[Freesurfer] Postdoctoral Research Scholar Position in Neuroimaging and Behavior Genetic

[Don Hagler]

The Department of Psychiatry at the University of California, San Diego is 
pleased to invite applications for a postdoctoral research scholar position in 
neuroimaging and behavior genetics under the direction of Drs. William Kremen 
(Psychiatry) and Anders Dale (Radiology and Neuroscience).  The position 
focuses on training in the application of sophisticated neuroimaging methods 
(structural MRI, DTI, fMRI, and ASL) and associated studies that will be 
applied to the NIH/NIA-funded Vietnam Era Twin Study of Aging (VETSA).  VETSA 
is a unique longitudinal study of middle-aged male twins that focuses on 
understanding cognitive and brain aging.  Over 500 twins have undergone 
neuroimaging and extensive neurocognitive assessment, personality and 
psychosocial measures, a medical history interview, in-lab physical health 
measures, and hormonal assays.  Genome-wide genotyping of all participants is 
currently underway. Wave 3 of the project, which was recently funded, will 
acquire new longitudinal and neuroimaging data. 
 
Applications from many disciplines may be considered, and the position is open 
to qualified international applicants.  Requirements for the position are: 1) 
completion of relevant Ph.D. research activities within the past five years; 2) 
advanced neuroimaging and programming skills, 3) statistical knowledge, 4) 
evidence of writing skills, and 5) an interest in imaging genetics research.  
Experience with multilevel data analysis and/or genetics is desirable.  The 
postdoctoral candidate will be encouraged to develop his or her own research 
projects that fit within the overall scope of the VETSA project.  The position 
will entail immersion in MR image analysis and opportunities to learn about 
twin modeling.  Experience with FreeSurfer and/or other neuroimaging software, 
R, and MATLAB is strongly preferred.
This advertisement is for a 2-year appointment beginning immediately.  Salary 
will be consistent with the NIH/NRSA levels in accordance with the University 
of California, San Diego for Postdoctoral trainees.  Compensation includes UCSD 
benefits, including health insurance and vacation time.  Review of applications 
will begin immediately and will continue until the position is filled.  As an 
Equal Opportunity/Affirmative Action Employer, the UCSD Department of 
Psychiatry seeks to recruit and retain a diverse workforce as a reflection of 
our strong commitment to the twin goals of achievement of excellence and 
diversity among its faculty and staff. We are thus interested in candidates who 
are committed to the highest standards of scholarship and professional 
activities, and to the development of a climate that supports equality and 
diversity.


To apply, please send a copy of your CV, a brief statement of research 
interests and goals, and any selected reprints to the email addresses below.  
Letters of reference will be required before final approval of hiring.  
Informal inquiries concerning this position are encouraged.  

Please e-mail Dr. Anders Dale (amd...@ucsd.edu) and Dr. William Kremen 
(wkre...@ucsd.edu) for more details.


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[Freesurfer] Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study

[Don Hagler]

Postdoc Positions for the Adolescent Brain Cognitive Development (ABCD) study

 

University of California, San Diego

 

Several funded postdoctoral positions are available in image analysis method 
development, including automated cortical- and subcortical segmentation, 
advanced diffusion tractography, and fMRI mapping and time series analysis. We 
are looking to build a team to help build the next generation of analysis 
pipelines and visualization tools for a newly funded study to follow 10,000 
children with longitudinal structural and functional imaging across 19 sites 
across the US. The study will use a cross-platform Harmonized Human Connectome 
Protocol, optimized for quantitative accuracy and consistency of imaging 
biomarkers across scanners and time. To learn more about the ABCD study, please 
see 
http://www.drugabuse.gov/news-events/news-releases/2015/09/nih-launches-landmark-study-substance-use-adolescent-brain-development
 
.

 

Requirements: Applicants should have research experience in any of the above 
fields, with a Ph.D. or equivalent degree. They should be comfortable working 
in a distributed team environment, and should have a track record of quality 
scientific publications. Candidates are expected to be experienced in 
programming with Matlab, Python, and/or <> C/C++. Experience with FreeSurfer, 
FSL, and the Human Connectome analysis pipelines is strongly preferred.

 

To formally apply, submit a current CV, a personal statement describing your 
research experience and interests, and contact information for 2-3 references 
to a...@ucsd.edu . Or feel free to email Dr. Donald 
Hagler (dhag...@ucsd.edu ) or Anders M. Dale 
(amd...@ucsd.edu ) for more information.

 

The University of California, San Diego is an Equal Opportunity/Affirmative 
Action Employer advancing inclusive excellence. All qualified applicants will 
receive consideration for employment without regard to race, color, religion, 
sex, sexual orientation, gender identity, national origin, disability, age, 
protected veteran status, or other protected categories covered by the UC 
nondiscrimination policy.___
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Re: [Freesurfer] write dipoles function

[Don Hagler]

Hi Bruce and Amy,

I think that menu command actually outputs a binary file, which I would give a 
.dip extension. Some matlab code for reading one is included below.

Don


function dipole_info=ts_read_dip_file(dip_file)
% ts_read_dip_file.m:   read dipole file for calculating forward solution
%
% dipole_info=ts_read_dip_file(dip_file)
%
% read freesurfer dip file for the location and orientation of the dipoles
% returns dipole_info containing x,y,z location and nx,ny,nz normal vector
%
% created:05/07/05 by Mingxiong Huang as read_dipdec.m
% early mod:  11/27/05 by Don Hagler as read_dip_file.m
% last mod:   08/01/06 by Don Hagler
%

dipole_info = [];

% make sure file exists
[status,message,messageid]=fileattrib(dip_file);
if (status==0)
  fprintf('%s: file %s not found... quitting\n',mfilename,dip_file);
  return;
end

% read dip file to get the location of the dipole
fprintf('ts_read_dip_file: reading file %s...\n',dip_file);
fp=fopen(dip_file,'r','ieee-be.l64');
[ch]=fread(fp,1,'uchar');
[n_dipole]=fread(fp,1,'int32');
dipole_info=fread(fp,[6,n_dipole],'float');
fclose(fp);

fprintf('%s: %d dipoles\n',mfilename,n_dipole);




> Date: Wed, 25 Jan 2012 17:35:22 -0500
> From: fis...@nmr.mgh.harvard.edu
> To: aguth...@lanl.gov
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] write dipoles function
> 
> Hi Amy
> 
> hmmm, no one has used that for ages that I know of! Looks like it is an 
> ascii file with:
> 
> #!ascii
> number of vertices
> x y z nx ny nz
> .
> .
> .
> vnum nbr_0 nbr_1 ... nbr_(vnum-1)
> .
> .
> .
> 
> 
> where ... means it is repeated for # of vertices,  are the vertex 
> coords and  is the surface normal
> 
> On Wed, 25 Jan 2012, 
> Guthormsen, Amy M wrote:
> 
> > Hello,
> >
> > I would like to try out the Tools-->surface-->write dipoles function, but I 
> > don't know how to read the file that it outputs.  Do I need to use a 
> > special file extension when I name the file?
> >
> > Thank you,
> >
> > Amy
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> ___
> 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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Re: [Freesurfer] write dipoles function

[Don Hagler]

Hi Bruce,

Yes, some in our group still use it, although I personally have switched to 
using a matlab function that computes the normal vectors directly from the 
surface files.

Don


Date: Wed, 25 Jan 2012 20:50:28 -0500
From: fis...@nmr.mgh.harvard.edu
To: dhagle...@hotmail.com
CC: aguth...@lanl.gov; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] write dipoles function

thanks Don
 
are you guys still using this function?
 
Bruce
On Wed, 25 Jan 2012, Don Hagler 
wrote:
 
> Hi Bruce and Amy,
> 
> I think that menu command actually outputs a binary file, which I would give
> a .dip extension. Some matlab code for reading one is included below.
> 
> Don
> 
> 
> function dipole_info=ts_read_dip_file(dip_file)
> % ts_read_dip_file.m:   read dipole file for calculating forward solution
> %
> % dipole_info=ts_read_dip_file(dip_file)
> %
> % read freesurfer dip file for the location and orientation of the dipoles
> % returns dipole_info containing x,y,z location and nx,ny,nz normal vector
> %
> % created:05/07/05 by Mingxiong Huang as read_dipdec.m
> % early mod:  11/27/05 by Don Hagler as read_dip_file.m
> % last mod:   08/01/06 by Don Hagler
> %
> 
> dipole_info = [];
> 
> % make sure file exists
> [status,message,messageid]=fileattrib(dip_file);
> if (status==0)
>   fprintf('%s: file %s not found... quitting\n',mfilename,dip_file);
>   return;
> end
> 
> % read dip file to get the location of the dipole
> fprintf('ts_read_dip_file: reading file %s...\n',dip_file);
> fp=fopen(dip_file,'r','ieee-be.l64');
> [ch]=fread(fp,1,'uchar');
> [n_dipole]=fread(fp,1,'int32');
> dipole_info=fread(fp,[6,n_dipole],'float');
> fclose(fp);
> 
> fprintf('%s: %d dipoles\n',mfilename,n_dipole);
> 
> 
> 
> 
> > Date: Wed, 25 Jan 2012 17:35:22 -0500
> > From: fis...@nmr.mgh.harvard.edu
> > To: aguth...@lanl.gov
> > CC: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] write dipoles function
> >
> > Hi Amy
> >
> > hmmm, no one has used that for ages that I know of! Looks like it is an
> > ascii file with:
> >
> > #!ascii
> > number of vertices
> > x y z nx ny nz
> > .
> > .
> > .
> > vnum nbr_0 nbr_1 ... nbr_(vnum-1)
> > .
> > .
> > .
> >
> >
> > where ... means it is repeated for # of vertices,  are the vertex
> > coords and  is the surface normal
> >
> > On Wed, 25 Jan 2012,
> > Guthormsen, Amy M wrote:
> >
> > > Hello,
> > >
> > > I would like to try out the Tools-->surface-->write dipoles function,
> but I don't know how to read the file that it outputs. Do I need to use a
> special file extension when I name the file?
> > >
> > > Thank you,
> > >
> > > Amy
> > > ___
> > > Freesurfer mailing list
> > > Freesurfer@nmr.mgh.harvard.edu
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> > >
> > >
> > >
> > ___
> > 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] In Qdec, what does the 'area' mean within 'Measure' menu in 'Design' tab

[Don Hagler]

Hi Doug,

What does the new version of mris_preproc do with area?

