[Freesurfer] Repeated measures ANOVA with covariate

[Mayuresh K]

Hi freesurfer experts,

Is there a way to perform a repeated measures ANOVA with a between subjects
factor (two groups)? I am interested in comparing cortical thickness
differences between the matched scans between the two groups i.e.
measures*group interaction.

How would I setup this design in freesurfer?

Thanks,
Mayuresh
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Re: [Freesurfer] fsaverage of freesurfer v5

[Douglas Greve]

yes, it is a 6th order icosahedron. Here is a list of the number of 
vertices with each order


3 642
42562
5   10242
6   40962
7  163842


On 5/25/11 11:08 PM, Dai Dai wrote:

hi, all
does freesurfer v5 have multiple fsaverage subjects with varying 
number of vertices?

see the following mails; where does fsaverage6 locate?

Nick Schmansky nicks at nmr.mgh.harvard.edu
Fri Sep 10 15:23:09 EDT 2010
* Previous message: [Freesurfer] two questions about freesurfer
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1. in freesurfer v5, there are now multiple fsaverage subjects with
varying number of vertices.  fsaverage6 has about 40,000 vertices per
hemi, so you can just include the flag:
--target fsaverage6
after the -qcache flag, and it will use that as the target instead of
fsaverage (producing files like 'rh.thickness.fsaverage6.mgh', which
will have 40K thickness samples).

On Fri, 2010-09-10 at 15:19 +0800, Dai Dai wrote:
> Hi, all
>
> I am a new user of freesurfer and now I have two questions.
>
> 1. For my work, the number of vertex in surface data is too much to
> process. How can I downsample the surface mesh as well as the
> curvation file (e.g. thickness)? The vertex number of fsaverage
> template is ~160,000, normally more than that of every subject. Can I
> construct an average surface of less vertexes or downsample the
> fsaverage surface to that of ~2 vertexes and then transform all
> the subjects using these templates with less vertexes (using recon-all
> -qcache)?
2011-05-26
Dai Dai


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[Freesurfer] fsaverage of freesurfer v5

[Dai Dai]

hi, all

does freesurfer v5 have multiple fsaverage subjects with varying number of 
vertices?

see the following mails; where does fsaverage6 locate? 


Nick Schmansky nicks at nmr.mgh.harvard.edu

Fri Sep 10 15:23:09 EDT 2010

* Previous message: [Freesurfer] two questions about freesurfer
* Next message: [Freesurfer] memory error and WM edits
* Messages sorted by: [ date ] [ thread ] [ subject ] [ author ]

1. in freesurfer v5, there are now multiple fsaverage subjects with
varying number of vertices.  fsaverage6 has about 40,000 vertices per
hemi, so you can just include the flag:

--target fsaverage6

after the -qcache flag, and it will use that as the target instead of
fsaverage (producing files like 'rh.thickness.fsaverage6.mgh', which
will have 40K thickness samples).


On Fri, 2010-09-10 at 15:19 +0800, Dai Dai wrote:
> Hi, all
>  
> I am a new user of freesurfer and now I have two questions. 
>  
> 1. For my work, the number of vertex in surface data is too much to
> process. How can I downsample the surface mesh as well as the
> curvation file (e.g. thickness)? The vertex number of fsaverage
> template is ~160,000, normally more than that of every subject. Can I
> construct an average surface of less vertexes or downsample the
> fsaverage surface to that of ~2 vertexes and then transform all
> the subjects using these templates with less vertexes (using recon-all
> -qcache)?

2011-05-26 



Dai Dai 
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Re: [Freesurfer] qdec error message

[Olivier Piguet]

Hi Nick
I run Qdec 1.2 and all cases have been processed with 
freesurfer-Linux-centos4_x86_64-stable-pub-v4.2.0
Olivier
On 25/05/2011, at 21:18, Nick Schmansky wrote:

> what version of freesurfer does this happen with?
> 
> n.
> On Wed, 2011-05-25 at 14:17 +1000, Olivier Piguet wrote:
>> Good afternoon, 
>> 
>> When running qdec, I receive the following error message:
>> 
>> Writing to 
>> /Volumes/workingdata/FTD/T1/subjects/qdec/Untitled/contrasts.sig.mgh
>> reading group avg surface area 822 cm^2 from file
>> ERROR: could not find volume 
>> /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig.  Does it 
>> exist?
>> Reading in average area 
>> /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/lh.white.avg.area.mgh
>> reading group avg surface area 1041 cm^2 from file
>> ERROR: could not find volume 
>> /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig.  Does it 
>> exist?
>> Reading in average area 
>> /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/lh.pial.avg.area.mgh
>> reading group avg surface area 822 cm^2 from file
>> ERROR: could not find volume 
>> /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig.  Does it 
>> exist?
>> 
>> I have run all subjects with qcache and I am using fsaverage. I have checked 
>> the files in the fsaverage folder. Although the file orig. does not exist, 
>> there is a file called orig.mgz in the mri folder. I have tried to rename 
>> this file (i.e., removing the 'mgz' part) but this did not remove the error. 
>> 
>> Any suggestion would be appreciated. 
>> 
>> Thanks
>> 
>> Olivier Piguet
>> Neuroscience Research Australia
>> Sydney NSW, Australia
>> 
>> 
>> 
>> 
>> 
>> 
>> 
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>> 
> 
> 
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[Freesurfer] for low resolution monitors, tksurfer dialog fix

[Krish Subramaniam]

Hi all,

It's been pointed out that tksurfer's "Configure Overlay Display"  
dialog gets clipped for low resolution monitors where it's impossible  
to see and interact with the buttons. This is how it looks: 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/tksurferclipped.jpg
 
  ( Thanks to Gonzalo Rojas Costa )

To fix this ( only for FS v5.1.0 ), copy the file 
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/tksurfer.tcl
 
  to $FREESURFER_HOME/lib/tcl/

The new dialog should look like this:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/misc/allplatforms/tksurfernew.tiff

-Krish
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[Freesurfer] Export table of cluster stats from Qdec

[Jeni Chen]

Hi,

I have 2 questions regarding Qdec:

1. We would like to save the results of  'cluster stats' (the printout on the 
terminal after pressing the "Find clusters and go to max" button) to a text 
file. Is there a way to do that? Or is it automatically saved in somewhere and 
where would that location be?
2. Also, would it be possible to save the plot information at cluster's max in 
a particular region and later on read them in a text or excel file?

