> sudo ln -s libjpeg.so.8 libjpeg.so.62
>
>
> in other words, link whatever libjpeg is already installed to the name
> libjpeg.so.62.
>
> Nick
>
>
>
> > Hi
> > I am getting an  error  while  using qdec. It  says  error while
> > loading shared libraries ,libjpeg.so.62  cannot open shared object
> > file No such file or directory
> > I ran reconall  with out any problem.
> > Any idea,
> > tx
> > chikku
> > ___
> > Freesurfer mailing list
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> >
> >
> >
>
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> is
> addressed. If you believe this e-mail was sent to you in error and the
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Re: [Freesurfer] mri_info crashing (bits stored vs bits allocated?)

[Bruce Fischl]

Hi John

if you email it to me I'll take a look
Bruce
On Wed, 20 Mar 2013, Ostuni, John 
(NIH/NINDS) [E] wrote:

> We have a data set that mri_info cannot work with.
>
> We've tried multiple architectures and freesurfer versions, but mri_info 
> either crashes with segmentation fault or generates errors such as
> *** glibc detected *** mri_info: free(): invalid pointer: 0x006b 
> ***
>
> One feature of the data set is that the bits stored(12) is different than the 
> bits allocated(16).
> Could this be the problem?
>
> I have an anonymized version of the data set I can upload if that helps.
>
> Thanks for any assistance,
>   John
>
>
>
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[Freesurfer] mri_info crashing (bits stored vs bits allocated?)

[Ostuni, John (NIH/NINDS) [E]]

We have a data set that mri_info cannot work with.

We've tried multiple architectures and freesurfer versions, but mri_info either 
crashes with segmentation fault or generates errors such as
*** glibc detected *** mri_info: free(): invalid pointer: 0x006b ***

One feature of the data set is that the bits stored(12) is different than the 
bits allocated(16).
Could this be the problem?

I have an anonymized version of the data set I can upload if that helps.

Thanks for any assistance,
   John



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Re: [Freesurfer] Reposting: interpreting clusters from 2 and 3 way interactions

[Douglas N Greve]

Try using this version of mri_segstats
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats
doug

On 03/20/2013 01:10 PM, Laura M. Tully wrote:
> the mri_segstats command did not work - below is the command and 
> output. It looks like it is searching for the .annot file in fsaverage 
> directory. How do I tell it to use fsaverage and to look for the 
> .annot elsewhere?
>
> cd glmdir
>
> mri_segstats --i beta.mgh --annot fsaverage lh
> ./SZcontrast_oneGrp_oneBehVar_4CVs/cache.th13.abs.sig.ocn.annot 
> --avgwf
> lh.SZ_CPT_area_betas.dat --excludeid 0
>
>
> $Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $
>
> cwd
>
> cmdline mri_segstats --i beta.mgh --annot fsaverage lh
> ./SZcontrast_oneGrp_oneBehVar_4CVs/cache.th13.abs.sig.ocn.annot 
> --avgwf
> lh.SZ_CPT_area_betas.dat --excludeid 0
>
> sysname  Linux
>
> hostname ncfws12.rc.fas.harvard.edu
> 
>
> machine  x86_64
>
> user ltully
>
> Constructing seg from annotation
>
> could not read annot file
> 
> /ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh../SZcontrast_oneGrp_oneBehVar_4CVs/cache.th13.abs.sig.ocn.annot.annot
>
> No such file or directory
>
>
> Thanks!
>
> LT
>
> On Wed, Mar 20, 2013 at 9:54 AM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> On 03/20/2013 12:09 PM, Laura M. Tully wrote:
>
> Sorry -  meant to respond to list.
>
> Thanks for the response Doug - I have a few follow up
> questions I hope you can clarify:
>
>   * is the xxx.ocn.annot file created by mri_glmfit-sim
> considered
> a "label" by freesurfer?
>
> It is an annotation
>
>
>   * or does it need to be converted to a label before I
> can use
> mri_segstats to extract the betas from the cluster(s)
> in the
> xxx.ocn.annot?
>
> No
>
>
>
>   * I tried using the following command line to attempt to
> extract
> the betas from the cluster annotation file created by
> mri_glmfit-sim, but received an error:
>
> mri_segstats --i beta.mgh --annot fsaverage hemi
> contrast/xxx.ocn.annot --avgwf avgwf.dat
>
> That looks correct. Did it work? Add --excludeid 0 to keep it from
> reporting on non-clusters
>
>
>
>   * how does one convert an xxx.ocn.annot file to a label?
>
> If needed, use mri_annotation2label
>
>
>   * If I have run 3 different glms looking at the
> relationship
>
> between thickness and 3 different behavioral
> variables, and
> found 1 (or more) cluster in each glm using
> mri_glmfit-sim can
> I create 1 annotation/label with all the clusters from the
> separate glms and then extract the betas from that one
> annotation using mri_segstats? Or do I need to treat
> each glm
> separately?
>
> It is probably easiest if you treat each glm separately. You can
> break the annotations into separate labels, then recombine the
> labels into another annotation (mris_label2annot), but it is a lot
> of work.
>
>
>  *
>
>
>   * I saw on the listserv some references to matlab
> functions that
>
> can calculate r square and partial correlations for
> glms with
> more than one predictor variable (e.g pcc between
> thickness
> and behavioral variable 1; pcc between thickness and
> behavioral variable2; Rsq for overall model) but I
> could not
> find the .m scripts for the functions (MRIread
> or fast_glm_pcc?) - would these functions be
> appropriate and
> if so where might I find them?
>
> Yes. They are in $FREESURFER_HOME/matlab and
> $FREESURFER_HOME/fsfast/toolbox
> doug
>
>
>  *
>
>
> Thanks in advance for your help!
>
> Laura.
>
>
> On Wed, Mar 20, 2013 at 8:29 AM, Douglas N Greve
>  
>  >> wrote:
>
>
> On 03/20/2013 10:17 AM, Laura M. Tully wrote:
> > Hi,
> >
> > I wanted to re-post my questions from a couple of
> days ago
> below, but
> > with some more specific questions following a search
> through the
> > archives.
> >
> > I want to be able to extract the beta values from a
> cluster
> identified
> 

Re: [Freesurfer] freeview warning: invalid drawable

[Ruopeng Wang]

On a Mac? You can just ignore those warning messages. Unfortunately we 
were unable to remove them.


Ruopeng

On 03/20/2013 04:07 PM, Glen Lee wrote:

Dear freesurfer experts,
I'm wondering why I get this warning message when I open up any surf 
template in either fsaverage or fsaverage_sym directory.