Don


Date: Mon, 27 Feb 2012 20:54:43 -0500
From: gr...@nmr.mgh.harvard.edu
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] In Qdec, what does the 'area' mean within 'Measure' 
menu in 'Design' tab


  



  
  
That is the area of the white surface. But don't use this unless you
have updated to the new version of mris_preproc.

doug



On 2/27/12 8:15 PM, ZhiLiangLong wrote:

  
Hi freesurfer experts:
 i'm using qdec to perform statistical analysis in
  Freesurfer 5.0.0, within 'Measure' menu in 'Design' tab, the
  default is 'thickness', however, there are other measurements
  such as 'area' and 'area.pial'.  the latter seems meaning area
  in pial surface. what does the former mean? does it mean area
  in white matter surface?
  
  

  

  
  

  
  

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[Freesurfer] aparc a2009s stats ROI names don't match ColorLUT for FS 6.0

[Don Hagler]

External Email - Use Caution

I have recently started using FreeSurfer 6.0 after previously working with 5.3 
for several years. I found that the lh.aparc.a2009s.stats files use different 
ROI names (e.g., G&S_frontomargin) than they did in FS5.3 
(G_and_S_frontomargin). However, the FreeSurferColorLUT.txt file still has the 
old names.

What caused the ROI names to change for the a2009s.stats files? Was the 
ColorLUT supposed to have been updated but wasn’t? Where do those shorter names 
come from? Is there already a mapping file for the different versions of the 
names?

Because some of the parcel names in the stats files no longer match the LUT, my 
existing code for compiling FreeSurfer results fails to load the results for 
those ROIs with new names.

I think I can find a work-around for this, such as using a mapping file or a 
renaming rule applied to the a2009s stats ROI names, before matching to the LUT.

But I thought I would email this list to raise the issue. I searched the 
archives and didn’t see something similar, so maybe no one else tries to match 
those names to the LUT.

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[Freesurfer] mri_vol2surf error

[Don Hagler]

Using version 4.5.0, I get this error message with mri_vol2surf:
INFO: Source volume detected as selxavg format
 number of frames is incorrect (0,1)

This error does not happen with version 3.0.5, and it only happens for input 
volumes with particular file names.

This fails:
mri_vol2surf \
 
 --src 
/space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTcalc/DTI5_corr_resDTI_DT_minb1000_FA.mgz
 \
  --src_type mgh \
  --srcreg 
/space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/rh-tmpreg.dat
 \
  --hemi lh \
  --surf white \
  --out 
/space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/DTI5_corr_resDTI_DT_minb1000_FA_pdist-1.0-lh.mgh
 \
  --out_type mgh \
  --trgsubject FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1 \
  --projdist -1.000 \
  --noreshape

But this works:
mri_vol2surf \
 
 --src 
/space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTcalc/DTI5_corr_resDTI_DT_minb1000_FA2.mgz
 \
  --src_type mgh \
  --srcreg 
/space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/rh-tmpreg.dat
 \
  --hemi lh \
  --surf white \
  --out 
/space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/DTI5_corr_resDTI_DT_minb1000_FA_pdist-1.0-lh.mgh
 \
  --out_type mgh \
  --trgsubject FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1 \
  --projdist -1.000 \
  --noreshape

In the second case, the input file is a direct copy of the input file for the 
first case.  It also works if the input file is copied to another location.


The complete messages when it fails:
srcvol
 = 
/space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTcalc/DTI5_corr_resDTI_DT_minb1000_FA.mgz
srctype = mgh
srcreg = 
/space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/rh-tmpreg.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1
surfreg = sphere.reg
ProjDist = -1
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
INFO: Source volume detected as selxavg format
 number of frames is incorrect (0,1)


Complete messages when it succeeds (second case):
srcvol
 = 
/space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTcalc/DTI5_corr_resDTI_DT_minb1000_FA2.mgz
srctype = mgh
srcreg = 
/space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/rh-tmpreg.dat
srcregold = 0
srcwarp unspecified
surf = white
hemi = lh
trgsubject = FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1
surfreg = sphere.reg
ProjDist = -1
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Reading surface 
/space/md4/5/halgdev/epiproj/FSRECONS/FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1/surf/lh.white
Done reading source surface
Reading thickness 
/space/md4/5/halgdev/epiproj/FSRECONS/FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1/surf/lh.thickness
Done
Mapping Source Volume onto Source Subject Surface
 1 -1 -1 -1
Done mapping volume to surface
Number of source voxels hit = 28720
Writing
 to 
/space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/DTI5_corr_resDTI_DT_minb1000_FA_pdist-1.0-lh.mgh
Dim: 145736 1 1


FYI:

FREESURFER_HOME: /usr/pubsw/packages/freesurfer/RH4-x86_64-R450

Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0

RedHat release: CentOS release 5.5 (Final)

Kernel info: Linux 2.6.18-194.8.1.el5 x86_64


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Re: [Freesurfer] mri_vol2surf error

[Don Hagler]

Hi Doug,

Yes indeed there is such a file (converted from mgz for DTIStudio).  Thanks for 
your explanation.

Don


> Date: Tue, 19 Oct 2010 11:40:47 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: dhagle...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] mri_vol2surf error
> 
> Hi Don, is there a file called DTI5_corr_resDTI_DT_minb1000_FA.dat? If 
> so, it thinks that that file is a file created by selxavg and it tries 
> to load it in. Doubtless it is not a selxavg file, and so that is 
> failing in an unpredictable way. This file is not used anymore, so I'll 
> have mri_vol2surf stop trying to load it. For now, just name your .dat 
> files differently than your other files.
> 
> doug
> 
> Don Hagler wrote:
> > Using version 4.5.0, I get this error message with mri_vol2surf:
> > INFO: Source volume detected as selxavg format
> >  number of frames is incorrect (0,1)
> >
> > This error does not happen with version 3.0.5, and it only happens for 
> > input volumes with particular file names.
> >
> > This fails:
> > mri_vol2surf \
> >   --src 
> > /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTcalc/DTI5_corr_resDTI_DT_minb1000_FA.mgz
> >  
> > \
> >   --src_type mgh \
> >   --srcreg 
> > /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/rh-tmpreg.dat
> >  
> > \
> >   --hemi lh \
> >   --surf white \
> >   --out 
> > /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/DTI5_corr_resDTI_DT_minb1000_FA_pdist-1.0-lh.mgh
> >  
> > \
> >   --out_type mgh \
> >   --trgsubject FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1 \
> >   --projdist -1.000 \
> >   --noreshape
> >
> > But this works:
> > mri_vol2surf \
> >   --src 
> > /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTcalc/DTI5_corr_resDTI_DT_minb1000_FA2.mgz
> >  
> > \
> >   --src_type mgh \
> >   --srcreg 
> > /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/rh-tmpreg.dat
> >  
> > \
> >   --hemi lh \
> >   --surf white \
> >   --out 
> > /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/DTI5_corr_resDTI_DT_minb1000_FA_pdist-1.0-lh.mgh
> >  
> > \
> >   --out_type mgh \
> >   --trgsubject FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1 \
> >   --projdist -1.000 \
> >   --noreshape
> >
> > In the second case, the input file is a direct copy of the input file 
> > for the first case.  It also works if the input file is copied to 
> > another location.
> >
> >
> > The complete messages when it fails:
> > srcvol = 
> > /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTcalc/DTI5_corr_resDTI_DT_minb1000_FA.mgz
> > srctype = mgh
> > srcreg = 
> > /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/rh-tmpreg.dat
> > srcregold = 0
> > srcwarp unspecified
> > surf = white
> > hemi = lh
> > trgsubject = FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1
> > surfreg = sphere.reg
> > ProjDist = -1
> > interp = nearest
> > float2int = round
> > GetProjMax = 0
> > INFO: float2int code = 0
> > Done loading volume
> > INFO: Source volume detected as selxavg format
> >  number of frames is incorrect (0,1)
> >
> >
> > Complete messages when it succeeds (second case):
> > srcvol = 
> > /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTcalc/DTI5_corr_resDTI_DT_minb1000_FA2.mgz
> > srctype = mgh
> > srcreg = 
> > /space/md8/10/data/epiproj/EPDTI/Containers/MRIPROCESSED_EPDTI_epd34_101002_20101002.185011_1/DTanalysis/rh-tmpreg.dat
> > srcregold = 0
> > srcwarp unspecified
> > surf = white
> > hemi = lh
> > trgsubject = FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1
> > surfreg = sphere.reg
> > ProjDist = -1
> > interp = nearest
> > float2int = round
> > GetProjMax = 0
> > INFO: float2int code = 0
> > Done loading volume
> > Reading surface 
> > /space/md4/5/halgdev/epiproj/FSRECONS/FREESURFERRECON_EPDTI_epd34_101002_20101002.185011_1/surf/lh.white
> > Done reading source surface
> > Reading thickness 
> > /space/md4/5/halgdev/epiproj

[Freesurfer] tksurfer error

[Don Hagler]

Hi,

In response to the message below, I have been getting the exact
same error when running tksurfer on a particular workstation.
tksurfer does display correctly, but the drawing is very slow, as if
running remotely (or not using the video card).  This happens with versions
3.0.5 and 4.5.0.

I tried uninstalling and reinstalling the nvidia driver, but that didn't help.

glxgears and glxinfo work fine, no warnings or error messages.

In Xorg.0.log, there is one warning:
(WW) NVIDIA(0): UBB is incompatible with the Composite extension.  Disabling
(WW) NVIDIA(0): UBB.

After googling, I found that UBB stands for Unified Back Buffer.
http://http.download.nvidia.com/XFree86/Linux-x86/1.0-8178/README/appendix-k.html
This only applies to Quadro GPUs.  This particular workstation has this type:
NVIDIA GPU Quadro FX 580

I haven't yet found a solution.  Evan, do you have a Quadro GPU?
Did you find a solution?


Don

_


Dear freesurfer community,

I am currently trying to view one of the surfaces generated by recon-all
command in tksurfer but when I enter the command:

tksurfer LuceHR_FS_SURF lh inflated.nofix

I receive a series of errors that look like this:

Received X error!
Error code   : 1
Request code : 147
Minor code   : 181

Error text : 'BadRequest (invalid request code or no such operation)'

Subsequently the surface window does not display what I would believe is the
surface I am trying to view and then the only way I can exit the tksurfer
environment is by exiting the terminal that I invoked it in.

Any ideas or solutions?

Thank you very much,

Evan Luther

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Re: [Freesurfer] tksurfer error

[Don Hagler]

A quick update on my earlier posting:  After disabling the "Composite" 
extension, I no longer
get the UBB warning in the Xorg.0.log, but I still get the error and slow 
drawing with tksurfer.