Thank you for your help.

Jeni
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Re: [Freesurfer] analysis interpretion question

[Bruce Fischl]

Hi Ilana

have you visually inspected the asegs? I would make sure that there are 
no systematic and/or biased segmentation results in which the 
putamen/insula are misassigned so that one is "stealing" from the other.

Bruce


On Wed, 25 May 2011, Ilana Hairston wrote:

> Hi there,
> I have two behavioural variables that are inversely related to each other. 
> One was correlated with thinning of the posterior insula (using glm_mri), 
> while the other is positively correlated with the putamen volume (extracting 
> aseg tables and running in SPSS).
> The region of the insula is basically adjacent to the putamen. So i'm 
> wondering whether these findings are related, and how would i go about 
> teasing this apart.
> Thanks
> ilana
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[Freesurfer] analysis interpretion question

[Ilana Hairston]

Hi there,
I have two behavioural variables that are inversely related to each other. One 
was correlated with thinning of the posterior insula (using glm_mri), while the 
other is positively correlated with the putamen volume (extracting aseg tables 
and running in SPSS). 
The region of the insula is basically adjacent to the putamen. So i'm wondering 
whether these findings are related, and how would i go about teasing this apart.
Thanks
ilana
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Re: [Freesurfer] rtview and color bar

[Douglas N Greve]

Can you send a picture?

Michelle Umali wrote:
> Hi Freesurfers!
> I ran rtview, and I couldn't find a color bar/legend.  I'm just  
> wondering how thow the colors get assigned.  Is each color a position  
> of wedge stimulus?
>
> I'm trying to define V1/V2/V3 boundaries and was wondering how to get  
> the  horizontal and vertical meridians.
>
>
> Any help would be most welcome.
>
> Thanks.
> Michelle
>
>
>
>
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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

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[Freesurfer] rtview and color bar

[Michelle Umali]

Hi Freesurfers!
I ran rtview, and I couldn't find a color bar/legend.  I'm just  
wondering how thow the colors get assigned.  Is each color a position  
of wedge stimulus?

I'm trying to define V1/V2/V3 boundaries and was wondering how to get  
the  horizontal and vertical meridians.


Any help would be most welcome.

Thanks.
Michelle




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Re: [Freesurfer] Freesurfer GLM and measurement of an interaction

[Douglas N Greve]

Hi Chris,

It is a t-test. In the case of one variate (a single row to the contrast 
matrix), an F-test is the same as an unsigned t-test.

doug

Chris Hyatt wrote:
> For a two factor GLM analysis with two levels, I'm uncertain as to why 
> the Freesurfer GLM measurement of the interaction effect of say, group 
> and gender, is a t-test and not an F-test. In my case, my factors are 
> group (healthies vs patients) and gender (male vs female). For a 2x2 
> two-way ANOVA analysis, the measurement of an interaction is always an 
> F-test.
>
> For example, on the following Freesurfer FSGD Wiki page (*Four Groups 
> (Two Factors/Two Levels), No Covariates)*
> http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G0V
> under Contrast 7, it claims the gender-x-handedness is a t-test.
>
> Is this contrast a t-test or actually an F-test?
>
> Thanks,
> Chris
> 
>
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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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Re: [Freesurfer] FS5.1 OSX: message during the first step : dyld: library not loaded

[Krish Subramaniam]

Hi,

And Mac users should wait for this instead of my suggested temporary  
fix earlier today.

Thanks,
-Krish

On May 25, 2011, at 2:57 PM, Nick Schmansky wrote:

> Hyunwoo (and Mac users),
>
> We're going to have to post a new build of v5.1 later today which  
> fixes
> this problem.  In general, our goal is to have a Mac build that doesnt
> require special libraries, like libgfortran, but both our build and  
> test
> machines had that lib for other reasons, so it slipped through the
> cracks during testing.
>
> I'll post to the list when its ready.  It will be identical in usage  
> to
> the current Mac 5.1, just without the libgfortran dynamic lib
> dependency.
>
> Nick
>
>
> On Wed, 2011-05-25 at 16:30 +, Hyunwoo Lee wrote:
>> Dear FreeSurfer
>>
>> Hello, I am currently trying the following freesurfer version:  
>> freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0>  
>> >
>> and I noticed the following.
>> During the first step ( recon-all -i invol1  -i invol2 -subjid  
>> your_subject_name ), the console displays the following messages:
>> ---
>> Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
>> Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
>> INFO: SUBJECTS_DIR is ***
>> Actual FREESURFER_HOME /Applications/freesurfer
>> Darwin mrs.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29  
>> 15:17:16 PST 2011; root:xnu-1504.9.37~1/RELEASE_I386 i386
>> dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib
>> Referenced from: /Applications/freesurfer/bin/mri_robust_register
>> Reason: image not found
>> Trace/BPT trap
>> dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib
>> Referenced from: /Applications/freesurfer/bin/mri_robust_register
>> Reason: image not found
>> Trace/BPT trap
>> -
>>
>> I confirmed that the above message does not appear on the linux  
>> version of FS5.1.
>>
>> So, I was wondering if the above situation will cause any problem  
>> down the pipeline? I just kept it running for ~18 hours and it  
>> seems to be going fine (i.e. at least no problem until the  
>> "mris_ca_label" step)
>>
>> Thank you very much, and I look forward to hearing from you.
>>
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>>
>
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Re: [Freesurfer] FS5.1 OSX: message during the first step : dyld: library not loaded

[Nick Schmansky]

Hyunwoo (and Mac users),

We're going to have to post a new build of v5.1 later today which fixes
this problem.  In general, our goal is to have a Mac build that doesnt
require special libraries, like libgfortran, but both our build and test
machines had that lib for other reasons, so it slipped through the
cracks during testing. 

I'll post to the list when its ready.  It will be identical in usage to
the current Mac 5.1, just without the libgfortran dynamic lib
dependency.