FYI, I'm using freeview v1.0
if anybody know, please help.
-Glen

$ freeview -f lh.inflated
2013-03-20 16:03:05.801 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.805 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.823 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.825 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.844 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.846 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.863 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.865 freeview.bin[52449:907] invalid drawable
QObject::connect: Connecting from QAbstractButton::toggled(bool) to 
COMPAT slot (QGroupBox::setShown(bool))
QObject::connect: Connecting from QAbstractButton::toggled(bool) to 
COMPAT slot (QGroupBox::setShown(bool))

2013-03-20 16:03:06.211 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:06.212 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:06.213 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:11.634 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:11.638 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:11.649 freeview.bin[52449:907] invalid drawable



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[Freesurfer] freeview warning: invalid drawable

[Glen Lee]

Dear freesurfer experts,
I'm wondering why I get this warning message when I open up any surf
template in either fsaverage or fsaverage_sym directory.
FYI, I'm using freeview v1.0
if anybody know, please help.
-Glen

$ freeview -f lh.inflated
2013-03-20 16:03:05.801 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.805 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.823 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.825 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.844 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.846 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.863 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:05.865 freeview.bin[52449:907] invalid drawable
QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT
slot (QGroupBox::setShown(bool))
QObject::connect: Connecting from QAbstractButton::toggled(bool) to COMPAT
slot (QGroupBox::setShown(bool))
2013-03-20 16:03:06.211 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:06.212 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:06.213 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:11.634 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:11.638 freeview.bin[52449:907] invalid drawable
2013-03-20 16:03:11.649 freeview.bin[52449:907] invalid drawable
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Re: [Freesurfer] Asymmetries of cortical thickness

[Douglas N Greve]

Hi Sophie, you can run the following command:

cd $SUBJECTS_DIR/yoursubject
  mris_apply_reg --src xhemi/surf/lh.thickness --streg 
xhemi/surf/lh.fsaverage_sym.sphere.reg surf/lh.fsaverage_sym.sphere.reg 
--tval surf/lh.rh.thickness.mgh

lh.rh.thickness.mgh will now have the rh thicknesses on the rh surface

mris_apply_reg is only available in 5.2. If you don't have 5.2, I can 
get you a version of this program if you tell me your OS. Also note that 
you need to go through the xhemi-reg procedure first.

doug


On 03/18/2013 10:40 AM, Sophie Maingault wrote:
> Yes if it is possible I would like to know how to do it ?
>
> Thanks !
>
> Sophie
>
> -Message d'origine-
> De : Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
> Envoyé : lundi 18 mars 2013 14:39
> À : Sophie Maingault; Freesurfer@nmr.mgh.harvard.edu
> Objet : Re: [Freesurfer] Asymmetries of cortical thickness
>
> It is possible, it is just not a good idea because if you map rh to lh
> and then compare to lh, the rh will have been interpolated to get it
> into the lh. Even if there are no differences between the two, you will
> see differences because of the interpolation. Mapping  both to
> fsaverage_sym means that both will be interpolated. If this
> interpolation does not bother you, then I can show you how to get it
> from rh to lh.
> doug
>
>
>
>
> On 03/18/2013 09:24 AM, Sophie Maingault wrote:
>> So i didn't understand what you mean by "just specify one subject when
> your
>> mris_preproc" ? Because, in fact I don't want to use the registration on
>> fsaverage_sym. I would like just to create a file lh.thickness less
>> rh.thickness vertex per vertex, maybe it is not possible ?
>>
>> -Message d'origine-
>> De : Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu]
>> Envoyé : lundi 18 mars 2013 14:15
>> À : Sophie Maingault; Freesurfer@nmr.mgh.harvard.edu
>> Objet : Re: [Freesurfer] Asymmetries of cortical thickness
>>
>> No, it is not, the target needs to be fsaverage_sym
>> doug
>>
>>
>> On 03/18/2013 09:13 AM, Sophie Maingault wrote:
>>> So I do : mris_preproc --target fsaverage --xhemi --hemi lh --paired-diff
>>> --meas thickness --out lh.lh-rh.thickness.sm00.mgh --s t0001 --s t0003
> --s
>>> t0009 --s t0027 --s t0031 --s t0033 --s t0126 --s t0148 --s t0171 --s
>> t0174
>>> --s t0199 --s t0203 --s t0212 --s t0215 --s t0242 --s t0245 --s t0253 --s
>>> t0254 --s t0256 --s t0268
>>>
>>> You think it's ok ?
>>>
>>> Sophie
>>>
>>> -Message d'origine-
>>> De : freesurfer-boun...@nmr.mgh.harvard.edu
>>> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] De la part de Douglas N
>>> Greve
>>> Envoyé : lundi 18 mars 2013 13:49
>>> À : freesurfer@nmr.mgh.harvard.edu
>>> Objet : Re: [Freesurfer] Asymmetries of cortical thickness
>>>
>>> you will have to use the same stream, just specify one subject when your
>>> mris_preproc
>>> doug
>>>
>>>
>>> On 03/18/2013 08:06 AM, Sophie Maingault wrote:
 Hello,

 Iobtained a map of cortical thickness asymmetries after the
 registration on the symmetric atlas. But I would to obtain the same
 map with raw data I mean just by subtract lh.thickness and
 rh.thickness. How can I modify the part #Create a stack of subjects in
 wiki page ? I have to register to fsaverage (and not fsaverage_sym)
 and then do the same thing ?

 Thanks you for your help.

 Sophie



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

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

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[Freesurfer] (no subject)

[martina.andellini]

Hi FreeSurfer experts,
I would need to use the registration tools in freesurfer because the fsl ones ga
ve me some problem.
Just to try I have run mri_ca_registration and mri_cvs_registration and so I hav
e three questions:


1) mri_ca_registration generates a talairach tansform file in .m3z format and I 
would need to apply it to my high res image. Any hint?
2) Converting RB_all_2008-03-26.gca to nii and opening it to mricron it seems to
 superimposable to the mni atlas. does it mean that what it comes out from mri_c
a_registration coincides to an mni atlas image?
3) Running mri_cvs_registration (on bert data...just to try) I do not know where
 to find the registered volume file (I have tried few volume .mgz but with no su
ccess...). Should i look for a transform file too?



Thanks so much!
Martina

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Re: [Freesurfer] Reposting: interpreting clusters from 2 and 3 way interactions

[Laura M. Tully]

the mri_segstats command did not work - below is the command and output. It
looks like it is searching for the .annot file in fsaverage directory. How
do I tell it to use fsaverage and to look for the .annot elsewhere?

cd glmdir

mri_segstats --i beta.mgh --annot fsaverage lh
./SZcontrast_oneGrp_oneBehVar_4CVs/cache.th13.abs.sig.ocn.annot --avgwf
lh.SZ_CPT_area_betas.dat --excludeid 0


$Id: mri_segstats.c,v 1.75.2.2 2011/04/27 22:18:58 nicks Exp $

cwd

cmdline mri_segstats --i beta.mgh --annot fsaverage lh
./SZcontrast_oneGrp_oneBehVar_4CVs/cache.th13.abs.sig.ocn.annot --avgwf
lh.SZ_CPT_area_betas.dat --excludeid 0

sysname  Linux

hostname ncfws12.rc.fas.harvard.edu

machine  x86_64

user ltully

Constructing seg from annotation

could not read annot file
/ncf/snp/04/SCORE/freesurfer_analysis/fsaverage/label/lh../SZcontrast_oneGrp_oneBehVar_4CVs/cache.th13.abs.sig.ocn.annot.annot

No such file or directory


Thanks!