From: dhagle...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Tue, 15 Mar 2011 12:07:56 -0700
Subject: [Freesurfer] tksurfer error








Hi,

In response to the message below, I have been getting the exact
same error when running tksurfer on a particular workstation.
tksurfer does display correctly, but the drawing is very slow, as if
running remotely (or not using the video card).  This happens with versions
3.0.5 and 4.5.0.

I tried uninstalling and reinstalling the nvidia driver, but that didn't help.

glxgears and glxinfo work fine, no warnings or error messages.

In Xorg.0.log, there is one warning:
(WW) NVIDIA(0): UBB is incompatible with the Composite extension.  Disabling
(WW) NVIDIA(0): UBB.

After googling, I found that UBB stands for Unified Back Buffer.
http://http.download.nvidia.com/XFree86/Linux-x86/1.0-8178/README/appendix-k.html
This only applies to Quadro GPUs.  This particular workstation has this type:
NVIDIA GPU Quadro FX 580

I haven't yet found a solution.  Evan, do you have a Quadro GPU?
Did you find a solution?


Don

_


Dear freesurfer community,

I am currently trying to view one of the surfaces generated by recon-all
command in tksurfer but when I enter the command:

tksurfer LuceHR_FS_SURF lh inflated.nofix

I receive a series of errors that look like this:

Received X error!
Error code   : 1
Request code : 147
Minor code   : 181

Error text : 'BadRequest (invalid request code or no such operation)'

Subsequently the surface window does not display what I would believe is the
surface I am trying to view and then the only way I can exit the tksurfer
environment is by exiting the terminal that I invoked it in.

Any ideas or solutions?

Thank you very much,

Evan Luther

  

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Re: [Freesurfer] distortion of flat map

[Don Hagler]

For retinotopy, I find it convenient to use the sphere surface.  It does not 
require a cut down the middle of V1 and it is flat enough to easily draw ROIs.  
Also, in my experience, the patch flattening algorithm often produces poor 
results (e.g. large distortions, twisting).

Date: Thu, 28 Apr 2011 23:03:50 -0400
From: liu.yan...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] distortion of flat map

Hi surfers, 

I am working on generating surface ROIs from the retinotopy surface. 
We cut the occipital lobe and draw paths on the flattened map to create labels. 
However, I found that there are distortions on the flat map that cause large 
errors when drawing these paths. I attached two pictures. The
 path_example2_dots.jpg are the dots that I selected to draw a path. 
Basically it is the method we use to demarcate the boundaries of visual 
areas. 

 And the path_example2_line.jpg are the line that is supposed to connect the 
dots and to be the correct boundary. 
Notice the dots and the line do not overlap!
so when I draw a line on the flat map, Freesurfer actually doesn't draw the 
line I want it to be.


Has anyone met this problem before? Is there a better solution to create 
surface ROIs? Drawing the boundary on inflated surface?

Yang


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Re: [Freesurfer] Retinotopy stimuli

[Don Hagler]

Hi Anders,

I agree with the points Jon made.  8 Hz flicker is also what I use.  I haven't 
tried lower frequencies, but
 I think you would definitely have reduced SNR if you did.  I also use rather 
thin wedges and rings and smoothly vary their position.


I would add that a longer cycle duration (e.g. 64 seconds) seems to provide 
better phase estimates.  I had been using a shorter duration (32 seconds) for 
awhile, and while you can get reasonable results (and better SNR because of 
more cycles/scan), I was also noticing irregularities in the maps (e.g. spots 
of upper field preference where it should be lower field).  When I did a direct 
comparison between the two cycle durations, the maps looked much cleaner with 
the longer cycle.

Because the data can be rather noisy (regardless of field strength), multiple 
scans are important.  I use 4 scans for polar angle (2 CW, 2 CCW) and 2 for 
eccentricity (1 expanding, 1 contracting), although I would do more in a 
session if I thought the typical subject could stand it.  My current settings 
are 5 cycles/scan, 64 second cycle duration, 128 TRs, TR = 2.5 sec, so ~5.5 
minutes / scan.  A 3 sec TR would work fine too, and allow for 6 cycles/scan, 
which would improve SNR (and increase total scan duration).

Don

> Date: Thu, 7 Jul 2011 11:30:13 -0400
> From: j...@nmr.mgh.harvard.edu
> To: ahouga...@dadlnet.dk
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Retinotopy stimuli
> 
> 
> hi anders,
> 
> the optimal set of stimulus parameters will depend somewhat on what
> cortical area(s) you are trying to map and on the details of your
> acquisition. in general, stimulating with both clockwise- and
> counterclockwise-rotating wedges for polar angle mapping and with both
> expanding and contracting rings for eccentricity mapping improves the
> accuracy of the maps, and the proper analysis of this data is implemented
> fsfast. the width of the wedge or the ring will depend on the cortical
> area you are trying to stimulate, but you may want to consider a thinner
> wedge. also, 8 Hz flickering has been shown to activate area V1 more
> strongly than other frequencies, and smoothly moving stimuli can also
> help. then, depending on your voxel size, field strength, coil array,
> etc., you could include more cycles and may need to average together
> multiple runs.
> 
> marty, roger et al. have a few nice papers that i'd recommend that discuss
> some of these details relating to phase-encoded retinotopic stimuli.
> 
>   Sereno & Tootell. Curr Opin Neurobiol. 2005;15(2):135-44.
>   Tootell et al. J Neurosci. 1997;17(18):7060-78.
>   Sereno et al. Science. 1995;268(5212):889-93.
> 
> (the '97 paper discusses the ring/wedge thickness, the '95 paper discusses
> the advantages of using both expanding + contracting stimuli, and the '05
> paper discusses the use of smoothly varying stimuli.)
> 
> hope this helps. were you able to get reasonable looking maps with the
> stimuli you described below?
> 
> 
> -jon
> 
> 
> 
> 
> On Thu, 7 Jul 2011, Anders Hougaard wrote:
> 
> > Dear freesurfers,
> >
> >
> > Which stimuli do you think provide the best retinotopic maps?
> >
> > I have done a retinotopy analysis using the following stimuli:
> >
> > Polar angle:
> >
> > - 45 deg counter-clockwise rotating wedge
> > - 8 unique positions
> > - flickering at 2 Hz
> > - stimulation period: 36 sec
> > - no. of cycles: 6
> > - TR = 3
> >
> > Eccentricity:
> >
> >  - expanding ring
> > - 8 unique positions
> > - flickering at 2 Hz
> > - stimulation period: 36 sec
> > - no. of cycles: 6
> > - TR = 3
> >
> > Any suggestions on how to optimize this stimulation?
> > E.g. different period length, more runs, bi-directional, different TR
> >
> > Thank you!
> >
> > Best regards,
> >
> > Anders
> >
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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 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] read_fscolorlut

[Don Hagler]

FYI, in version 5.1.0, FreeSurferColorLUT.txt has a space (" ") instead of an 
empty line at line 1189.  This causes the matlab funciton read_fscolorlut to 
throw an error.

An easy fix is to change this line:
if(~isempty(tline) & tline(1) ~= '#') break; end

to this:
if(~isempty(deblank(tline)) & tline(1) ~= '#') break; end



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[Freesurfer] mri_surf2surf ico to ico

[Don Hagler]

I am trying to use mri_surf2surf to resample surface data in mgh format 
from ico4 to ico3. There is an apparent bug, however, in that the output
 file has the same dimensions as the input file despite srcicoorder = 4 
and trgicoorder = 3. I am using ico for both srcsubject and trgsubject. 
 This problem occurs in versions 4.5.0 and 5.1.0 (and presumably other 
versions as well). I have the same problem when trying to go from ico4 
to ico7.

command line:
mri_surf2surf --srcsubject ico 
--trgsubject ico --srcicoorder 4 --trgicoorder 3 --sval 
dSPM_cond17-lh.mgh --tval dSPM_cond17_ico3-lh.mgh --hemi lh

output:
srcsubject = ico
srcval = dSPM_cond17-lh.mgh
srctype= 
trgsubject = ico
trgval = dSPM_cond17_ico3-lh.mgh
trgtype= 
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
   Reading icosahedron 
/usr/pubsw/packages/freesurfer/RH4-x86_64-R450/lib/bem/ic4.tri
Source Ico Order = 4
Loading source data
INFO: trgsubject = srcsubject
Saving target data


A work-around is to specify the trgsubject as an "average" subject in the 
desired (e.g. ico 3) resolution.

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Re: [Freesurfer] mri_surf2surf ico to ico

[Don Hagler]

My suggested work-around in my earlier email does not actually work. It outputs 
as ico7 even though my "average" subject is ico3.


From: dhagle...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Thu, 17 Nov 2011 11:52:22 -0800
Subject: [Freesurfer] mri_surf2surf ico to ico








I am trying to use mri_surf2surf to resample surface data in mgh format 
from ico4 to ico3. There is an apparent bug, however, in that the output
 file has the same dimensions as the input file despite srcicoorder = 4 
and trgicoorder = 3. I am using ico for both srcsubject and trgsubject. 
 This problem occurs in versions 4.5.0 and 5.1.0 (and presumably other 
versions as well). I have the same problem when trying to go from ico4 
to ico7.

command line:
mri_surf2surf --srcsubject ico 
--trgsubject ico --srcicoorder 4 --trgicoorder 3 --sval 
dSPM_cond17-lh.mgh --tval dSPM_cond17_ico3-lh.mgh --hemi lh

output:
srcsubject = ico
srcval = dSPM_cond17-lh.mgh
srctype= 
trgsubject = ico
trgval = dSPM_cond17_ico3-lh.mgh
trgtype= 
srcsurfreg = sphere.reg
trgsurfreg = sphere.reg
srchemi= lh
trghemi= lh
frame  = 0
fwhm-in= 0
fwhm-out   = 0
label-src  = (null)
label-trg  = (null)
   Reading icosahedron 
/usr/pubsw/packages/freesurfer/RH4-x86_64-R450/lib/bem/ic4.tri
Source Ico Order = 4
Loading source data
INFO: trgsubject = srcsubject
Saving target data


A work-around is to specify the trgsubject as an "average" subject in the 
desired (e.g. ico 3) resolution.

  

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RE: [Freesurfer] difficulty readings DICOM files from CD

[Don Hagler]

matlab's dicomread can handle 8 bit images, so if you have matlab, one could 
write a script to convert your dicoms to mgh format (using save_mgh).