Nick


On Wed, 2011-05-25 at 16:30 +, Hyunwoo Lee wrote:
> Dear FreeSurfer
> 
> Hello, I am currently trying the following freesurfer version: 
> freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> and I noticed the following.
> During the first step ( recon-all -i invol1  -i invol2 -subjid 
> your_subject_name ), the console displays the following messages:
> ---
> Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> INFO: SUBJECTS_DIR is ***
> Actual FREESURFER_HOME /Applications/freesurfer
> Darwin mrs.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:17:16 PST 
> 2011; root:xnu-1504.9.37~1/RELEASE_I386 i386
> dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib
> Referenced from: /Applications/freesurfer/bin/mri_robust_register
> Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib
> Referenced from: /Applications/freesurfer/bin/mri_robust_register
> Reason: image not found
> Trace/BPT trap
> -
> 
> I confirmed that the above message does not appear on the linux version of 
> FS5.1.
> 
> So, I was wondering if the above situation will cause any problem down the 
> pipeline? I just kept it running for ~18 hours and it seems to be going fine 
> (i.e. at least no problem until the "mris_ca_label" step)
> 
> Thank you very much, and I look forward to hearing from you.
> 
> ___
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> 
> 

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[Freesurfer] Freesurfer GLM and measurement of an interaction

[Chris Hyatt]

For a two factor GLM analysis with two levels, I'm uncertain as to why the 
Freesurfer GLM measurement of the interaction effect of say, group and gender, 
is a t-test and not an F-test. In my case, my factors are group (healthies vs 
patients) and gender (male vs female). For a 2x2 two-way ANOVA analysis, the 
measurement of an interaction is always an F-test. 

For example, on the following Freesurfer FSGD Wiki page (Four Groups (Two 
Factors/Two Levels), No Covariates)
http://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G0V
under Contrast 7, it claims the gender-x-handedness is a t-test.

Is this contrast a t-test or actually an F-test?

Thanks,
Chris

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[Freesurfer] Stats for HC and lobar volumes in template space

[caoaize]

Hello,
 
We are thinking about the hippocampal and lobar volumes in FS template space, 
do we have such stats? Thanks.
 
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[Freesurfer] job opportunity

[Paige Scalf]

Beginning August 15th, a two-year position is available for a highly
motivated and talented postdoctoral fellow in the Department of
Psychology at the University of Arizona.

The goal of this research program is to study the neural processes
that support vision, perception and attention using functional
neuoimaging (including ultra high resolution and time resolved fMRI)
and behavioral (including eye-tracking) methods. Candidates will be
expected to support the research goals of the PI, but will also be
given the opportunity to develop more independent lines of research.

The candidate will be encouraged to take advantage of the highly
collaborative departmental environment. The Department of Psychology
is part of the School of Mind, Brain, and Behavior (MBB), and is a
member of the College of Science, in keeping with its strong
research-oriented approach and scientifically-derived knowledge base.
Its faculty and students interact and collaborate with those of other
MBB programs and departments—Neuroscience, Cognitive Science, and
Speech, Language and Hearing Science—as well as with other academic
units across campus. The fMRI facilities at the University of Arizona
includes a GE 3.0T Signa scanner that is fully available for research
use 5 days per week.

The University of Arizona is a premier (NSF ranking: # 16) public
research university located in Tucson, Arizona. The sun shines nearly
every day in Tucson, which is surrounded by four mountain ranges that
include the southernmost downhill ski resort in the USA. Tucson also
supports great opportunities for hiking and cycling, and is one of the
most bicycle friendly cities in the US.

Candidates must have a PhD in neuroscience or a related field and the
capacity to make a substantive intellectual contribution to the
research program. Candidates with previous neuroimaging experience and
strong programming skills will will be preferred. Of particular
interest are those candidates with experience using python-based
programs such as the Vision Egg and SciPy. For more information,
contact Dr. Paige Scalf (psc...@gmail.com). Applications may be
submitted to job #47659 at http://www.uacareertrack.com.

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Re: [Freesurfer] FS5.1 OSX: message during the first step : dyld: library not loaded

[Krish Subramaniam]

Hi Hyunwoo

Our build system seems to pick up the dynamic gfortran libraries for  
OSX. We'll post a fixed mri_robust_register ( and similar binaries  
which depend on that dynamic library) soon.

For a temporary fix:

save 
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/krish/libgfortran.2.0.0.dylib
 
  to a path.. ( say ~/Downloads )

sudo mkdir -p /usr/local/lib

sudo cp ~/Downloads/libgfortran.2.0.0.dylib /usr/local/lib

cd /usr/local/lib

sudo ln -s libgfortran.2.0.0.dylib libgfortran.2.dylib

You need write permissions for /usr/local/lib . Let us know if it  
fixes this

-Krish


On May 25, 2011, at 12:30 PM, Hyunwoo Lee wrote:

> Dear FreeSurfer
>
> Hello, I am currently trying the following freesurfer version:  
> freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0  
> >
> and I noticed the following.
> During the first step ( recon-all -i invol1  -i invol2 -subjid  
> your_subject_name ), the console displays the following messages:
> ---
> Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> INFO: SUBJECTS_DIR is ***
> Actual FREESURFER_HOME /Applications/freesurfer
> Darwin mrs.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29  
> 15:17:16 PST 2011; root:xnu-1504.9.37~1/RELEASE_I386 i386
> dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib
> Referenced from: /Applications/freesurfer/bin/mri_robust_register
> Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib
> Referenced from: /Applications/freesurfer/bin/mri_robust_register
> Reason: image not found
> Trace/BPT trap
> -
>
> I confirmed that the above message does not appear on the linux  
> version of FS5.1.
>
> So, I was wondering if the above situation will cause any problem  
> down the pipeline? I just kept it running for ~18 hours and it seems  
> to be going fine (i.e. at least no problem until the "mris_ca_label"  
> step)
>
> Thank you very much, and I look forward to hearing from you.
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>

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Re: [Freesurfer] FS5.1 OSX: message during the first step : dyld: library not loaded

[Martin Reuter]

Hi,

I am not familiar with the mac build and think Krish can probably give more 
details. 
You are missing the libgfortran dynamic library. I don't think it is installed 
on the mac by default. On the mac we use the veclib framework, not sure why the 
error shows up and what consequences it has.

You can try registering two images with mri_robust_register (which is not used 
in recon-all). Recon-all might be influenced because mri_robust_template should 
show the same problems and that is used for motion correction of several inputs 
and in the longitudinal stream.