LT

On Wed, Mar 20, 2013 at 9:54 AM, Douglas N Greve
wrote:

>
> On 03/20/2013 12:09 PM, Laura M. Tully wrote:
>
>> Sorry -  meant to respond to list.
>>
>> Thanks for the response Doug - I have a few follow up questions I hope
>> you can clarify:
>>
>>   * is the xxx.ocn.annot file created by mri_glmfit-sim considered
>> a "label" by freesurfer?
>>
>>  It is an annotation
>
>
>>   * or does it need to be converted to a label before I can use
>> mri_segstats to extract the betas from the cluster(s) in the
>> xxx.ocn.annot?
>>
>>  No


>
>>   * I tried using the following command line to attempt to extract
>> the betas from the cluster annotation file created by
>> mri_glmfit-sim, but received an error:
>>
>> mri_segstats --i beta.mgh --annot fsaverage hemi
>> contrast/xxx.ocn.annot --avgwf avgwf.dat
>>
>>  That looks correct. Did it work? Add --excludeid 0 to keep it from
> reporting on non-clusters
>
>>
>>
>>   * how does one convert an xxx.ocn.annot file to a label?
>>
>>  If needed, use mri_annotation2label
>
>>
>>   * If I have run 3 different glms looking at the relationship
>>
>> between thickness and 3 different behavioral variables, and
>> found 1 (or more) cluster in each glm using mri_glmfit-sim can
>> I create 1 annotation/label with all the clusters from the
>> separate glms and then extract the betas from that one
>> annotation using mri_segstats? Or do I need to treat each glm
>> separately?
>>
>>  It is probably easiest if you treat each glm separately. You can break
> the annotations into separate labels, then recombine the labels into
> another annotation (mris_label2annot), but it is a lot of work.
>
>>
>>  *
>>
>>
>>   * I saw on the listserv some references to matlab functions that
>>
>> can calculate r square and partial correlations for glms with
>> more than one predictor variable (e.g pcc between thickness
>> and behavioral variable 1; pcc between thickness and
>> behavioral variable2; Rsq for overall model) but I could not
>> find the .m scripts for the functions (MRIread
>> or fast_glm_pcc?) - would these functions be appropriate and
>> if so where might I find them?
>>
>>  Yes. They are in $FREESURFER_HOME/matlab and $FREESURFER_HOME/fsfast/**
> toolbox
> doug
>
>>
>>  *
>>
>>
>> Thanks in advance for your help!
>>
>> Laura.
>>
>>
>> On Wed, Mar 20, 2013 at 8:29 AM, Douglas N Greve
>> > >
>> wrote:
>>
>>
>> On 03/20/2013 10:17 AM, Laura M. Tully wrote:
>> > Hi,
>> >
>> > I wanted to re-post my questions from a couple of days ago
>> below, but
>> > with some more specific questions following a search through the
>> > archives.
>> >
>> > I want to be able to extract the beta values from a cluster
>> identified
>> > using mc-z in a group by behavioral variable interaction so
>> that I can
>> > 1) plot the relationship of thickness to behavioral variable
>> data by
>> > group in that cluster, 2) conduct post hoc tests to examine the
>> > interaction, and 3) calculate the Rsquare and partial
>> correlations for
>> > each variable in the glm (i.e. how much variation in
>> thickness is
>> > explained by my behavioral variable).
>> >
>> > To extract the beta values from a cluster identified by mc-z
>> would I
>> > treat the cluster like a label and use mri_segstats to
>> extract the
>> > beta weights from the cluster? Would I need to make a label
>> of all the
>> > clusters that I want to do this for first?
>> You can do it label by label. Or, if the annotation created by
>> mri_glmfit-sim has all the clusters you want, you can use that
>> (also in
>> mri_segstats). You can also creat

Re: [Freesurfer] Brainsuite --> FreeSurfer

[Bruce Fischl]

it depends on what measures you want
Bruce
On Wed, 20 Mar 2013, Valtina Pouegue 
wrote:



Hi Bruces, 
It's because i'm doing a comparison between brainsuite and freesrufer. So , I 
would like to export results of
segmentation with Brainsuite and make measurements with FreeSurfer. In Fact, 
with freesurfer I can have more parameters
than with freesurfer. 
Does it exist another way for get measurements with surfaces ( not generated by 
Freesurfer)? 
Thx . 

VP
Date: Wed, 20 Mar 2013 08:38:26 -0400
From: fis...@nmr.mgh.harvard.edu
To: pval...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Brainsuite --> FreeSurfer

Hi Valtina

you can try opening it with freeview if all you want is visualization. If 
you are trying to produce anatomical stats you will need a lot more than 
just the pial surface, as mris_anatomical_stats computes many things from 
an array of inputs (such as the wm.mgz, the aseg.mgz, etc). Why not 
just run recon-all and generate them?

Bruce


On Tue, 19 Mar 2013, Valtina Pouegue wrote:

> I could  see the  created surface in MAtlab ( 'read_surf,) but I could't open 
the file in Freesurfer with tksurfer 
> 
> VP
> 
> ___

__
> From: pval...@hotmail.com
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Brainsuite --> FreeSurfer
> Date: Tue, 19 Mar 2013 22:34:39 -0400
> 
> Hi, 
> 
> I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to get measurements with FreeSurfer. SO, I

> convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be 
usable with Freesurfer. Then, I tried to get
> measurements with the command .'mris_anatomical_stats' .  with the file 
created previously in Matlab (I called it
>  'rh.pial'). But I got this error like the system is not able to read wm.mgz.
> That's why I thought I could juste replace th 'rh.pial' of the segmentation 
with Freesurfey by the 'rh.pial' created wi
th
> Matalb and then run mris_anatomical_Stats. IS this a good approximation. 
Could you recommand another way.
> 
> 
> VP
> 
>


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Re: [Freesurfer] Reposting: interpreting clusters from 2 and 3 way interactions

[Douglas N Greve]