> Date: Fri, 30 Jan 2009 16:06:52 -0500
> From: gr...@nmr.mgh.harvard.edu
> To: senu...@fas.harvard.edu
> Subject: Re: [Freesurfer] difficulty readings DICOM files from CD
> CC: freesurfer@nmr.mgh.harvard.edu
> 
> 
> This might not work with our tools. As the message implies, they cannot 
> unpack 8bit images (I think it is fixed at 16). I'm not sure how to 
> change it (or if it can be changed). We use a 3rd party dicom reader, 
> and it is not an easy thing modify.
> 
> sorry
> 
> doug
> 
> Sam Enumah wrote:
> >
> > Hello,
> >
> > My name is Sam Enumah and I am an undergraduate working in the A.A. 
> > Martinos Imaging Center at MGH Navy Yard.  I have become familiar with 
> > Freesurfer's tkmedit function and I am able to analyze my data once I 
> > am given a set of 144 MR  dicom files.  While the mri_convert tool 
> > works for the dicom files that are on the local machine, I cannot seem 
> > to get it to work for the files I have tried to retrieve from a CD.  
> > The files on my local host machine all display the extension  ".dcm"   
> > while the files from the CD do not display a file extension and are 
> > files with names that consist of 8 unique numbers (e.g 48480095)
> >
> > As you may know, when running mri_convert, the user need only input 
> > one of the files in a series and it recognizes all the other files and 
> > creates the desired output (in this case the ".nii" file type to be 
> > read by tkmedit).  However, when I tried to input these 8 digit file 
> > names into mri_convert, I received the following error:
> >
> > [gordo:1225] (nmr-std-env) mri_convert 48480995.dcm adc.nii
> > mri_convert 48480995.dcm adc.nii
> > $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $
> > reading from 48480995.dcm...
> > Starting DICOMRead2()
> > dcmfile = /autofs/homes/014/xmlentz/
> > Desktop/dicom/08110217/1225/48480995.dcmdcmdir = 
> > /autofs/homes/014/xmlentz/Desktop/dicom/08110217/1225
> > Ref Series No = 805
> > ERROR: bits = 8 not supported.
> > Send email to freesurfer@nmr.mgh.harvard.edu 
> > 
> >
> >   I tried
> >  "mri_convert  --in_type ge adc.nii"
> > but kept getting the error:
> > genesisRead(): can't determine file name format
> >
> > Essentially, my problem is that I have roughly 1000 dicom files (as 
> > evidenced by command "file" in terminal) without an identifiable 
> > extension and I need to find a way to change these into one of any of 
> > the set MR001.dcm - MR144.dcm   to be read by mri_convert.
> >
> > As it stands now, I don't know what series (average DC, isotropic, FA, 
> > etc.) these 8 digit numbers correspond to so I'm unsure of how to proceed.
> > Suggestions?
> >
> > Thanks for your time.
> >
> > -Sam
> >
> > -- 
> > Sam Enumah
> > Harvard College Class of 2010
> > Concentrator in Neurobiology
> > senu...@fas.harvard.edu 
> > 
> >
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RE: [Freesurfer] Qdec area measure

[Don Hagler]

It seems to me that vertex areas in the native subject space are not 
meaningful.  The orig surfaces should be uniformly tesselated; however, 
topology correction and final surface finding should introduce complicated and 
probably uninteresting variation.

But, if a subject's surfaces are resampled to atlas (i.e. make_average_subject 
with only one subject as input), then the vertex areas should indicate the 
degree to which squishing or stretching is required to match the atlas (as 
Bruce said), which could be quite interesting.  Or put another way, vertex area 
represents the relative size of a patch of cortex compared to the collection of 
subjects that went into the atlas.  This measure of vertex area may vary 
between groups and may be correlated to certain genetic markers.

Since volume depends on both area and thickness, it seems redundant to use all 
three measures.


> Date: Tue, 17 Feb 2009 23:16:33 -0600
> Subject: Re: [Freesurfer] Qdec area measure
> From: mha...@conte.wustl.edu
> To: fis...@nmr.mgh.harvard.edu
> CC: d.gitel...@gmail.com; freesurfer@nmr.mgh.harvard.edu
> 
> 
> Here is a question related to this whole discussion (prompted by what
> Darren wrote):
> As a practical matter, have you found the localized (i.e., vertex-based)
> measures of area and volume to be biologically useful and meaningful? 
> Have they been used in any published studies?  (I don't recall seeing any
> surface maps of "area" or "volume" differences between groups, whereas
> there are obviously many published studies showing surface maps of
> thickness differences).
> 
> cheers,
> Mike H.
> 
> > Hi Darren
> >
> > the curvature is related to the angles of the edges connected to each
> > vertex (also called the "angle deficit"). The surface area should just be
> > given by how much compression expansion the individual surface undergoes
> > when it aligns to a spot in the atlas. We'll compute it and correct for
> > it sometime soon.
> >
> > cheers,
> > Bruce
> > On Tue, 17 Feb 2009, Darren Gitelman wrote:
> >
> >> Devdutta, Nick, Bruce, Mike
> >>
> >> I'm trying to understand these measures in terms of how they would map
> >> to
> >> the brain physically.
> >>
> >> Would it be correct that the size of the triangles touching a vertex
> >> would
> >> be related to the amount curvature near a particular vertex and
> >> therefore
> >> the amount of unfolding that takes place? Thus surface area would seem
> >> to
> >> relate to both brain size and the foldiness of the brain, and brain size
> >> could relate to a variety of factors including the cortical thickness
> >> but
> >> also the amount of underlying white matter.  So overall surface area
> >> seems
> >> to be a complex metric that could reflect changes in underlying white
> >> matter, cortical thickness and foldiness. Is this correct?
> >>
> >> I guess one would have to correct for overall brain size (using TIV or
> >> similar measure as a covariate) when examining surface area because of
> >> the
> >> effect of amount of gray and/or white matter.
> >>
> >> Volume then would be the amount of cortex underlying a vertex and the
> >> triangles connected to it (estimated as an average of the pial and white
> >> matter surface areas).
> >>
> >> Darren
> >>
> >>
> >>
> >>
> >>> I think the area probably should be corrected to preserve the native
> >>> area
> > of the subject, but as you say we haven't gotten to the correction
> > yet. On
> > Tue, 17 Feb 2009, Nick Schmansky wrote:
> >
> >Devdutta,
> >
> >The 'area' of a vertex on a surface in freesurfer is just the
> > average
> > of
> >the area of the triangles which touch that vertex .
> >
> >The volume data associated with a vertex created for a subject is
> > not
> >buggy in how it is calculated now.  it is the area of the
> > mid-point
> >between the white and pial surfaces times the thickness at the
> > vertex.
> >The question that has been bandied about internally is whether
> > this
> >volume calculation should be corrected when it is mapped to the
> >fsaverage surface during a group analysis (qdec does this mapping
> > of
> > the
> >volume calcs of each subject to the fsaverage surface, when you
> > select
> >'volume' as one of the measures).  At some point we will visit
> > this
> >issue (and determine if it is an issue) but other stuff seems to
> > take
> >priority.  Maybe someone on the list can chime in.
> >
> >Nick
> >
> >On Tue, 2009-02-17 at 11:28 -0600, Devdutta W wrote:
> >
> >Hi,
> >In Qdec, what exactly does the area option measure?  As I
> > understand,
> >qdec does its calculations vertex by vertex, which makes sense
> > in
> > case
> >of cortical thickness.  But if area refers to surface area how
> > does
> >that change from 

RE: [Freesurfer] qdec thickness and repeatability

[Don Hagler]

You could extend the analysis described on that wiki page by calculating tstats 
and pvalues (in addition to mean and stdev).  Then you have a paired t-test, 
whereas mri_glmfit with qdec would be doing an unpaired t-test.  I think 
preproc has an option to calculate within subject differences for a paired 
t-test with mri_glmfit as well.  As you may know, paired t-tests are more 
sensitive than unpaired t-tests, and are generally more appropriate when you 
make within subject comparisons.  On the other hand, if you intend your 
exercise to be a test for the likelihood of false positive differences between 
groups, the unpaired t-test may be more appropriate.

> Subject: Re: [Freesurfer] qdec thickness and repeatability
> From: ni...@nmr.mgh.harvard.edu
> To: bell0...@umn.edu
> Date: Fri, 20 Feb 2009 15:15:10 -0500
> CC: freesurfer@nmr.mgh.harvard.edu
> 
> The two methods are very different.  In the method described on the
> thickness repeatability page, its computing a mean and stddev of the
> thickness for your group.  This a direct and easily interpretable
> measure, but doesn't give you a statistical measure (but you could do
> that on your own with some external package).
> 
> In qdec (mri_glmfit), it would be conducting a GLM-based analysis
> looking for statistical significance, expressed as a p-value at each
> vertex, in thickness between groups.  Here, raw thickness differences
> are hidden in the analysis.  
> 
> However, you can of course do both analysis, and compare them, which I
> would suggest you do.  You would hope the areas of change are the same.
> Note that you can load external surface maps, such as a thickness-
> diff.mgh map, onto the fsaverage surface in qdec, so that you can view
> both analysis (or just load the thickness-diff.mgh map in tksurfer).
> 
> Its on the list of things to add to qdec to create two-group thickness
> difference maps, as well as just viewing the mean group thickness, to
> save some work for this sort of thing.
> 
> Nick
> 
> 
> On Fri, 2009-02-20 at 12:53 -0600, bell0...@umn.edu wrote:
> > All,
> > 
> > I am going to run an analysis of cortical thickness reproducibility; there 
> > are at least two methods that seem obvious. I could run qdec analysis with 
> > time1 and time2 as different groups or I could run the methods below. Are 
> > the commands below the same ones used in the qdec GUI? As far as I can 
> > tell, they will both give me cortical thickness differences on a vertex by 
> > vertex basis. There are probably some subtle differences in the way they 
> > are coded, but any major changes? Thanks.
> > 
> > http://surfer.nmr.mgh.harvard.edu/fswiki/ThicknessRepeatibility
> > 
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> > 
> 
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RE: [Freesurfer] determining sizes of clusters on surface data

[Don Hagler]

Assuming Worsley did not make any changes to his basic method since 2003 (the 
version I copied), then the difference here is probably, as you said, because 
of the resels.

If you use resels, then the cluster thresholds are in resels and the
surface area of two clusters with the same number of resels can be different 
(by design).  If you want your threshold
to be a constant mm^2, don't use resels.


His function has an option to either supply the total surface area in
mm^2 or in resels.  If you specify in resels, then you area supossed to set 
fwhm = 1.  This is in the comments of his function that is buried in mine.  I 
haven't used his most recent toolbox.  Does it give the option to specify 
surface area and fwhm in mm^2?

By the way, when I made surface maps of resels I calculated for my own surface 
data, they looked very spiky and I decided not to use them, but instead made 
the simplifying assumption of uniform smoothness across the surface.