Best, Martin


On May 25, 2011, at 12:30 PM, Hyunwoo Lee wrote:

> Dear FreeSurfer
> 
> Hello, I am currently trying the following freesurfer version: 
> freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> and I noticed the following.
> During the first step ( recon-all -i invol1  -i invol2 -subjid 
> your_subject_name ), the console displays the following messages:
> ---
> Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
> INFO: SUBJECTS_DIR is ***
> Actual FREESURFER_HOME /Applications/freesurfer
> Darwin mrs.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:17:16 PST 
> 2011; root:xnu-1504.9.37~1/RELEASE_I386 i386
> dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib
> Referenced from: /Applications/freesurfer/bin/mri_robust_register
> Reason: image not found
> Trace/BPT trap
> dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib
> Referenced from: /Applications/freesurfer/bin/mri_robust_register
> Reason: image not found
> Trace/BPT trap
> -
> 
> I confirmed that the above message does not appear on the linux version of 
> FS5.1.
> 
> So, I was wondering if the above situation will cause any problem down the 
> pipeline? I just kept it running for ~18 hours and it seems to be going fine 
> (i.e. at least no problem until the "mris_ca_label" step)
> 
> Thank you very much, and I look forward to hearing from you.
> 
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
> 


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[Freesurfer] FS5.1 OSX: message during the first step : dyld: library not loaded

[Hyunwoo Lee]

Dear FreeSurfer

Hello, I am currently trying the following freesurfer version: 
freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
and I noticed the following.
During the first step ( recon-all -i invol1  -i invol2 -subjid 
your_subject_name ), the console displays the following messages:
---
Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0
INFO: SUBJECTS_DIR is ***
Actual FREESURFER_HOME /Applications/freesurfer
Darwin mrs.local 10.7.0 Darwin Kernel Version 10.7.0: Sat Jan 29 15:17:16 PST 
2011; root:xnu-1504.9.37~1/RELEASE_I386 i386
dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib
Referenced from: /Applications/freesurfer/bin/mri_robust_register
Reason: image not found
Trace/BPT trap
dyld: Library not loaded: /usr/local/lib/libgfortran.2.dylib
Referenced from: /Applications/freesurfer/bin/mri_robust_register
Reason: image not found
Trace/BPT trap
-

I confirmed that the above message does not appear on the linux version of 
FS5.1.

So, I was wondering if the above situation will cause any problem down the 
pipeline? I just kept it running for ~18 hours and it seems to be going fine 
(i.e. at least no problem until the "mris_ca_label" step)

Thank you very much, and I look forward to hearing from you.

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Re: [Freesurfer] flattened patch ascii file & matlab

[Cris Lanting]

Actually, it goes beyond visualisation. That works fine using
tksurfer; although, while we're at it: I'd like to use a different
colormap (say the jet colormap) but don't seem to be able to do so...
suggestions?.
I'd like to resample the activation maps and do some surface based
searchlight analysis.

Cris

On Wed, May 25, 2011 at 4:45 PM, Bruce Fischl
 wrote:
> Hi Cris,
>
> why not just visualize it in tksurfer instead?
>
> cheers
> Bruce
> On Wed, 25 May 2011, Cris Lanting wrote:
>
>> Dear all,
>>
>> I'm trying to read a flattened patch (ascii) using matlab but I'm
>> slightly confused:
>> after performing mris_flatten and
>> mris_convert -p rh.patch.flat rh.patch.flat.asc
>>
>> I get the following file:
>>
>> #!ascii version of patch ./rh.orig. The 1st index is not a vertex number
>> 12755 25052
>> -46888 vno=46887
>> -47.306606  -24.583883  0.00
>> -46894 vno=46893
>> -44.649334  -26.691339  0.00
>> ...
>> 94637
>> 48206 48190 46887
>> 94661
>> 48221 48205 46896
>>
>> And based on the read_patch script (freesurfer_dir/matlab) I'm able to
>> extract the vertices and faces.
>> vertices_flatmap:
>> -47.3066  -24.5839         0
>> -44.6493  -26.6913         0
>> -45.1151  -25.9817         0
>> ...
>> &
>> faces_flatmap
>>  48206       48190       46887
>>  48221       48205       46896
>>  46893       48218       48219
>> ...
>>
>> Yet, if I call
>>
>> Hpa = patch('vertices',vert_flat,'faces',face_flat,...
>>    'EdgeColor',edgecolor,'FaceColor',facecolor);
>>
>> it comes up with an error: Warning: Values in patch Faces must be in
>> [1 : rows(Vertices)] - not rendering.
>> I suppose this relates to the fact that it is a subset of the actual
>> complete surface and that it therefore does not start with index 1
>> (but 48206 instead). Any suggestions how to proceed from here?
>> In the end, I'd like to visualise an overlay (saved as .w file) onto
>> the flattened patch instead of on the inflated surface.
>>
>> Kind regards and thanks in advance,
>> Cris Lanting
>> ___
>> 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
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> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
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Re: [Freesurfer] flattened patch ascii file & matlab

[Bruce Fischl]

Hi Cris,

why not just visualize it in tksurfer instead?

cheers
Bruce
On Wed, 25 May 2011, Cris 
Lanting wrote:

> Dear all,
>
> I'm trying to read a flattened patch (ascii) using matlab but I'm
> slightly confused:
> after performing mris_flatten and
> mris_convert -p rh.patch.flat rh.patch.flat.asc
>
> I get the following file:
>
> #!ascii version of patch ./rh.orig. The 1st index is not a vertex number
> 12755 25052
> -46888 vno=46887
> -47.306606  -24.583883  0.00
> -46894 vno=46893
> -44.649334  -26.691339  0.00
> ...
> 94637
> 48206 48190 46887
> 94661
> 48221 48205 46896
>
> And based on the read_patch script (freesurfer_dir/matlab) I'm able to
> extract the vertices and faces.
> vertices_flatmap:
> -47.3066  -24.5839 0
> -44.6493  -26.6913 0
> -45.1151  -25.9817 0
> ...
> &
> faces_flatmap
>  48206   48190   46887
>  48221   48205   46896
>  46893   48218   48219
> ...
>
> Yet, if I call
>
> Hpa = patch('vertices',vert_flat,'faces',face_flat,...
> 'EdgeColor',edgecolor,'FaceColor',facecolor);
>
> it comes up with an error: Warning: Values in patch Faces must be in
> [1 : rows(Vertices)] - not rendering.
> I suppose this relates to the fact that it is a subset of the actual
> complete surface and that it therefore does not start with index 1
> (but 48206 instead). Any suggestions how to proceed from here?
> In the end, I'd like to visualise an overlay (saved as .w file) onto
> the flattened patch instead of on the inflated surface.
>
> Kind regards and thanks in advance,
> Cris Lanting
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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[Freesurfer] flattened patch ascii file & matlab