On 03/20/2013 12:09 PM, Laura M. Tully wrote:
> Sorry -  meant to respond to list.
>
> Thanks for the response Doug - I have a few follow up questions I hope 
> you can clarify:
>
>   * is the xxx.ocn.annot file created by mri_glmfit-sim considered
> a "label" by freesurfer?
>
It is an annotation
>
>   * or does it need to be converted to a label before I can use
> mri_segstats to extract the betas from the cluster(s) in the
> xxx.ocn.annot?
>
No
>
>   * I tried using the following command line to attempt to extract
> the betas from the cluster annotation file created by
> mri_glmfit-sim, but received an error:
>
> mri_segstats --i beta.mgh --annot fsaverage hemi
> contrast/xxx.ocn.annot --avgwf avgwf.dat
>
That looks correct. Did it work? Add --excludeid 0 to keep it from 
reporting on non-clusters
>
>
>   * how does one convert an xxx.ocn.annot file to a label?
>
If needed, use mri_annotation2label
>
>   * If I have run 3 different glms looking at the relationship
> between thickness and 3 different behavioral variables, and
> found 1 (or more) cluster in each glm using mri_glmfit-sim can
> I create 1 annotation/label with all the clusters from the
> separate glms and then extract the betas from that one
> annotation using mri_segstats? Or do I need to treat each glm
> separately?
>
It is probably easiest if you treat each glm separately. You can break 
the annotations into separate labels, then recombine the labels into 
another annotation (mris_label2annot), but it is a lot of work.
>
>  *
>
>
>   * I saw on the listserv some references to matlab functions that
> can calculate r square and partial correlations for glms with
> more than one predictor variable (e.g pcc between thickness
> and behavioral variable 1; pcc between thickness and
> behavioral variable2; Rsq for overall model) but I could not
> find the .m scripts for the functions (MRIread
> or fast_glm_pcc?) - would these functions be appropriate and
> if so where might I find them?
>
Yes. They are in $FREESURFER_HOME/matlab and $FREESURFER_HOME/fsfast/toolbox
doug
>
>  *
>
> Thanks in advance for your help!
>
> Laura.
>
>
> On Wed, Mar 20, 2013 at 8:29 AM, Douglas N Greve
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
>
> On 03/20/2013 10:17 AM, Laura M. Tully wrote:
> > Hi,
> >
> > I wanted to re-post my questions from a couple of days ago
> below, but
> > with some more specific questions following a search through the
> > archives.
> >
> > I want to be able to extract the beta values from a cluster
> identified
> > using mc-z in a group by behavioral variable interaction so
> that I can
> > 1) plot the relationship of thickness to behavioral variable
> data by
> > group in that cluster, 2) conduct post hoc tests to examine the
> > interaction, and 3) calculate the Rsquare and partial
> correlations for
> > each variable in the glm (i.e. how much variation in
> thickness is
> > explained by my behavioral variable).
> >
> > To extract the beta values from a cluster identified by mc-z
> would I
> > treat the cluster like a label and use mri_segstats to
> extract the
> > beta weights from the cluster? Would I need to make a label
> of all the
> > clusters that I want to do this for first?
> You can do it label by label. Or, if the annotation created by
> mri_glmfit-sim has all the clusters you want, you can use that
> (also in
> mri_segstats). You can also create an annotation from
> individual labels
> with mris_label2annot.
> >
> > Is there a way to calculate the basic statistics for the glm and
> > extract in table form? i.e. Fs and ps for peaks of each
> cluster? What
> > about Rsquare, or the correlation between thickness and my
> behavioral
> > variable in the clusters? or would I need to compute these
> outside of
> > freesurfer using the extracted betas?
> You will need to do it outside of FS. What are Fs and ps?
> doug
>
> >
> > Thank you!
> >
> > Laura.
> >
> >
> >
> >
> >
> >
> > On Mon, Mar 18, 2013 at 5:05 PM, Laura M. Tully
> >  
>  >> wrote:
> >
> > Hi Freesurfer experts,
> >
> > I'm hoping you can help me understand how to interpret
> > interactions in clusters identified in whole brain
> analysis

Re: [Freesurfer] Reposting: interpreting clusters from 2 and 3 way interactions

[Laura M. Tully]

Sorry -  meant to respond to list.

Thanks for the response Doug - I have a few follow up questions I hope you
can clarify:

>
>- is the xxx.ocn.annot file created by mri_glmfit-sim considered a
>"label" by freesurfer? or does it need to be converted to a label before I
>can use mri_segstats to extract the betas from the cluster(s) in the
>xxx.ocn.annot? I tried using the following command line to attempt to
>extract the betas from the cluster annotation file created by
>mri_glmfit-sim, but received an error:
>
> mri_segstats --i beta.mgh --annot fsaverage hemi contrast/xxx.ocn.annot
> --avgwf avgwf.dat
>
>
>- how does one convert an xxx.ocn.annot file to a label?
>
>
>- If I have run 3 different glms looking at the relationship between
>thickness and 3 different behavioral variables, and found 1 (or more)
>cluster in each glm using mri_glmfit-sim can I create 1 annotation/label
>with all the clusters from the separate glms and then extract the betas
>from that one annotation using mri_segstats? Or do I need to treat each glm
>separately?
>
>
>- I saw on the listserv some references to matlab functions that
>can calculate r square and partial correlations for glms with more than one
>predictor variable (e.g pcc between thickness and behavioral variable 1;
>pcc between thickness and behavioral variable2; Rsq for overall model) but
>I could not find the .m scripts for the functions (MRIread
>or fast_glm_pcc?) - would these functions be appropriate and if so where
>might I find them?
>
> Thanks in advance for your help!
>
> Laura.
>
>
> On Wed, Mar 20, 2013 at 8:29 AM, Douglas N Greve <
> gr...@nmr.mgh.harvard.edu> wrote:
>
>>
>> On 03/20/2013 10:17 AM, Laura M. Tully wrote:
>> > Hi,
>> >
>> > I wanted to re-post my questions from a couple of days ago below, but
>> > with some more specific questions following a search through the
>> > archives.
>> >
>> > I want to be able to extract the beta values from a cluster identified
>> > using mc-z in a group by behavioral variable interaction so that I can
>> > 1) plot the relationship of thickness to behavioral variable data by
>> > group in that cluster, 2) conduct post hoc tests to examine the
>> > interaction, and 3) calculate the Rsquare and partial correlations for
>> > each variable in the glm (i.e. how much variation in thickness is
>> > explained by my behavioral variable).
>> >
>> > To extract the beta values from a cluster identified by mc-z would I
>> > treat the cluster like a label and use mri_segstats to extract the
>> > beta weights from the cluster? Would I need to make a label of all the
>> > clusters that I want to do this for first?
>> You can do it label by label. Or, if the annotation created by
>> mri_glmfit-sim has all the clusters you want, you can use that (also in
>> mri_segstats). You can also create an annotation from individual labels
>> with mris_label2annot.
>> >
>> > Is there a way to calculate the basic statistics for the glm and
>> > extract in table form? i.e. Fs and ps for peaks of each cluster? What
>> > about Rsquare, or the correlation between thickness and my behavioral
>> > variable in the clusters? or would I need to compute these outside of
>> > freesurfer using the extracted betas?
>> You will need to do it outside of FS. What are Fs and ps?
>> doug
>>
>> >
>> > Thank you!
>> >
>> > Laura.
>> >
>> >
>> >
>> >
>> >
>> >
>> > On Mon, Mar 18, 2013 at 5:05 PM, Laura M. Tully
>> > mailto:tully.la...@googlemail.com>> wrote:
>> >
>> > Hi Freesurfer experts,
>> >
>> > I'm hoping you can help me understand how to interpret
>> > interactions in clusters identified in whole brain analysis using
>> > glmfit and glmfit-sim. Below I describe what I've done and what
>> > I'd like to be able to do. Any suggestions would be most
>> appreciated!
>> >
>> >   * I have two groups (patients, controls) and a behavioral
>> > variable of interest (social functioning). I am interested in
>> > cortical thickness differences between groups (main effect of
>> > group), whether cortical thickness relate to social
>> > functioning across the group (main effect of social
>> > functioning), and whether this relationship differs by group
>> > (group x social functioning interaction).
>> >   * I ran whole brain analysis using mri_glmfit with group and
>> > functioning as variables of interest whilst controlling
>> > for/regressing out gender, age, and mean thickness. i.e. 4
>> > classes (conmale,confemale, ptmale, ptfemale) and 3 continuous
>> > variables (age, AvgThickness, Functioning) = 16 regressors.
>> >   * I tested the group x functioning interaction with the
>> > following contrast - is it correct?
>> >
>> > 0.50.5-0.5-0.5
>> >
>> >   * I then ran mri_glmfit-sim to identify clusters that survive
>> > multiple comparisons. Th