Date: Fri, 3 Apr 2009 11:03:04 +0800
From: jid...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] determining sizes of clusters on surface data

Hi, 

I was trying to figure out if there is any way to determine the exact size at 
which clusters becomes significant given a specified significance on the 
surface data.


Then i found there is a subject talking about this: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2007-August/005855.html


In that talk,Don Hagler mentioned Keith Worsley's "Random Field Theory" method 
(http://www.math.mcgill.ca/keith/fmristat/toolbox/stat_threshold.m) can be used 
to directly (in seconds) estimate the cluster size thresholds given:

..total surface area
..number of vertices
..fwhm smoothness.
function [cluster_threshold,peak_threshold] =  
fs_calc_cluster_thresh(nverts,area,fwhm,df,alpha,pval);
> % alpha: corrected p-value

> % {default = 0.05}
> % pval: uncorrected p-value
> % {default = 0.001}

I tried this function, and it does give me a cluster size with mm^2, say 100 
mm^2.  But I don't know whether this is the right thing to do. 


As I'm doing some statistical analysis using GLM, so I also try the method from 
Keith Worsley's statistical toolbox, then I can get the cluster's No. of 
vertices and the corrected p-value(alpha=0.05) for the cluster.


Here is one example:
 
  clusid  nverts  resels P 
---
   1  2205  18.2781  2.1299e-06
   2   208  1.421050.013359
   3   127  1.155330.026747

   458   1.04430.036658
   5 5 0.519762 0.20884
   6   105 0.464429  0.2571

The thing I don't understand is , if we are looking for a cluster size 
threshold, then we can say that, the clusters above that threshold size is what 
we want to keep. And also, the p-value of the clusters above that threshold 
size should 

be below alpha we set, say 0.05. But when checking the tale above, the first 
four clusters' p- value is smaller than 0.05, then we should keep it. But 
according to the no. of vertices, we can caculate the cluster size in mm^2. 
Then the 4th 

cluster size is obviously below 100mm^2, the threshold we found using the 
function fs_calc_cluster_thresh. Oppositely, the 6th cluster has a large no. of 
vertices and its cluster size is above 100mm^2, while it's
not kept because its p value is above 0.05.I know what happened here is because 
of the 'resels', but it really confuse me which one is the right one. Since you 
said we can use the function, then why is the result  conflicted with each 
other?


Could you tell me what's wrong here or what did I miss ?
Thanks a lot,

Jidan


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RE: [Freesurfer] determining sizes of clusters on surface data

[Don Hagler]

Hi Jidan,

The cluster size is the correction, so I don't think you can get an uncorrected 
p-value for a cluster size.  You could apply a threshold equivalent to 0.05 
uncorrected and then see what the size of the cluster is.

By the way, you can vary the pval (uncorrected) used for calculating the 
cluster threshold.  A smaller, more stringent pval (e.g. 0.0001) will result in 
a smaller cluster size threshold than a more liberal pval (e.g. 0.05).  It may 
seem like cheating to adjust the pval until you get the result you want, and it 
probably is, but if you initially used pval=0.05, it would probably have been 
better to use something like 0.01 or 0.001.  If pval is too large, your 
clusters will clump together and your centroids would not be meaningful.


Don



Date: Fri, 3 Apr 2009 13:09:50 +0800
Subject: Re: [Freesurfer] determining sizes of clusters on surface data
From: jid...@gmail.com
To: dhagle...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu

Hi Don,Thanks for your reply. I'm using the same program you mentioned. Now I 
understand why the cluster size in mm^2 is not a constant. 
I'm curious about the alpha, which is corrected p- value threshold for the 
cluster. In fact, is there any method to get the uncorrected p-value of the 
cluster or its size ? If I use alpha=0.05 (corrected), there would be a problem 
that the cluster size is too stringent to show the result. I'm thinking whether 
I can get the cluster size with uncorrected p-value (say,0.05) to compare this 
size with the corrected one, to see how difference they are. 
function [cluster_threshold,peak_threshold] =  
fs_calc_cluster_thresh(nverts,area,fwhm,df,alpha,pval);


Thanks, regards,
Jidan



On Fri, Apr 3, 2009 at 11:49 AM, Don Hagler  wrote:






Assuming Worsley did not make any changes to his basic method since 2003 (the 
version I copied), then the difference here is probably, as you said, because 
of the resels.

If you use resels, then the cluster thresholds are in resels and the
surface area of two clusters with the same number of resels can be different 
(by design).  If you want your threshold
to be a constant mm^2, don't use resels.


His function has an option to either supply the total surface area in
mm^2 or in resels.  If you specify in resels, then you area supossed to set 
fwhm = 1.  This is in the comments of his function that is buried in mine.  I 
haven't used his most recent toolbox.  Does it give the option to specify 
surface area and fwhm in mm^2?


By the way, when I made surface maps of resels I calculated for my own surface 
data, they looked very spiky and I decided not to use them, but instead made 
the simplifying assumption of uniform smoothness across the surface.



Date: Fri, 3 Apr 2009 11:03:04 +0800
From: jid...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu

Subject: [Freesurfer] determining sizes of clusters on surface data

Hi, 

I was trying to figure out if there is any way to determine the exact size at 
which clusters becomes significant given a specified significance on the 
surface data.



Then i found there is a subject talking about this: 
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2007-August/005855.html



In that talk,Don Hagler mentioned Keith Worsley's "Random Field Theory" method 
(http://www.math.mcgill.ca/keith/fmristat/toolbox/stat_threshold.m) can be used 
to directly (in seconds) estimate the cluster size thresholds given:


..total surface area
..number of vertices
..fwhm smoothness.
function [cluster_threshold,peak_threshold] =  
fs_calc_cluster_thresh(nverts,area,fwhm,df,alpha,pval);
> % alpha: corrected p-value


> % {default = 0.05}
> % pval: uncorrected p-value
> % {default = 0.001}

I tried this function, and it does give me a cluster size with mm^2, say 100 
mm^2.  But I don't know whether this is the right thing to do. 



As I'm doing some statistical analysis using GLM, so I also try the method from 
Keith Worsley's statistical toolbox, then I can get the cluster's No. of 
vertices and the corrected p-value(alpha=0.05) for the cluster.



Here is one example:
 
  clusid  nverts  resels P 
---
   1  2205  18.2781  2.1299e-06
   2   208  1.421050.013359
   3   127  1.155330.026747


   458   1.04430.036658
   5 5 0.519762 0.20884
   6   105 0.464429  0.2571

The thing I don't understand is , if we are looking for a cluster size 
threshold, then we can say that, the clusters above that threshold size is what 
we want to keep. And also, the p-value of the clusters above that threshold 
size should 


be below alpha we set, say 0.05. But when checking the tale above, the first 
four clusters' p- value is smaller than 0.05, then we should keep it. But 
according to the no. of vertices, we can caculate the cluster size in mm^2. 
Then the 4th

RE: [Freesurfer] Can fieldsigns be added across sessions?

[Don Hagler]

I think you should average your polar angle and eccentricity maps across 
session and then calculate fieldsign from that.  You do a complex average (a 
separate average for real and imaginary components).

By the way, the sign of the fieldsign measure should have a fixed meaning; the 
orientation of the cross product of the gradients of polar angle and 
eccenctricity, relative to the cortical surface.  Are you sure you didn't 
reverse the stimulus order or something? Was the projector's image upside down 
or flipped left/right?

Date: Thu, 7 May 2009 18:47:32 -0400
From: jeffrey.s.phill...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Can fieldsigns be added across sessions?

Hi all,

I would like to add fieldsigns across multiple retinotopy sessions in the same 
subject, in order to get a metric of the reliability of the mapping.  However, 
when I tried to do this in one subject, I found that fieldsigns from two 
sessions largely canceled one another out.  This led to a discussion in our lab 
of whether the fieldsign 1) has a consistent meaning across sessions and 
subjects, or 2) whether the fieldsign in a given region, say V1, may switch 
from positive to negative due to noise or between-subject differences.  For 
example, a colleague speculated that paint-sess could start with +1 at an 
arbitrary starting point on the edge of an occipital patch, then flip the sign 
whenever the polar angle/eccentricity gradients reversed themselves.  Thus, V5 
might be +1, V4 = -1, V3 = +1, V2 = -1, and V1 would be +1.  However, if noise 
in a given session resulted in a failure to detect V4, then V1 would end up 
being the opposite fieldsign, -1.  Is this correct?  If so, then I might be 
shooting myself in the foot by adding fieldsign maps from different sessions.  
I would really appreciate any insight about how the fieldsign is assigned, and 
whether circumstances like the ones I describe could cause it to flip for a 
given functional region.


Thanks,

Jeff Phillips

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RE: [Freesurfer] Can fieldsigns be added across sessions?

[Don Hagler]

1. Fieldsign is supposed to be -1 or 1, without values in between.  It is the 
sign of the cross product.  I don't see why you would want to average the 
fieldsign.  You will get the best estimate of the fieldsign by calculating it 
from the average of all your available data.
2. Reversing the stimulus direction would definitely affect the fieldsign 
calculation.  And you will have to take it into account if you average across 
scans or sessions.   By that I mean you need to reverse the phase (by setting 
the imaginary component negative) of one direction before adding to the other.  
I also subtract a few seconds worth of phase to account for hemodynamic delay.
3. The sign may be arbitrary, but it is not random.  The fieldsign depends on 
whether you consider clockwise a positive or negative rotation and expansion 
positive or negative.  If you change either of those conventions, the fieldsign 
will flip.  Also, the color wheel in tksurfer depends on those conventions.  
Red is supposed to be upper field and green is suppoed to be lower field.  That 
too is an arbitrary assignment, but it only holds true for clockwise rotations. 
 For counterclockwise, you need to reverse the phase for the colors to look 
right.
4. Someone else may know if the fsfast tools can handle this type of situation.

Date: Mon, 11 May 2009 12:40:41 -0400
Subject: Re: [Freesurfer] Can fieldsigns be added across sessions?
From: jeffrey.s.phill...@gmail.com
To: dhagle...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu

Hi Don,

Thanks for your comments.  I will try operating on the eccentricity and polar 
angle maps first--however, if I calculate a fieldsign from average maps, I 
presume that the fieldsign map will not be similarly graded, but rather binary. 
 I'll have to think about how to adapt that to our purposes.  


I'm confident that the stimulus order was not reversed between sessions.  One 
difference which did exist was that the first session involved unidirectional 
stimulation (i.e., only clockwise wedges and only expanding rings), while the 
second session involved bidirectional stimulation in alternating runs (i.e., 
both clockwise/counterclockwise and expanding/contracting rings).  Would this 
difference create any problems?