[Cris Lanting]

Dear all,

I'm trying to read a flattened patch (ascii) using matlab but I'm
slightly confused:
after performing mris_flatten and
mris_convert -p rh.patch.flat rh.patch.flat.asc

I get the following file:

#!ascii version of patch ./rh.orig. The 1st index is not a vertex number
12755 25052
-46888 vno=46887
-47.306606  -24.583883  0.00
-46894 vno=46893
-44.649334  -26.691339  0.00
...
94637
48206 48190 46887
94661
48221 48205 46896

And based on the read_patch script (freesurfer_dir/matlab) I'm able to
extract the vertices and faces.
vertices_flatmap:
 -47.3066  -24.5839 0
 -44.6493  -26.6913 0
 -45.1151  -25.9817 0
...
&
faces_flatmap
  48206   48190   46887
  48221   48205   46896
  46893   48218   48219
...

Yet, if I call

Hpa = patch('vertices',vert_flat,'faces',face_flat,...
 'EdgeColor',edgecolor,'FaceColor',facecolor);

it comes up with an error: Warning: Values in patch Faces must be in
[1 : rows(Vertices)] - not rendering.
I suppose this relates to the fact that it is a subset of the actual
complete surface and that it therefore does not start with index 1
(but 48206 instead). Any suggestions how to proceed from here?
In the end, I'd like to visualise an overlay (saved as .w file) onto
the flattened patch instead of on the inflated surface.

Kind regards and thanks in advance,
Cris Lanting
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Re: [Freesurfer] Error compiling freesurfer

[Jordi Delgado]

The lXmu libraries are installed on my system.

Now the error is:

Making all in mri_em_register
make[2]: Entering directory `/tmp/dev/mri_em_register'
/bin/sh ../libtool --tag=CC   --mode=link g++ -I../include
-I../include/dicom  -I/usr/local/cuda/include -DFS_CUDA
-L/tmp/packages/mni/current/lib -L/tmp/packages/vxl/current/lib-o
mri_em_register_cuda   mri_em_register_cuda-mri_em_register.o
em_register_cuda.o ../utils/libutils_cuda.a ../rgb/librgb.a
../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a
../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a
../expat/libexpat.a -L/usr/local/cuda/lib -lcuda -lcudart -lz -lm -lcrypt
-ldl -lpthread -lnetcdf -lvolume_io -lminc -lvnl_algo -lvnl -lvcl
-lnetlib -lv3p_netlib
libtool: link: warning: library `/tmp/packages/mni/current/lib/
libvolume_io.la' was moved.
libtool: link: warning: library `/tmp/packages/mni/current/lib/libminc.la'
was moved.
libtool: link: warning: library `/tmp/packages/mni/current/lib/
libvolume_io.la' was moved.
libtool: link: warning: library `/tmp/packages/mni/current/lib/libminc.la'
was moved.
g++ -I../include -I../include/dicom -I/usr/local/cuda/include -DFS_CUDA -o
mri_em_register_cuda mri_em_register_cuda-mri_em_register.o
em_register_cuda.o  -L/tmp/packages/mni/current/lib
-L/tmp/packages/vxl/current/lib ../utils/libutils_cuda.a ../rgb/librgb.a
../unix/libunix.a ../dicom/libdicom.a ../hipsstubs/libhipsstubs.a
../log/liblog.a ../xml2/libxml2.a ../jpeg/libjpeg.a ../tiff/libtiff.a
../expat/libexpat.a -L/usr/local/cuda/lib -lcuda -lcudart -lz -lcrypt -ldl
-lpthread /tmp/packages/mni/current/lib/libvolume_io.a
-L/usr/pubsw/packages/mni/current/lib
/tmp/packages/mni/current/lib/libminc.a -lnetcdf -lm -lvnl_algo -lvnl -lvcl
-lnetlib -lv3p_netlib
/usr/bin/ld: Warning: size of symbol `min' changed from 37 in
em_register_cuda.o to 8 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `umin' changed from 37 in
em_register_cuda.o to 8 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `llmin' changed from 46 in
em_register_cuda.o to 11 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `ullmin' changed from 46 in
em_register_cuda.o to 11 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `max' changed from 37 in
em_register_cuda.o to 8 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `umax' changed from 37 in
em_register_cuda.o to 8 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `llmax' changed from 46 in
em_register_cuda.o to 11 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `ullmax' changed from 46 in
em_register_cuda.o to 11 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `rsqrt' changed from 67 in
em_register_cuda.o to 42 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `rsqrtf' changed from 45 in
em_register_cuda.o to 22 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `erfinv' changed from 2130 in
em_register_cuda.o to 926 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `erfinvf' changed from 45 in
em_register_cuda.o to 22 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `erfcinv' changed from 1636 in
em_register_cuda.o to 805 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `erfcinvf' changed from 45 in
em_register_cuda.o to 22 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `sinpi' changed from 402 in
em_register_cuda.o to 260 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `sinpif' changed from 45 in
em_register_cuda.o to 22 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `rcbrt' changed from 352 in
em_register_cuda.o to 220 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: Warning: size of symbol `rcbrtf' changed from 45 in
em_register_cuda.o to 22 in ../utils/libutils_cuda.a(mriframegpu.o)
/usr/bin/ld: warning: i386:x86-64 architecture of input file
`em_register_cuda.o' is incompatible with i386 output
*/usr/bin/ld: warning: i386:x86-64 architecture of input file
`../utils/libutils_cuda.a(libutils_cuda_a-polevl.o)' is incompatible with
i386 output
/usr/bin/ld: warning: i386:x86-64 architecture of input file
`../utils/libutils_cuda.a(mriframegpu.o)' is incompatible with i386 output
/usr/bin/ld: warning: i386:x86-64 architecture of input file
`../utils/libutils_cuda.a(devicemanagement.o)' is incompatible with i386
output
/usr/bin/ld: warning: i386:x86-64 architecture of input file
`../utils/libutils_cuda.a(gcamorphenergygpu.o)' is incompatible with i386
output
/usr/bin/ld: warning: i386:x86-64 architecture of input file
`../utils/libutils_cuda.a(mrilabels_cuda.o)' is incompatible with i386
output
/usr/bin/l