[Freesurfer] non-parallel version of LME models MATLAB scripts

[Lalonde, Francois (NIH/NIMH) [E]]

In running a mass-univariate LME models analysis I keep running into calls to 
the parallel computing toolbox (parfor, matlabpool, etc…).  I was able to 
comment out these lines in some of the scripts but I've run up to one that is 
particularly difficult to modify (I am not an expert in MATLAB).  The script 
called lme_mass_fit_Rgw has proven to be too difficult.  Would it be possible 
to get a version of the of the LME models analysis that runs on the base MATLAB 
program only?  It will admittedly take longer but will make the analysis more 
accessible.

Also, I was unable to find the function "for_progress" which is called along 
with "parfor_progress".

Thanks,
Francois

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Re: [Freesurfer] Problem with tracula: incomplete or lacking tracts

[Anastasia Yendiki]

Hi Stefano - Have you checked that your gradient table is correct by 
looking at the output of the tensor fit?


a.y

On Wed, 20 Mar 2013, std...@virgilio.it wrote:


Hi list and Anastasia,
if you remember the last week I had same problems with tracula output: the  
final tract are lacking or
incomplete for same subjects. Some of these are less wrong (only forceps 
major), other have more evident
error (you can see this in picture that I have attacked). 

To resolve this issue I have:

1-checked the correct overlap of dwi and dwi_mask
2-rerun data with new version 5.2
3-rerun new registration using bbregister (fsl/spm option): for example, in the 
subject of the picture
attacked, the .mincost file now contains as first value 0.87 (previous it was 
1.1)

Please, give me an advise

Thanks


Stefano




Messaggio originale
Da: std...@virgilio.it
Data: 12-mar-2013 17.47
A: 
Cc: 
Ogg: [Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlap

I got it from mri directory but I'm understanding that this directory isn't 
ok.I'm attacking the image
from dlabel/diff/aparc+aseg.bbr.nii


Stefano



Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 12-mar-2013 17.19
A: 
Cc: 
Ogg: Re: [Freesurfer] R: Re:  Question on tracula and dwi-T1 overlap


Can you please answer my question? I can't really tell if the issue is due 
poor dwi-aseg overlap unless you tell me where you got that aseg volume 
from.

On Tue, 12 Mar 2013, std...@virgilio.it wrote:

> Thank you Anastasia. What do you think about the issue in the file attacked
> (I'm noting that same subjects are lacking of same
>  tracts or same tracts are incomplete)
> 
> 
> Stefano
> 
> 
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 12-mar-2013 17.02
> A: 
> Cc: 
> Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap
> 
> 
> Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's in
> the dlabel/diff/ directory has been mapped to the same space as the DWI,
> so those are the volumes that can be compared directly to dwi.nii.gz.
> 
> a.y
> 
> On Tue, 12 Mar 2013, std...@virgilio.it wrote:
> 
> > Hi list,
> >
> > I have two questions, please.
> >
> > I'm using version 5.1 to complete my analysis.
> >
> > 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of the same
> > subject (figure 1 and 3). You can note the dwi do not overlap to the aseg.
> > How can I resolve this issue? 
> >
> > 2-After TRACULA analysis, I'm noting that same subjects are lacking of
> same
> > tracts or same tracts are incomplete (figure 3).
> >
> > Could it depends from the issue in question 1? I'm thinking to rerun all
> > using version 5.2 but before starting new analyses, I'd like to ask you
> > which is the possible error.
> >
> >
> > Stefano
> >
> >___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to you in
> error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
> 
> 
> 
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Re: [Freesurfer] TRACULA missings tracts

[Anastasia Yendiki]

Hi Benjamin - Have you checked that your gradient table is correct by 
looking at the output of the tensor fit?

a.y

On Wed, 20 Mar 2013, Roschinski, Benjamin wrote:

> Dear Freesurfer users and experts,
>
> we have some problems using TRACULA. This means that tracks are missing or 
> that they are too short.
> I hope you can advise me how to fix these problems.
>
> Thanks and kind regards
> Benjamin
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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Re: [Freesurfer] Reposting: interpreting clusters from 2 and 3 way interactions

[Douglas N Greve]

On 03/20/2013 10:17 AM, Laura M. Tully wrote:
> Hi,
>
> I wanted to re-post my questions from a couple of days ago below, but 
> with some more specific questions following a search through the 
> archives.
>
> I want to be able to extract the beta values from a cluster identified 
> using mc-z in a group by behavioral variable interaction so that I can 
> 1) plot the relationship of thickness to behavioral variable data by 
> group in that cluster, 2) conduct post hoc tests to examine the 
> interaction, and 3) calculate the Rsquare and partial correlations for 
> each variable in the glm (i.e. how much variation in thickness is 
> explained by my behavioral variable).
>
> To extract the beta values from a cluster identified by mc-z would I 
> treat the cluster like a label and use mri_segstats to extract the 
> beta weights from the cluster? Would I need to make a label of all the 
> clusters that I want to do this for first?
You can do it label by label. Or, if the annotation created by 
mri_glmfit-sim has all the clusters you want, you can use that (also in 
mri_segstats). You can also create an annotation from individual labels 
with mris_label2annot.
>
> Is there a way to calculate the basic statistics for the glm and 
> extract in table form? i.e. Fs and ps for peaks of each cluster? What 
> about Rsquare, or the correlation between thickness and my behavioral 
> variable in the clusters? or would I need to compute these outside of 
> freesurfer using the extracted betas?
You will need to do it outside of FS. What are Fs and ps?
doug