More generally, I'm still a bit confused about the calculation of the 
fieldsign.  The wiki notes that "positive" and "negative" are arbitrarily 
defined--in other words, these terms don't bear any relation to 
clockwise/counterclockwise stimulation.  It also appears (but please correct me 
if I'm wrong) that the meanings of these terms are not linked across the polar 
angle and eccentricity manipulations--that is, I haven't read of any rule that 
says if you call clockwise wedges positive, then expanding rings must also be 
termed positive.  I thought that knowing this directionality would be important 
to interpreting the cross-product.  


I have been unable to find a document, wiki page, etc. which explains some of 
these details--if you happen to know of one, I would appreciate the reference.

Thanks,

Jeff

On Fri, May 8, 2009 at 3:32 PM, Don Hagler  wrote:






I think you should average your polar angle and eccentricity maps across 
session and then calculate fieldsign from that.  You do a complex average (a 
separate average for real and imaginary components).

By the way, the sign of the fieldsign measure should have a fixed meaning; the 
orientation of the cross product of the gradients of polar angle and 
eccenctricity, relative to the cortical surface.  Are you sure you didn't 
reverse the stimulus order or something? Was the projector's image upside down 
or flipped left/right?


Date: Thu, 7 May 2009 18:47:32 -0400
From: jeffrey.s.phill...@gmail.com
To: freesurfer@nmr.mgh.harvard.edu

Subject: [Freesurfer] Can fieldsigns be added across sessions?

Hi all,

I would like to add fieldsigns across multiple retinotopy sessions in the same 
subject, in order to get a metric of the reliability of the mapping.  However, 
when I tried to do this in one subject, I found that fieldsigns from two 
sessions largely canceled one another out.  This led to a discussion in our lab 
of whether the fieldsign 1) has a consistent meaning across sessions and 
subjects, or 2) whether the fieldsign in a given region, say V1, may switch 
from positive to negative due to noise or between-subject differences.  For 
example, a colleague speculated that paint-sess could start with +1 at an 
arbitrary starting point on the edge of an occipital patch, then flip the sign 
whenever the polar angle/eccentricity gradients reversed themselves.  Thus, V5 
might be +1, V4 = -1, V3 = +1, V2 = -1, and V1 would be +1.  However, if noise 
in a given session resulted in a failure to detect V4, then V1 would end up 
being the opposite fieldsign, -1.  Is this correct?  If so, then I might be 
shooting myself in the foot by adding fieldsign maps from differen

RE: [Freesurfer] Can fieldsigns be added across sessions?

[Don Hagler]

I am not familiar with fsfast, so someone with intimate knowledge of the code 
(Doug?) could help more.  But if you can specify the stimulus order in your 
paradigm files, then you should not have to do any phase reversals yourself.  
It seems strange (i.e. bug-like) that your fieldsign comes out different for 
the two sessions in this situation.  When you view the resulting polar angle 
and eccentricity maps in tksurfer, are the colors reversed as well?

Date: Mon, 11 May 2009 15:01:53 -0400
Subject: Re: [Freesurfer] Can fieldsigns be added across sessions?
From: jeffrey.s.phill...@gmail.com
To: dhagle...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu

Hi Don,

Thanks for writing back again.  Let me clarify:  in our last session, we had a 
scanning menu like this:

1 run polar/clockwise

1 run eccen/expanding
1 run polar/counter-clockwise

1 run eccen/contracting

The difference in direction was reflected in our paradigm files (*.par), with 
clockwise & expanding runs categorized as positive, and the others as negative. 
I have assumed that if the paradigm files specify this difference, it will not 
be necessary to manually flip the signs for negative runs.  Is this correct?


Jeff

On Mon, May 11, 2009 at 2:45 PM, Don Hagler  wrote:






1. Fieldsign is supposed to be -1 or 1, without values in between.  It is the 
sign of the cross product.  I don't see why you would want to average the 
fieldsign.  You will get the best estimate of the fieldsign by calculating it 
from the average of all your available data.

2. Reversing the stimulus direction would definitely affect the fieldsign 
calculation.  And you will have to take it into account if you average across 
scans or sessions.   By that I mean you need to reverse the phase (by setting 
the imaginary component negative) of one direction before adding to the other.  
I also subtract a few seconds worth of phase to account for hemodynamic delay.

3. The sign may be arbitrary, but it is not random.  The fieldsign depends on 
whether you consider clockwise a positive or negative rotation and expansion 
positive or negative.  If you change either of those conventions, the fieldsign 
will flip.  Also, the color wheel in tksurfer depends on those conventions.  
Red is supposed to be upper field and green is suppoed to be lower field.  That 
too is an arbitrary assignment, but it only holds true for clockwise rotations. 
 For counterclockwise, you need to reverse the phase for the colors to look 
right.

4. Someone else may know if the fsfast tools can handle this type of situation.

Date: Mon, 11 May 2009 12:40:41 -0400
Subject: Re: [Freesurfer] Can fieldsigns be added across sessions?
From: jeffrey.s.phill...@gmail.com

To: dhagle...@hotmail.com
CC: freesurfer@nmr.mgh.harvard.edu


Hi Don,

Thanks for your comments.  I will try operating on the eccentricity and polar 
angle maps first--however, if I calculate a fieldsign from average maps, I 
presume that the fieldsign map will not be similarly graded, but rather binary. 
 I'll have to think about how to adapt that to our purposes.  



I'm confident that the stimulus order was not reversed between sessions.  One 
difference which did exist was that the first session involved unidirectional 
stimulation (i.e., only clockwise wedges and only expanding rings), while the 
second session involved bidirectional stimulation in alternating runs (i.e., 
both clockwise/counterclockwise and expanding/contracting rings).  Would this 
difference create any problems?



More generally, I'm still a bit confused about the calculation of the 
fieldsign.  The wiki notes that "positive" and "negative" are arbitrarily 
defined--in other words, these terms don't bear any relation to 
clockwise/counterclockwise stimulation.  It also appears (but please correct me 
if I'm wrong) that the meanings of these terms are not linked across the polar 
angle and eccentricity manipulations--that is, I haven't read of any rule that 
says if you call clockwise wedges positive, then expanding rings must also be 
termed positive.  I thought that knowing this directionality would be important 
to interpreting the cross-product.  



I have been unable to find a document, wiki page, etc. which explains some of 
these details--if you happen to know of one, I would appreciate the reference.

Thanks,

Jeff

On Fri, May 8, 2009 at 3:32 PM, Don Hagler  wrote:







I think you should average your polar angle and eccentricity maps across 
session and then calculate fieldsign from that.  You do a complex average (a 
separate average for real and imaginary components).

By the way, the sign of the fieldsign measure should have a fixed meaning; the 
orientation of the cross product of the gradients of polar angle and 
eccenctricity, relative to the cortical surface.  Are you sure you didn't 
reverse the stimulus order or something? Was the projector's image upside down

[Freesurfer] vtkMultiThreader error

[Don Hagler]

When we run v430 on our cluster, running rocks redhat 4.3, we get the error 
message below when mris_volmask is run.  From a google search, I see that 
someone had the same error message back in Oct 2007.  Was a solution found for 
this?  It runs fine on our desktop machines as well as when we log in directly 
to a node and run the job interactively.



 mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 
--label_right_ribbon 42 --save_ribbon --save_distance 
FREESURFERRECON_NTNU_PRE_095v2_20071126.173245.968000_1

SUBJECTS_DIR is /home/dhagler/data_test
ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 
372
vtkMultiThreader (0x1306ec80): Unable to create a thread.  pthread_create() 
returned 12

ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 
372
vtkMultiThreader (0x1306ec80): Unable to create a thread.  pthread_create() 
returned 12

ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 
372
vtkMultiThreader (0x1306ec80): Unable to create a thread.  pthread_create() 
returned 12

ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 
372
vtkMultiThreader (0x1306ec80): Unable to create a thread.  pthread_create() 
returned 12

ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 
372
vtkMultiThreader (0x1306ec80): Unable to create a thread.  pthread_create() 
returned 12

ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 
372
vtkMultiThreader (0x1306ec80): Unable to create a thread.  pthread_create() 
returned 12

ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx, line 
372
vtkMultiThreader (0x1306ec80): Unable to create a thread.  pthread_create() 
returned 12

Segmentation fault
Linux compute-0-12.local 2.6.9-55.0.2.ELsmp #1 SMP Tue Jun 26 14:14:47 EDT 2007 
x86_64 x86_64 x86_64 GNU/Linux

recon-all exited with ERRORS at Fri Jun  5 18:58:09 PDT 2009





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RE: [Freesurfer] vtkMultiThreader error

[Don Hagler]

Hi Nick,

Thanks for the reply.  I will look into the memory limit issue some more (we 
recently instituted per job memory limits), but I have done a test run with a 
16GB memory limit (running one job per node).

Meanwhile, thanks for the novtk suggestion.  Our fallback option is to just 
disable the ribbon generation.  I don't think we ever use them for anything.