Re: [Freesurfer] temporal pole label

[Bruce Fischl]

the easiest thing to do is to convert all the annotations to labels, then just 
use the temporal pole one. I don't think there is an option at the moment to 
only extract a single label, but Doug will correct me if I'm wrong :)

cheers
Bruce
On Wed, 25 May 2011 k...@rice.edu wrote:

> Dear Bruce,
> 
> Thanks for the prompt response again. With mri_annotation2label how do I 
> specify just the TP label vertices to export as a .label file? I'm assuming I 
> would use the hemisphere-specific annotation and label files but I'm not sure 
> how to do that.
> 
> Best,
> Kareem
> 
> Quoting Bruce Fischl :
> 
>> Hi Kareen,
>> 
>> I'll cc the list as others may be interested. You can use 
>> mri_annotation2label to extract the label you want. As for which to use, it 
>> depends what you want to do with it, but I would expect the individual 
>> labels are what you want since they are adjusted to account for individual 
>> variations in the anatomy.
>> 
>> cheers
>> Bruce
>> 
>> 
>> On Wed, 25 May 2011 k...@rice.edu wrote:
>> 
>>> Dear Bruce,
>>> 
>>> How can I access these temporal pole labels within each subject? For each 
>>> of these TP labels I would like a .label file -- how can I export a file in 
>>> this format for the R and L TPs? Furthermore, do you recommend the use of 
>>> this fsaverage subject that you have to apply to all our subjects?
>>> 
>>> Thank you very much for your help,
>>> Kareem
>>> 
>>> 
>>> Quoting Bruce Fischl :
>>> 
 Hi Kareem,
 
 both the annotations we automatically compute contain temporal pole 
 labels. Also, the average subject we provide (fsaverage) has both 
 parcellations, so you could just use one of them
 
 cheers
 Bruce
 
 
 On Wed, 25 May 2011 k...@rice.edu wrote:
 
> Hello,
> 
> I have a question about the labeling in tksurfer. My goal is to take
> an average inflated surface of 10 controls and then make a temporal
> pole label out of that average.
> 
> Alternatively, if FS provides a label for the TP for each patient I
> could average the labels together.
> 
> Do you have any idea how best to do this?
> 
> Thanks in advance.
> 
> Warm regards,
> Kareem
> 
> ___
> 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] temporal pole label

[Bruce Fischl]

Hi Kareen,

I'll cc the list as others may be interested. You can use mri_annotation2label 
to extract the label you want. As for which to use, it depends what you want to 
do with it, but I would expect the individual labels are what you want since 
they are adjusted to account for individual variations in the anatomy.

cheers
Bruce


On Wed, 25 May 2011 k...@rice.edu wrote:

> Dear Bruce,
> 
> How can I access these temporal pole labels within each subject? For each of 
> these TP labels I would like a .label file -- how can I export a file in this 
> format for the R and L TPs? Furthermore, do you recommend the use of this 
> fsaverage subject that you have to apply to all our subjects?
> 
> Thank you very much for your help,
> Kareem
> 
> 
> Quoting Bruce Fischl :
> 
>> Hi Kareem,
>> 
>> both the annotations we automatically compute contain temporal pole labels. 
>> Also, the average subject we provide (fsaverage) has both parcellations, so 
>> you could just use one of them
>> 
>> cheers
>> Bruce
>> 
>> 
>> On Wed, 25 May 2011 k...@rice.edu wrote:
>> 
>>> Hello,
>>> 
>>> I have a question about the labeling in tksurfer. My goal is to take
>>> an average inflated surface of 10 controls and then make a temporal
>>> pole label out of that average.
>>> 
>>> Alternatively, if FS provides a label for the TP for each patient I
>>> could average the labels together.
>>> 
>>> Do you have any idea how best to do this?
>>> 
>>> Thanks in advance.
>>> 
>>> Warm regards,
>>> Kareem
>>> 
>>> ___
>>> 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] new FreeSurfer release, v5.1

[Bruce Fischl]

glad to hear it. Let us know how it goes.

Bruce
On Wed, 25 May 2011, Alan Francis 
wrote:

> Hi Nick and Bruce:
>
> Congratulations and thanks for releasing FS 5.1. We have a longitudinal
> study of First Episode Schizophrenia that was awaiting this release.
>
> best,
>
> Alan Francis
> Beth Israel Deaconess Medical Center
>
> On Tue, May 24, 2011 at 4:28 PM, Nick Schmansky
> wrote:
>
>> FreeSurfer Users,
>>
>> The long anticipated, much awaited, release v5.1 of FreeSurfer is
>> finally here.  It's everything 5.0 should have been, and now much more!
>>
>> The ReleaseNotes page describes the new features and changes:
>>
>> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
>>
>> and the Download page will take you to the tarballs:
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>>
>> As always, we recommended not mixing results in a group study processed
>> with other versions or across OS platforms.  This new version can still
>> be used to view and post-process results, or to re-run recon-all (edits
>> are retained).
>>
>>
>> The FreeSurfer Team
>>
>>
>> ___
>> 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] new FreeSurfer release, v5.1

[Alan Francis]

Hi Nick and Bruce:

Congratulations and thanks for releasing FS 5.1. We have a longitudinal
study of First Episode Schizophrenia that was awaiting this release.

best,

Alan Francis
Beth Israel Deaconess Medical Center

On Tue, May 24, 2011 at 4:28 PM, Nick Schmansky
wrote:

> FreeSurfer Users,
>
> The long anticipated, much awaited, release v5.1 of FreeSurfer is
> finally here.  It's everything 5.0 should have been, and now much more!
>
> The ReleaseNotes page describes the new features and changes:
>
> http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes
>
> and the Download page will take you to the tarballs:
>
> https://surfer.nmr.mgh.harvard.edu/fswiki/Download
>
> As always, we recommended not mixing results in a group study processed
> with other versions or across OS platforms.  This new version can still
> be used to view and post-process results, or to re-run recon-all (edits
> are retained).
>
>
> The FreeSurfer Team
>
>
> ___
> 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] Error compiling freesurfer

[Yaroslav Halchenko]

lacking -lXmu
?