>
> Thank you!
>
> Laura.
>
>
>
>
>
>
> On Mon, Mar 18, 2013 at 5:05 PM, Laura M. Tully 
> mailto:tully.la...@googlemail.com>> wrote:
>
> Hi Freesurfer experts,
>
> I'm hoping you can help me understand how to interpret
> interactions in clusters identified in whole brain analysis using
> glmfit and glmfit-sim. Below I describe what I've done and what
> I'd like to be able to do. Any suggestions would be most appreciated!
>
>   * I have two groups (patients, controls) and a behavioral
> variable of interest (social functioning). I am interested in
> cortical thickness differences between groups (main effect of
> group), whether cortical thickness relate to social
> functioning across the group (main effect of social
> functioning), and whether this relationship differs by group
> (group x social functioning interaction).
>   * I ran whole brain analysis using mri_glmfit with group and
> functioning as variables of interest whilst controlling
> for/regressing out gender, age, and mean thickness. i.e. 4
> classes (conmale,confemale, ptmale, ptfemale) and 3 continuous
> variables (age, AvgThickness, Functioning) = 16 regressors.
>   * I tested the group x functioning interaction with the
> following contrast - is it correct?
>
> 0.50.5-0.5-0.5
>
>   * I then ran mri_glmfit-sim to identify clusters that survive
> multiple comparisons. This revealed 4 clusters (3 in LH; 1 in
> RH) that represent regions showing significant group x
> functioning interaction.
>   * I visualized the clusters in tksurfer, and by loading the
> y.fsgd file was able to visualize the plotted data to get a
> sense of the interaction, but this is as much as I know in
> terms of how to examine interactions in the cluster data..
>
> My specifc questions include:
>
>   * I understand that the values in xxx.sig.cluster.mgh overlay
> reflect log10 p values, the signs of which indicate the
> direction of the relationship (i.e. -3 = negative correlation
> between thickness & variable) but I'm not sure how to
> interpret this in the context of an interaction with group?
>   * I understand that the values in xxx.y.ocn.dat contain the
> average thickness value for each subject in that cluster and
> that in a simple between groups test this data could be used
> to conduct post hoc t-tests to show the direction of the
> difference, but again I'm not sure how to use this data in the
> context of the interaction. What do the values represent in a
> group x variable interaction?
>
> Ideally, I'd like to extract the contrast estimates for each
> subject in the group x functioning contrast and plot it in another
> program and conduct pairwise comparisons (t-tests) in order to get
> a better understanding of the interaction). I'm not sure how to do
> this - is it possible? My thinking is that I do something similar
> in fMRI analysis in spm where I can plot the contrasts in a
> significant cluster and then extract both the average contrast
> estimates for each group and the contrast estimates for each
> individual subject.
>
> Thanks in advance!
>
> Laura.
>
>
> -- 
> --
> Laura 

[Freesurfer] Problem with tracula: incomplete or lacking tracts

[stdp82]

Hi list and Anastasia,
if you remember the last week I had same problems with tracula output: the  
final tract are lacking or incomplete for same subjects. Some of these are less 
wrong (only forceps major), other have more evident error (you can see this in 
picture that I have attacked). 
To resolve this issue I have:
1-checked the correct overlap of dwi and dwi_mask2-rerun data with new version 
5.23-rerun new registration using bbregister (fsl/spm option): for example, in 
the subject of the picture attacked, the .mincost file now contains as first 
value 0.87 (previous it was 1.1)
Please, give me an advise
Thanks

Stefano

Messaggio originaleDa: stdp82@virgilio.itData: 12-mar-2013 17.47A: 
Cc: Ogg: 
[Freesurfer] R: Re: R: Re: Question on tracula and dwi-T1 overlapI got it from 
mri directory but I'm understanding that this directory isn't ok.I'm attacking 
the image from dlabel/diff/aparc+aseg.bbr.nii


Stefano


Messaggio originale
Da: ayend...@nmr.mgh.harvard.edu
Data: 12-mar-2013 17.19
A: 
Cc: 
Ogg: Re: [Freesurfer] R: Re:  Question on tracula and dwi-T1 overlap


Can you please answer my question? I can't really tell if the issue is due 
poor dwi-aseg overlap unless you tell me where you got that aseg volume 
from.

On Tue, 12 Mar 2013, std...@virgilio.it wrote:

> Thank you Anastasia. What do you think about the issue in the file attacked
> (I'm noting that same subjects are lacking of same
>  tracts or same tracts are incomplete)
> 
> 
> Stefano
> 
> 
> Messaggio originale
> Da: ayend...@nmr.mgh.harvard.edu
> Data: 12-mar-2013 17.02
> A: 
> Cc: 
> Ogg: Re: [Freesurfer] Question on tracula and dwi-T1 overlap
> 
> 
> Hi Stefano - Where did you get the aseg.nii.gz from? Anything that's in
> the dlabel/diff/ directory has been mapped to the same space as the DWI,
> so those are the volumes that can be compared directly to dwi.nii.gz.
> 
> a.y
> 
> On Tue, 12 Mar 2013, std...@virgilio.it wrote:
> 
> > Hi list,
> >
> > I have two questions, please.
> >
> > I'm using version 5.1 to complete my analysis.
> >
> > 1- I have attacked two images from aseg.nii.gz and dwi.nii.gz of the same
> > subject (figure 1 and 3). You can note the dwi do not overlap to the aseg.
> > How can I resolve this issue? 
> >
> > 2-After TRACULA analysis, I'm noting that same subjects are lacking of
> same
> > tracts or same tracts are incomplete (figure 3).
> >
> > Could it depends from the issue in question 1? I'm thinking to rerun all
> > using version 5.2 but before starting new analyses, I'd like to ask you
> > which is the possible error.
> >
> >
> > Stefano
> >
> >___
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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
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> contains patient information, please contact the Partners Compliance
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[Freesurfer] Reposting: interpreting clusters from 2 and 3 way interactions

[Laura M. Tully]

Hi,

I wanted to re-post my questions from a couple of days ago below, but with
some more specific questions following a search through the archives.