Don


> Subject: Re: [Freesurfer] vtkMultiThreader error
> From: ni...@nmr.mgh.harvard.edu
> To: martin.ka...@gmail.com; dhagle...@hotmail.com
> Date: Mon, 8 Jun 2009 11:15:51 -0400
> CC: freesurfer@nmr.mgh.harvard.edu
> 
> Don and Martin,
> 
> I dont have a good solution for you to this problem.  The error code
> indicates an 'out-of-memory' error returned by pthread_create, and I do
> know the mris_vol_mask uses a lot of memory (at least 1GB).
> 
> I have not been able to find any clues to the source of this problem on
> the web either.  The only curious thing to it is that in the source
> code, that section is conditionally compiled to ignore the return code
> if 'VTK_HP_PTHREADS' is defined, which implies some sort of odd behavior
> on some special HP platform build.
> 
> mris_vol_mask has been a real thorn in the side of the recon-all stream,
> but its not easy to replace because it does a subjectively better job of
> finding the voxels which intersect the pial and white surfaces.  For
> comparison, or even to solve your problem, you can use
> mris_vol_mask_novtk to create the ribbon.mgz files.  The output is not
> the same as that produced by mris_vol_mask though.  Perhaps you can run
> it, and compare the results side-by-side and give us your opinion on
> which is the better ribbon (as there is no objective measure on what a
> 'correct' ribbon.mgz should like like, ie, should it include voxels that
> intersect more than half way through a surface, or not at all?).
> 
> Nick
> 
> 
> On Mon, 2009-06-08 at 09:16 +0200, Martin Kavec wrote:
> > Hi Don,
> > 
> > I am in a similar situation. I am on a IBM BladeCenter cluster (though with 
> > one blade only) with 2 Quad core Intels, and I experience intermittent 
> > crashes of mri_volmask as well. Similarly as you, when I run the 
> > mri_volmask 
> > on the crashed subject on a desktop, this passes perfectly fine and 
> > sometimes 
> > also on the cluster as well.
> > 
> > I am wonder whether how do you obtain the debug information about the cause 
> > of 
> > the crash (being in the vtkMultiThreader)?
> > 
> > I also wonder, whether the crashes could be due to different compilation 
> > environments of the VTK libraries used in teh FS distribution (centos) and 
> > your redhat. I went on the bug-report site of VTK and there really isn't 
> > anythink major reported on this class. 
> > 
> > In my experience the mri_volmask runs fine for quite a while and then 
> > crashes. 
> > >From the debug messages you show it would thus could be that the process 
> > >may 
> > hit some limit of the threads which could be allocated to a process.
> > 
> > What do you think?
> > 
> > Martin  
> > 
> > On Saturday 06 June 2009 04:19:51 Don Hagler wrote:
> > > When we run v430 on our cluster, running rocks redhat 4.3, we get the 
> > > error
> > > message below when mris_volmask is run.  From a google search, I see that
> > > someone had the same error message back in Oct 2007.  Was a solution found
> > > for this?  It runs fine on our desktop machines as well as when we log in
> > > directly to a node and run the job interactively.
> > >
> > >
> > >
> > >  mris_volmask --label_left_white 2 --label_left_ribbon 3
> > > --label_right_white 41 --label_right_ribbon 42 --save_ribbon
> > > --save_distance FREESURFERRECON_NTNU_PRE_095v2_20071126.173245.968000_1
> > >
> > > SUBJECTS_DIR is /home/dhagler/data_test
> > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> > > pthread_create() returned 12
> > >
> > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> > > pthread_create() returned 12
> > >
> > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThreader.cxx,
> > > line 372 vtkMultiThreader (0x1306ec80): Unable to create a thread. 
> > > pthread_create() returned 12
> > >
> > > ERROR: In /usr/pubsw/packages/vtk/5.2.0/src/Common/vtkMultiThrea

RE: [Freesurfer] vtkMultiThreader error

[Don Hagler]

On one cluster that has default memory limits, I get this error, even when I 
override those limits with qsub up to 16GB.  On another cluster, without any 
pre-set limits, I do not get the error.  But when I qsub with a memory limit 
(even 8GB), then the errors happen on this cluster too.So there is plenty 
of memory, but somehow just having a limit at all seems to cause problems for 
vtkmultithreader.

For now, I guess the solution will be to disable the ribbon making.  Thanks, 
Nick, for pointing out the downstream dependencies.


From: christopher.nu...@loni.ucla.edu
To: freesurfer@nmr.mgh.harvard.edu
Date: Tue, 9 Jun 2009 10:16:39 -0700
Subject: FW: RE: [Freesurfer] vtkMultiThreader error

I am getting similar error messages when running on our grid and pipeline 
systems (see below).  Our tech people had previously thought this could be 
related to memory capacity issues, but after increasing memory to 8gb when 
submitting my jobs with a qsub command, the problem is still not resolved.  I'm 
beginning to have doubts about this being related to memory capacity.
 
 
Could somebody please provide instructions on disabling the ribbon processing?  
Thank you.
 
 
#...@# Cortical ribbon mask Sun May 31 18:21:54 PDT 2009
/ifs/edevel/CN_SAN_DIEGO/FREESURFER/OUTPUT/164/mri
\n mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 
41 --label_right_ribbon 42 --save_ribbon --save_distance 164 \n
ERROR: In 
/usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line 372
vtkMultiThreader (0x3279bb60): Unable to create a thread.  pthread_create() 
returned 12
 
ERROR: In 
/usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line 372
vtkMultiThreader (0x3279bb60): Unable to create a thread.  pthread_create() 
returned 12
 
ERROR: In 
/usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line 372
vtkMultiThreader (0x3279bb60): Unable to create a thread.  pthread_create() 
returned 12
 
ERROR: In 
/usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line 372
vtkMultiThreader (0x3279bb60): Unable to create a thread.  pthread_create() 
returned 12
 
ERROR: In 
/usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line 372
vtkMultiThreader (0x3279bb60): Unable to create a thread.  pthread_create() 
returned 12
 
ERROR: In 
/usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line 372
vtkMultiThreader (0x3279bb60): Unable to create a thread.  pthread_create() 
returned 12
 
ERROR: In 
/usr/pubsw/packages/vtk/5.1.0-CVS/src/VTK/Common/vtkMultiThreader.cxx, line 372
vtkMultiThreader (0x3279bb60): Unable to create a thread.  pthread_create() 
returned 12
 
 
 
 
---
S. Christopher Nuñez, PhD
Postdoctoral Fellow
Developmental Cognitive Neuroimaging Group
Laboratory of Neuro Imaging
UCLA Dept of Neurology
Neuroscience Research Building 1, Suite 225
635 Charles Young Drive South
Los Angeles, CA 90095-7334
(310) 267-
---

From: hranilov...@ucla.edu [hranilov...@ucla.edu]
Sent: Monday, June 08, 2009 12:13 PM
To: Christopher Nunez
Subject: Fwd: RE: [Freesurfer] vtkMultiThreader error
 
Pretty much what I was saying the other day.  It looks like maybe you
can disable this step if you don't want this output, though?
 
- Forwarded message from dhagle...@hotmail.com -
 Date: Mon, 8 Jun 2009 11:19:43 -0700
     From: Don Hagler 
Reply-To: Don Hagler 
  Subject: RE: [Freesurfer] vtkMultiThreader error
   To: ni...@nmr.mgh.harvard.edu, martin.ka...@gmail.com
   Cc: freesurfer maillist 
 
 
Hi Nick,
 
Thanks for the reply.  I will look into the memory limit issue some
more (we recently instituted per job memory limits), but I have done a
test run with a 16GB memory limit (running one job per node).
 
Meanwhile, thanks for the novtk suggestion.  Our fallback option is to
just disable the ribbon generation.  I don't think we ever use them
for anything.
 
Don
 
 
> Subject: Re: [Freesurfer] vtkMultiThreader error
> From: ni...@nmr.mgh.harvard.edu
> To: martin.ka...@gmail.com; dhagle...@hotmail.com
> Date: Mon, 8 Jun 2009 11:15:51 -0400
> CC: freesurfer@nmr.mgh.harvard.edu
>
> Don and Martin,
>
> I dont have a good solution for you to this problem.  The error code
> indicates an 'out-of-memory' error returned by pthread_create, and I do
> know the mris_vol_mask uses a lot of memory (at least 1GB).
>
> I have not been able to find any clues to the source of this problem on
> the web either.  The only curious thing to it is that in the source
> code, that section is conditionally compiled to ignore the return code
> if 'VTK_HP_PTHREADS' is defined, which implies some sort of odd behavior
> on some special HP platform build.
>
> mris_vol_m

Re: [Freesurfer] Overlay surface onto EPI

[Don Hagler]

thickness
%   1.00   # ?
%   9.969735e-01 -7.713004e-02 -9.725398e-03 1.009433e+00  # transformation matrix
%   2.020466e-02 3.778771e-01 -9.256357e-01 2.806142e+01
%   7.506926e-02 9.226375e-01 3.782920e-01 9.858908e+00
%   0.00e+00 0.00e+00 0.00e+00 1.00e+00
%   round   # how to handle float to int conversion
%
%  See fs_write_regdat.m
%
%  created:   07/18/08   by Don Hagler
%  last modified: 07/18/08   by Don Hagler
%


%%%

M = []; subj = []; inplane = []; slicethick = [];
if (~mmil_check_nargs(nargin,1)) return; end;
parms = mmil_args2parms( varargin, {...
  'tk2ras_flag',false,sort([false true]),...
  'M_ref',eye(4),[],...
  'M_reg',eye(4),[],...
  'nvox_ref',[256 256 256],[],...
  'nvox_reg',[256 256 256],[],...
});

%%%

% read register.dat file
if ~exist(fname,'file')
  error('file %s not found',fname);
end;
fid=fopen(fname,'rt');
if fid==-1
  error('failed to open file %s for writing',fname);
end;
subj = fscanf(fid,'%s',1);
inplane = fscanf(fid,'%f',1);
slicethick = fscanf(fid,'%f',1);
tmp = fscanf(fid,'%f',1);
M = fscanf(fid,'%f',[4,4])';
fclose(fid);

%%%

if parms.tk2ras_flag
  % modify transformation matrix from tkregister to ras2ras

  M_ref = parms.M_ref;
  voxres_ref = sqrt(sum(M_ref(1:3,1:3).^2,1));
  nx = parms.nvox_ref(1);
  ny = parms.nvox_ref(2);
  nz = parms.nvox_ref(3);
  ps = voxres_ref(1);
  st = voxres_ref(3);
  M_ref_tk = [-ps 0 0 (nx/2+1)*ps; 0 0 st -(nz/2+1)*st; 0 -ps 0 (ny/2+1)*ps; 0 0 0 1];

  M_reg = parms.M_reg;
  voxres_reg = sqrt(sum(M_reg(1:3,1:3).^2,1));
  nx = parms.nvox_reg(1);
  ny = parms.nvox_reg(2);
  nz = parms.nvox_reg(3);
  ps = voxres_reg(1);
  st = voxres_reg(3);
  M_reg_tk = [-ps 0 0 (nx/2+1)*ps; 0 0 st -(nz/2+1)*st; 0 -ps 0 (ny/2+1)*ps; 0 0 0 1];

  % convert from tkras2tkras to ras2ras
  M_ref_to_reg = M_reg * inv(M_reg_tk) * M * M_ref_tk * inv(M_ref);

  % reverse translations
  Y = diag([-1 -1 -1]);
  M_ref_to_reg(1:3,4) = Y*M_ref_to_reg(1:3,4);

  % reverse x rotation (by flipping z)
  X = diag([1 1 -1 1]);
  M_ref_to_reg = X*M_ref_to_reg*X;

  M = M_ref_to_reg;
end;

%%%

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[Freesurfer] Postdoctoral Position, University of California, San Diego

[Don Hagler]

Postdoctoral Research Scholar Position in Behavior Genetics and
Neuroimaging

Departments
of Psychiatry and Radiology, University of California, San Diego

 

The Departments
of Psychiatry and Radiology at the University of California, San Diego are
pleased to invite applications for a postdoctoral research scholar position in
neuroimaging and behavior genetics under the direction of Drs. Anders Dale
(Neuroscience and Radiology) and William Kremen (Psychiatry). Responsibilities
will include analysis of MRI, genetic, and behavioral data collected for the
NIH/NIA-funded Vietnam-Era Twin Study of Aging (VETSA). The successful
candidate will receive training in psychometric techniques (particularly twin
analyses) and the application and development of analysis tools for
neuroimaging data (including structural MRI, DTI, fMRI, and ASL). The
postdoctoral candidate will be encouraged to develop his or her own research
projects that fit within the overall scope of the project.