On Wed, 25 May 2011, Jordi Delgado wrote:
>../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a
>../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lGLU -lGL
>-L/usr/X11R6/lib -lX11  -lm  ../glut/libglut.a -lz -lm -lcrypt -ldl
>-lpthread -lnetcdf -lvolume_io -lminc -lvnl_algo -lvnl -lvcl
>-lnetlib -lv3p_netlib
>libtool: link: warning: library
>`/tmp/packages/mni/current/lib/[1]libvolume_io.la' was moved.
>libtool: link: warning: library
>`/tmp/packages/mni/current/lib/[2]libminc.la' was moved.
>libtool: link: warning: library
>`/tmp/packages/mni/current/lib/[3]libvolume_io.la' was moved.
>libtool: link: warning: library
>`/tmp/packages/mni/current/lib/[4]libminc.la' was moved.
>g++ -o mris_show mris_show.o  -L/tmp/packages/mni/current/lib
>-L/tmp/packages/vxl/current/lib -L/usr/X11R6/lib ../utils/libutils.a
>../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a
>../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a
>../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lGLU
>/usr/lib/libGL.so -lXext -lX11 ../glut/libglut.a -lz -lcrypt -ldl
>-lpthread /tmp/packages/mni/current/lib/libvolume_io.a
>-L/usr/pubsw/packages/mni/current/lib
>/tmp/packages/mni/current/lib/libminc.a -lnetcdf -lm -lvnl_algo -lvnl
>-lvcl -lnetlib -lv3p_netlib
>/usr/bin/ld: warning: i386:x86-64 architecture of input file
>`../utils/libutils.a(pgmstubs.o)' is incompatible with i386 output
>../glut/libglut.a(glut_cmap.o): In function `__glutSetupColormap':
>/tmp/dev/glut/glut_cmap.c:253: undefined reference to
>`XmuLookupStandardColormap'
-- 
Yaroslav O. Halchenko
Postdoctoral Fellow,   Department of Psychological and Brain Sciences
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834   Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik
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Re: [Freesurfer] FS5.1 for CentOS4 works for CentOS5-like OS?

[Pedro Paulo de Magalhães Oliveira Junior]

Yes. It works

-- iOS 4.3

Em 25/05/2011, às 10:14, Xinian Zuo  escreveu:

> Dear FS team, Only see new 5.1 version for CentOS4 in the website. Thanks, XN.
>
> --
> Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn)
> ___
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>
>
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
>

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Re: [Freesurfer] temporal pole label

[Bruce Fischl]

Hi Kareem,

both the annotations we automatically compute contain temporal pole 
labels. Also, the average subject we provide (fsaverage) has both 
parcellations, so you could just use one of them

cheers
Bruce


On Wed, 25 May 2011 k...@rice.edu wrote:

> Hello,
>
> I have a question about the labeling in tksurfer. My goal is to take
> an average inflated surface of 10 controls and then make a temporal
> pole label out of that average.
>
> Alternatively, if FS provides a label for the TP for each patient I
> could average the labels together.
>
> Do you have any idea how best to do this?
>
> Thanks in advance.
>
> Warm regards,
> Kareem
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
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[Freesurfer] FS5.1 for CentOS4 works for CentOS5-like OS?

[Xinian Zuo]

Dear FS team, Only see new 5.1 version for CentOS4 in the website. Thanks, XN.

-- 
Xi-Nian Zuo, Ph.D of Applied Mathematics (http://lfcd.psych.ac.cn)
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[Freesurfer] Error compiling freesurfer

[Jordi Delgado]

Hi Freesurfers,

I've downloaded FS from CVS, and I have Cent OS 5.5 (32 bits)

I've done:

./configure --prefix="/tmp/freesurfer"
--with-mni-dir="/tmp/packages/mni/current"
--with-tcl-dir="/tmp/packages/tcltktixblt/current"
--with-vtk-dir="/tmp/packages/vtk/current"
--with-vxl-dir="/tmp/packages/vxl/current" --enable-fermi-gpu

make -j 9

Then the process throws this error:

make[2]: Leaving directory `/tmp/dev/nmovie'
Making all in mris_show
make[2]: Entering directory `/tmp/dev/mris_show'
/bin/sh ../libtool --tag=CC --mode=link g++
-L/tmp/packages/mni/current/lib -L/tmp/packages/vxl/current/lib-o
mris_show -L/usr/X11R6/lib -lX11 mris_show.o ../utils/libutils.a
../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a
../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a
../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lGLU -lGL
-L/usr/X11R6/lib -lX11  -lm  ../glut/libglut.a -lz -lm -lcrypt -ldl
-lpthread -lnetcdf -lvolume_io -lminc -lvnl_algo -lvnl -lvcl -lnetlib
-lv3p_netlib
libtool: link: warning: library `/tmp/packages/mni/current/lib/
libvolume_io.la' was moved.
libtool: link: warning: library `/tmp/packages/mni/current/lib/libminc.la'
was moved.
libtool: link: warning: library `/tmp/packages/mni/current/lib/
libvolume_io.la' was moved.
libtool: link: warning: library `/tmp/packages/mni/current/lib/libminc.la'
was moved.
g++ -o mris_show mris_show.o  -L/tmp/packages/mni/current/lib
-L/tmp/packages/vxl/current/lib -L/usr/X11R6/lib ../utils/libutils.a
../rgb/librgb.a ../unix/libunix.a ../dicom/libdicom.a
../hipsstubs/libhipsstubs.a ../log/liblog.a ../xml2/libxml2.a
../jpeg/libjpeg.a ../tiff/libtiff.a ../expat/libexpat.a -lGLU
/usr/lib/libGL.so -lXext -lX11 ../glut/libglut.a -lz -lcrypt -ldl -lpthread
/tmp/packages/mni/current/lib/libvolume_io.a
-L/usr/pubsw/packages/mni/current/lib
/tmp/packages/mni/current/lib/libminc.a -lnetcdf -lm -lvnl_algo -lvnl -lvcl
-lnetlib -lv3p_netlib
/usr/bin/ld: warning: i386:x86-64 architecture of input file
`../utils/libutils.a(pgmstubs.o)' is incompatible with i386 output
../glut/libglut.a(glut_cmap.o): In function `__glutSetupColormap':
/tmp/dev/glut/glut_cmap.c:253: undefined reference to
`XmuLookupStandardColormap'
collect2: ld returned 1 exit status
make[2]: *** [mris_show] Error 1
make[2]: Leaving directory `/tmp/dev/mris_show'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/tmp/dev'
make: *** [all] Error 2


Any idea?