I want to be able to extract the beta values from a cluster identified
using mc-z in a group by behavioral variable interaction so that I can 1)
plot the relationship of thickness to behavioral variable data by group in
that cluster, 2) conduct post hoc tests to examine the interaction, and 3)
calculate the Rsquare and partial correlations for each variable in the glm
(i.e. how much variation in thickness is explained by my behavioral
variable).

To extract the beta values from a cluster identified by mc-z would I treat
the cluster like a label and use mri_segstats to extract the beta weights
from the cluster? Would I need to make a label of all the clusters that I
want to do this for first?

Is there a way to calculate the basic statistics for the glm and extract in
table form? i.e. Fs and ps for peaks of each cluster? What about Rsquare,
or the correlation between thickness and my behavioral variable in the
clusters? or would I need to compute these outside of freesurfer using the
extracted betas?

Thank you!

Laura.






On Mon, Mar 18, 2013 at 5:05 PM, Laura M. Tully
wrote:

> Hi Freesurfer experts,
>
> I'm hoping you can help me understand how to interpret interactions in
> clusters identified in whole brain analysis using glmfit and glmfit-sim.
> Below I describe what I've done and what I'd like to be able to do. Any
> suggestions would be most appreciated!
>
>
>- I have two groups (patients, controls) and a behavioral variable of
>interest (social functioning). I am interested in cortical thickness
>differences between groups (main effect of group), whether cortical
>thickness relate to social functioning across the group (main effect of
>social functioning), and whether this relationship differs by group (group
>x social functioning interaction).
>- I ran whole brain analysis using mri_glmfit with group and
>functioning as variables of interest whilst controlling for/regressing out
>gender, age, and mean thickness. i.e. 4 classes (conmale,confemale, ptmale,
>ptfemale) and 3 continuous variables (age, AvgThickness, Functioning) = 16
>regressors.
>- I tested the group x functioning interaction with the following
>contrast - is it correct?
>
> 0 0 0 0 0 0 0 0 0 0 0 0 0.5 0.5 -0.5 -0.5
>
>- I then ran mri_glmfit-sim to identify clusters that survive multiple
>comparisons. This revealed 4 clusters (3 in LH; 1 in RH) that represent
>regions showing significant group x functioning interaction.
>- I visualized the clusters in tksurfer, and by loading the y.fsgd
>file was able to visualize the plotted data to get a sense of the
>interaction, but this is as much as I know in terms of how to examine
>interactions in the cluster data..
>
> My specifc questions include:
>
>- I understand that the values in xxx.sig.cluster.mgh overlay reflect
>log10 p values, the signs of which indicate the direction of the
>relationship (i.e. -3 = negative correlation between thickness & variable)
>but I'm not sure how to interpret this in the context of an interaction
>with group?
>- I understand that the values in xxx.y.ocn.dat contain the average
>thickness value for each subject in that cluster and that in a simple
>between groups test this data could be used to conduct post hoc t-tests to
>show the direction of the difference, but again I'm not sure how to use
>this data in the context of the interaction. What do the values represent
>in a group x variable interaction?
>
> Ideally, I'd like to extract the contrast estimates for each subject in
> the group x functioning contrast and plot it in another program and
> conduct pairwise comparisons (t-tests) in order to get a better
> understanding of the interaction). I'm not sure how to do this - is it
> possible? My thinking is that I do something similar in fMRI analysis in
> spm where I can plot the contrasts in a significant cluster and then
> extract both the average contrast estimates for each group and the contrast
> estimates for each individual subject.
>
> Thanks in advance!
>
> Laura.
>
>
> --
> --
> Laura M. Tully, MA
> Social Neuroscience & Psychopathology, Harvard University
> Center for the Assessment and Prevention of Prodromal States, UCLA Semel
> Institute of Neuroscience
> ltu...@mednet.ucla.edu
> ltu...@fas.harvard.edu
> 310-267-0170
> --
> My musings as a young clinical scientist:
> http://theclinicalbrain.blogspot.com/
> Follow me on Twitter: @tully_laura
>



-- 
--
Laura M. Tully, MA
Social Neuroscience & Psychopathology, Harvard University
Center for the Assessment and Prevention of Prodromal States, UCLA Semel
Institute of Neuroscience
ltu...@mednet.ucla.edu
ltu...@fas.harvard.edu
310-267-0170
--
My musings as a young clinical scientist:
http://theclinicalbrain.blogspot.com/
F

[Freesurfer] TRACULA missings tracts

[Roschinski, Benjamin]

Dear Freesurfer users and experts,

we have some problems using TRACULA. This means that tracks are missing or that 
they are too short.
I hope you can advise me how to fix these problems.

Thanks and kind regards
Benjamin

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Re: [Freesurfer] Brainsuite --> FreeSurfer

[Valtina Pouegue]

Hi Bruces, It's because i'm doing a comparison between brainsuite and 
freesrufer. So , I would like to export results of segmentation with Brainsuite 
and make measurements with FreeSurfer. In Fact, with freesurfer I can have more 
parameters than with freesurfer. Does it exist another way for get measurements 
with surfaces ( not generated by Freesurfer)? Thx . 
VP
Date: Wed, 20 Mar 2013 08:38:26 -0400
From: fis...@nmr.mgh.harvard.edu
To: pval...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Brainsuite --> FreeSurfer

Hi Valtina
 
you can try opening it with freeview if all you want is visualization. If 
you are trying to produce anatomical stats you will need a lot more than 
just the pial surface, as mris_anatomical_stats computes many things from 
an array of inputs (such as the wm.mgz, the aseg.mgz, etc). Why not 
just run recon-all and generate them?
Bruce
 
 
On Tue, 19 Mar 2013, Valtina Pouegue wrote:
 
> I could  see the  created surface in MAtlab ( 'read_surf,) but I could't open 
> the file in Freesurfer with tksurfer 
> 
> VP
> 
> _
> From: pval...@hotmail.com
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Brainsuite --> FreeSurfer
> Date: Tue, 19 Mar 2013 22:34:39 -0400
> 
> Hi, 
> 
> I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like 
> to get measurements with FreeSurfer. SO, I
> convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be 
> usable with Freesurfer. Then, I tried to get
> measurements with the command .'mris_anatomical_stats' .  with the file 
> created previously in Matlab (I called it
>  'rh.pial'). But I got this error like the system is not able to read wm.mgz.
> That's why I thought I could juste replace th 'rh.pial' of the segmentation 
> with Freesurfey by the 'rh.pial' created with
> Matalb and then run mris_anatomical_Stats. IS this a good approximation. 
> Could you recommand another way.
> 
> 
> VP
> 
>

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Re: [Freesurfer] make a volume template from the surface-based template for non-human primates

[Bruce Fischl]

yes, I have it
On Tue, 19 Mar 2013, Longchuan Li wrote:


Hi, Bruce

The command line I used is: 

mris_fill -r 1 -c rh.white rh.white.nii.gz

I attached the rh.white in my previous mail. Could you see it in the attachment?