Thank you!
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[Freesurfer] temporal pole label

[kwa1]

Hello,

I have a question about the labeling in tksurfer. My goal is to take  
an average inflated surface of 10 controls and then make a temporal  
pole label out of that average.

Alternatively, if FS provides a label for the TP for each patient I  
could average the labels together.

Do you have any idea how best to do this?

Thanks in advance.

Warm regards,
Kareem

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Re: [Freesurfer] Error from cudadetect

[Pedro Paulo de Magalhães Oliveira Junior]

5.1 was released yesterday

-- iOS 4.3

Em 25/05/2011, às 09:42, R Edgar  escreveu:

> On Wed, May 25, 2011 at 7:59 AM, Howison, Mark  wrote:
>
>> We have installed Freesurfer 5.0.0 (CentOS x86_64) on our compute
>> cluster at Brown and are seeing the following error when running
>> 'cudadetect':
>>
>> ERROR: cuda driver does not appear to be installed!
>> Detecting CUDA... There are 2 devices supporting CUDA:
>> Device 0: "Tesla M2050"
>> CUDA Driver Version: 3.20
>> (etc.)
>
> Did you do a binary install, or compile from source? If the former,
> then it might be a problem with us using a different version of CUDA
> at the time of compilation. Things are supposed to work, but we've
> seen a lot of problems like this.
>
> I believe that 5.1 is about to be released, which should be compiled
> against the driver/library you're using. Otherwise, the best solution
> might be to get the source, and compile directly from that.
>
> Richard
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>
>
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> at
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Re: [Freesurfer] Error from cudadetect

[R Edgar]

On Wed, May 25, 2011 at 7:59 AM, Howison, Mark  wrote:

> We have installed Freesurfer 5.0.0 (CentOS x86_64) on our compute
> cluster at Brown and are seeing the following error when running
> 'cudadetect':
>
> ERROR: cuda driver does not appear to be installed!
> Detecting CUDA... There are 2 devices supporting CUDA:
> Device 0: "Tesla M2050"
> CUDA Driver Version: 3.20
> (etc.)

Did you do a binary install, or compile from source? If the former,
then it might be a problem with us using a different version of CUDA
at the time of compilation. Things are supposed to work, but we've
seen a lot of problems like this.

I believe that 5.1 is about to be released, which should be compiled
against the driver/library you're using. Otherwise, the best solution
might be to get the source, and compile directly from that.

Richard
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Re: [Freesurfer] overlay properties tksurfer window incomplete...

[Ilana Hairston]

i had a similar problem with my macbook (i think), and was told to use spacebar 
in lieu of enter.  


On 23 May 2011, at 01:04, Gonzalo Rojas Costa wrote:

> Hi:
> 
>   I have an ubuntu based computer with Freesurfer 5, and it seems that 
> because the font size or the screen resolution, the lowest part of the 
> "Overlay Properties" window in tksurfer didn't appears (Ok and Cancel 
> buttons, for example, etc)... Any solution ?...
> 
>   Sincerely,
> 
> 
> 
> Gonzalo Rojas Costa
> Laboratory for Advanced Medical Image Processing
> Department of Radiology
> Las Condes Clinic
> Lo Fontecilla 441, Las Condes, Santiago, Chile.
> Tel: 56-2-2105170
> Cel: 56-9-97771785
> www.clc.cl
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> 
> 
> The information in this e-mail is intended only for the person to whom it is
> addressed. If you believe this e-mail was sent to you in error and the e-mail
> contains patient information, please contact the Partners Compliance HelpLine 
> at
> http://www.partners.org/complianceline . If the e-mail was sent to you in 
> error
> but does not contain patient information, please contact the sender and 
> properly
> dispose of the e-mail.
> 


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[Freesurfer] Error from cudadetect

[Howison, Mark]

Dear Freesurfer developers,

We have installed Freesurfer 5.0.0 (CentOS x86_64) on our compute
cluster at Brown and are seeing the following error when running
'cudadetect':

ERROR: cuda driver does not appear to be installed!
Detecting CUDA... There are 2 devices supporting CUDA:
Device 0: "Tesla M2050"
CUDA Driver Version: 3.20
(etc.)

However, the NVIDIA driver is installed and other CUDA programs
function correctly:

[mhowison@gpu001 ~]$ nvidia-smi

==NVSMI LOG==


Timestamp : Fri May 13 10:19:48 2011

Driver Version : 260.19.29


You can see our hardware specs here:

http://www.brown.edu/Departments/CCV/doc/techspecs

And output from bugr is:

-

FREESURFER_HOME: /gpfs/runtime/opt/freesurfer/5.0.0

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0

RedHat release: CentOS release 5.4 (Final)

Kernel info: Linux 2.6.18-164.el5 x86_64

-

We are using CentOS 5.4 and CUDA 3.2.16. Any ideas why Freesurfer
cannot use our GPUs?

Thanks,

Mark Howison
Application Scientist
Center for Computation & Visualization
Brown University
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Re: [Freesurfer] qdec error message

[Nick Schmansky]

what version of freesurfer does this happen with?

n.
On Wed, 2011-05-25 at 14:17 +1000, Olivier Piguet wrote:
> Good afternoon, 
> 
> When running qdec, I receive the following error message:
> 
> Writing to 
> /Volumes/workingdata/FTD/T1/subjects/qdec/Untitled/contrasts.sig.mgh
> reading group avg surface area 822 cm^2 from file
> ERROR: could not find volume 
> /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig.  Does it 
> exist?
> Reading in average area 
> /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/lh.white.avg.area.mgh
> reading group avg surface area 1041 cm^2 from file
> ERROR: could not find volume 
> /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig.  Does it 
> exist?
> Reading in average area 
> /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/lh.pial.avg.area.mgh
> reading group avg surface area 822 cm^2 from file
> ERROR: could not find volume 
> /Volumes/workingdata/FTD/T1/subjects/fsaverage/surf/../mri/orig.  Does it 
> exist?
> 
> I have run all subjects with qcache and I am using fsaverage. I have checked 
> the files in the fsaverage folder. Although the file orig. does not exist, 
> there is a file called orig.mgz in the mri folder. I have tried to rename 
> this file (i.e., removing the 'mgz' part) but this did not remove the error. 
> 
> Any suggestion would be appreciated. 
> 
> Thanks
> 
> Olivier Piguet
> Neuroscience Research Australia
> Sydney NSW, Australia
> 
> 
> 
> 
> 
> 
> 
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> 

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