Thank you!

Longchuan

_
From: Bruce Fischl 
To: Longchuan Li 
Cc: FreeSurfer 
Sent: Tuesday, March 19, 2013 8:10 PM
Subject: Re: [Freesurfer] make a volume template from the surface-based 
template for non-human primates

can you send your mris_fill command line? And maybe the lh.white surface
you are trying to fill?
Bruce
On Tue, 19 Mar 2013, Longchuan Li wrote:

> Hi, Bruce
>
> This is the lh.white that gives me the empty volume when I use mris_fill to
> sample it to the volume space. Could you help diagnose what is causing it?
> Thank you very much in advance!
>
> Lognchuan
>
>
> 
> From: Bruce Fischl 
> To: Longchuan Li 
> Cc: FreeSurfer 
> Sent: Sunday, March 17, 2013 11:47 AM
> Subject: Re: [Freesurfer] make a volume template from the surface-based
> template for non-human primates
>
> Hi Longchuan
>
> I'm not sure what space the volume average is constructed in - Doug would
> know. Probably talairach, in which case it won't match the surfaces well.
> Can you send along your mris_fill command line? It shouldn't produce an
> empty volume. There's no reason to look at the inflated surfaces in the
> volume though - they have no volumetric meaning.
>
> cheers
> Bruce
>
>
> On Fri, 15 Mar 2013, Longchuan Li wrote:
>
> > Hi, Bruce
> >
> > Sorry for the late reply as I was trying to figure it out by myself.
> > I mean the average of the subjects in the volume space that were used for
> > generating the surface template. Actually I kind of found a volume average
> > in the mri folder named as T1.mgz that seems to correspond to the surface
> > template for the non-human primates. Perhaps because my ?h.white and
> ?.pial
> > surface files do not have the identical origins as that of the volume
> > template, when I used the function "mri_surf2vol" to project the mgh
> surface
> > file to the volume average, I always got the outputs telling me there is 0
> > hits. I tried to diagnose it by projecting the ?h.white and ?h.pial to the
> > volume using "mri_fill" and I got an empty volume. I then tried to project
> > ?h.inflated to the volume space using the "mri_fill" and this time, I got
> a
> > mask in the output volume space. Therefore, i suspect that there is a
> > mismatch of the origins between the ?h.white and the volume template in
> the
> > mri folder.
> >
> > Could you please show me what are the best strategies to correctly project
> > the mgh file to the volume template in the 'mri' folder?
> >
> > Many thanks
> >
> > Longchuan 
> >
> >___
> _
> > From: Bruce Fischl 
> > To: Longchuan Li 
> > Cc: FreeSurfer 
> > Sent: Friday, March 15, 2013 4:56 PM
> > Subject: Re: [Freesurfer] make a volume template from the surface-based
> > template for non-human primates
> >
> > Hi Longchuan
> >
> > what kind of volume template do you mean?
> > Bruce
> > On Fri, 15 Mar 2013, Longchuan Li
> > wrote:
> >
> > > Hi, FreeSurfer experts
> > >
> > > I have a question regarding making a volume template based on the
> surface
> > > template for non-human primates. I have made a surface template using a
> > > group of monkeys and now, we want to see the result, which is a mgh
> > surface
> > > file, on the coronal slices of the template. So I am planning to
> generate
> > a
> > > volume template corresponding to the surface template and then project
> the
> > > mgh file to the volume for viewing. Could someone tell me what is the
> best
> > > way to generate such a volume template?
> > >
> > > Many thanks in advance!
> > >
> > > Longchuan
> > >
> > >
> > >
> >
> >
> > 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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>
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> error
> but d

Re: [Freesurfer] Brainsuite --> FreeSurfer

[Bruce Fischl]

Hi Valtina

you can try opening it with freeview if all you want is visualization. If 
you are trying to produce anatomical stats you will need a lot more than 
just the pial surface, as mris_anatomical_stats computes many things from 
an array of inputs (such as the wm.mgz, the aseg.mgz, etc). Why not 
just run recon-all and generate them?

Bruce


On Tue, 19 Mar 2013, Valtina Pouegue wrote:


I could  see the  created surface in MAtlab ( 'read_surf,) but I could't open 
the file in Freesurfer with tksurfer 

VP

_
From: pval...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: Brainsuite --> FreeSurfer
Date: Tue, 19 Mar 2013 22:34:39 -0400

Hi, 

I've done a segmentation with Brainsuite ( and FreeSurfer) and I would like to 
get measurements with FreeSurfer. SO, I
convert my rile ( readdfs --> write_surf ) from BRainsuite in Matlab to be 
usable with Freesurfer. Then, I tried to get
measurements with the command .'mris_anatomical_stats' .  with the file created 
previously in Matlab (I called it
 'rh.pial'). But I got this error like the system is not able to read wm.mgz.
That's why I thought I could juste replace th 'rh.pial' of the segmentation 
with Freesurfey by the 'rh.pial' created with
Matalb and then run mris_anatomical_Stats. IS this a good approximation. Could 
you recommand another way.


VP

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[Freesurfer] ELF class

[Varghese Chikku]

Hi Fs Team,
I am getting this  errow  while  trying to use freeview.
reesurfer@freesurfer-VirtualBox:~$ freeview
freeview.bin: error while loading shared libraries: libjpeg.so.62: wrong
ELF class: ELFCLASS32
Any Help
Tx
chikku
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[Freesurfer] Updated info for freesurfer 5.2 on Fedora 18. update from Bugzilla. Freesurfer used unsupported, nonstandard salt to crypt()

[Knut J Bjuland]

HI

I have copied the info from Bugzilla.


Product: Fedora https://bugzilla.redhat.com/show_bug.cgi?id=905638 Patsy 
Franklin  changed: What |Removed |Added 
 
Flags|needinfo?(pfrankli@redhat.c | |om) | 
Flags|needinfo?(pfrankli@redhat.c | |om) | --- Comment #27 from Patsy 
Franklin  --- The most immediate solution is for 
the application to be changed to use a compliant crypt salt value. After 
further investigation, we found that the application is passing 
unsupported, nonstandard salt to crypt(). This will result in crypt() 
returning NULL and setting errno to EINVAL. It does not appear that the 
application is checking for a NULL return value from crypt. It also 
appears that the application is using this NULL return value in a 
subsequent function call resulting in a segmentation fault. Previously 
glibc would accept unsupported salt values, but newer versions of the 
library have become stricter. We are currently reviewing the 
implementation to see if the accepted salt values can be expanded while 
still meeting our standards compliance requirements.
--

Knut J
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