 

VETSA is a
unique longitudinal study of over 600 middle-aged male twin pairs that focuses
on understanding cognitive and brain aging.  Over 500 twins have undergone
structural MRI and DTI in VETSA wave 1. A variety of additional information was
also collected, including neurocognitive, personality, and psychosocial
assessments, medical history interviews, blood pressure, pulmonary function,
and hormonal levels. DNA has been obtained from all subjects and they have been
genotyped for APOE. Genome-wide genotyping of all VETSA subjects is planned.
Wave 2 of the project will acquire five-year follow-up data, and also include
fMRI and ASL scans.

 

Applicants for the position must have completed relevant Ph.D. research 
activities within
the past five years. Applications from many disciplines may be considered, and
the position is open to qualified international applicants.

 

Experience or
expertise in the following areas is highly desired:

1. 
computer
programming (especially MATLAB, C/C++, or similar)

2. 
neuroimaging
analysis methods (especially FreeSurfer)

3. 
structural
MRI, DTI, fMRI, ASL

4. 
scientific
writing

5. 
advanced
statistical analyses

6. 
twin
modeling (especially using Mx software)

7. 
genetics

 

This posting is
for a 2-year appointment beginning immediately. Salary will be consistent
with the NIH/NRSA levels in accordance with the University of California, San
Diego policies for Postdoctoral trainees. Compensation includes full staff
benefits, including health insurance, and vacation time. Review of applications
will begin immediately and will continue until the position is filled. To apply,
please send your CV, a brief statement of research
interests and goals, and any selected reprints to wkre...@ucsd.edu and
amd...@ucsd.edu with the subject line "VETSA
Postdoctoral position".  Letters of
reference will be required before final approval of hiring. Informal inquiries
for more details are welcome.

 


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[Freesurfer] mris_expand

[Don Hagler]

Bruce recently wrote that you could run mris_expand like this:
mris_expand -t lh.white 0.5 lh.graymid

I found that didn't work, but this did:
mris_expand -thickness lh.white 0.5 lh.graymid

I am using version 4.4.


By the way, is there a way to increase the resolution of the surfaces before 
creating final surfs?


  
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[Freesurfer] glut

[Don Hagler]

I recently started getting this error message when running tkmedit:
GLUT: Fatal Error in tkmedit.bin: failed to create OpenGL rendering context.

This is with v4.4 on a machine running RHE5.  Recent updates to RHE5 may be to 
blame.

I get this error when running v3.0.5:
freeglut 
(/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R305/bin/tkmedit.bin): 
Unable to create direct context rendering for window 'Medit: '
This may hurt performance.
X Error of failed request:  BadMatch (invalid parameter attributes)
  Major opcode of failed request:  143 (GLX)
  Minor opcode of failed request:  5 (X_GLXMakeCurrent)
  Serial number of failed request:  37
  Current serial number in output stream:  37

I see that there have been previous posts about similar errors, but I haven't 
found any replies with solutions.

tkmedit does work when I use a different user account than the one I log into 
the xserver with.  In that case, I get these messages:
NVIDIA: could not open the device file /dev/nvidiactl (Permission denied).
freeglut 
(/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R305/bin/tkmedit.bin): 
Unable to create direct context rendering for window 'Medit: '
This may hurt performance.


Does anyone know of a solution for this problem?
  
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Re: [Freesurfer] glut

[Don Hagler]

I was able to resolve my issue related to OpenGL causing tksurfer and tkmedit 
to have problems, and the solution may be helpful to others.

The problem was that the kernel had been updated (e.g. yum update), causing 
problems for the nvidia display driver.  The solution was to uninstall the 
nvidia driver (e.g. yum erase dell-nvidia) and then to reinstall the nvidia 
driver downloaded from support.dell.com (e.g. rpm -ihv 
dell-nvidia-180.29-1dkms_rhel5.3.a01.x86_64.rpm).  The uninstall and reinstall 
should be done as root in init mode 3 (e.g. Ctl-Alt-F1).



From: dhagle...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Date: Fri, 9 Oct 2009 17:29:32 -0700
Subject: [Freesurfer] glut








I recently started getting this error message when running tkmedit:
GLUT: Fatal Error in tkmedit.bin: failed to create OpenGL rendering context.

This is with v4.4 on a machine running RHE5.  Recent updates to RHE5 may be to 
blame.

I get this error when running v3.0.5:
freeglut 
(/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R305/bin/tkmedit.bin): 
Unable to create direct context rendering for window 'Medit: '
This may hurt performance.
X Error of failed request:  BadMatch (invalid parameter attributes)
  Major opcode of failed request:  143 (GLX)
  Minor opcode of failed request:  5 (X_GLXMakeCurrent)
  Serial number of failed request:  37
  Current serial number in output stream:  37

I see that there have been previous posts about similar errors, but I haven't 
found any replies with solutions.

tkmedit does work when I use a different user account than the one I log into 
the xserver with.  In that case, I get these messages:
NVIDIA: could not open the device file /dev/nvidiactl (Permission denied).
freeglut 
(/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R305/bin/tkmedit.bin): 
Unable to create direct context rendering for window 'Medit: '
This may hurt performance.


Does anyone know of a solution for this problem?
  
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[Freesurfer] PostDoc Positions at UCSD MultiModal Imaging Laboratory (MMIL)

[Don Hagler]

Postdoctoral Research Scholar Position, Multimodal Imaging
Laboratory, University of California, San Diego

 

The
Multimodal Imaging Laboratory (MMIL) at the University of California, San Diego
invites applications for multiple postdoctoral research scholar positions under
the direction of Dr. Anders Dale. The successful candidates will join a
multi-disciplinary team of scientists, programmers, and support staff
addressing a variety of neuroscience questions using multimodal brain imaging,
electrophysiology, behavior, and genetics. 
An important component of the work done at MMIL, and the primary role
for the currently announced positions, is the development and improvement of
methods for the analysis of neuroimaging data. 
Postdoctoral researchers will receive training in brain imaging and
methods development, and will be encouraged to develop their own research
projects.

 

The
primary areas of development will include:

1.
Segmentation of pediatric brain scans

2. Tractography and diffusion MRI analysis and modeling

3. Multispectral lesion segmentation and quantification

4. Longitudinal registration & analysis of contrast change

5. EEG/MEG/fMRI integration and modeling

6. Resting state fMRI & ASL analysis, quantification within
anatomically-defined ROIs

7.
Validation of non-invasive imaging measures using ex vivo histology and 
stereology 



Applicants for the position must have completed relevant Ph.D. research
activities within the past five years. Applications from many disciplines may
be considered, and the position is open to qualified international applicants.

 

Experience
or expertise in the following areas is highly desired:

1.  computer programming experience
(MATLAB, C/C++, Python, OpenGL, tcl/tk)

2.  neuroimaging analysis methods
(especially FreeSurfer)

3.  structural MRI, DTI, fMRI, ASL

4.  MRI physics and/or pulse
programming

5.  scientific writing

 

This
posting is for 2-year appointments beginning immediately. Salary will be
consistent with the NIH/NRSA levels in accordance with the University of
California, San Diego policies for Postdoctoral trainees. Compensation includes
full staff benefits, including health insurance, and vacation time. Review of
applications will begin immediately and will continue until the position is
filled. To apply, please send your CV, a
brief statement of research interests and goals, and any selected reprints to
amd...@ucsd.edu with the subject line "MMIL
postdoctoral position".  Letters
of reference will be required before final approval of hiring. Informal
inquiries for more details are welcome.

  
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Re: [Freesurfer] thickness maps: FDR versus Monte Carlo - different results

[Don Hagler]

Who says FDR is more conservative?  It all depends on the thresholds you choose.

Note that the FDR threshold is different from the cluster-based p
threshold, and it isn't necessarily appropriate to use the same for
both.

The cluster-based p threshold controls the overall probability that you will 
get 1 or more false positives.  With p<0.05, the idea is that if you repeated 
your study 20 times, 19 times out of 20, you would have NO false positives.

With an FDR threshold of 0.05, you are guaranteed that 5% of your
"significant" vertices are false positives.  A more conservative
threshold would be 0.01.


By the way, for cluster thresholding, there are two p thresholds that are 
important.  The first is the p threshold applied to the z-stats or t-stats 
before finding clusters.  0.05 would usually be too liberal.  0.01 or 0.001 
would be better.  The second is the multiple comparison corrected p value, for 
which you would usually use 0.05.

Date: Fri, 29 Jan 2010 10:02:45 -0500
From: stefan.bra...@googlemail.com
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] thickness maps: FDR versus Monte Carlo - different
results

Hi there,


we are struggling with one question and haven't yet heard back. We would be 
very grateful for any advice or recommendation.
We were running an analysis (95 subjects) examining a group effect (two groups, 
controlling for the effects of a covariate and two cofactors, DODS model) on 
cortical thickness with mri_glmfit. We then corrected our results for multiple 
comparisons using two methods, FDR and Monte Carlo simulation with 4000 
repeats. The threshold was set at p=0.05 respectively. Although examining the 
same population we got results in very different regions.


command for the simulation:


mri_glmfit-sim --glmdir .glmdir --sim mc-z 4000 1.301 mc-z abs.1.301 
--sim-sign abs


the fdr results were obtained setting the fdr-threshold at p=0.05 with the 
tksurfer script command (sclv_set current_threshold_using_fdr 0.05 0)


With the fdr method we found a spot in the left supramarginal gyrus and with 
the clusterwise correction we got a cluster in the right middle temporal lobe 
(see pictures of corrected and uncorrected results attached). No other 
clusters/findings survived one of the correction methods.




We are well aware of the fact that FDR and Monte Carlo simulation are very 
different statistical methods and that FDR is more conservative. Does that 
explain the discrepant results? Would you expect a highly robust FDR finding to 
not show up at all when using Monte Carlo? What additional information could be 
used to decide which method to use for the final models?  

 Thank you,
Stefan



  
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Re: [Freesurfer] thickness maps: FDR versus Monte Carlo - different results

[Don Hagler]

In my experience, which is more in fMRI than thickness analyses, 0.05 can yield 
very large mega-clusters that should actually be considered a conglomeration of 
smaller clusters.  I found that regardless of whether one does Monte Carlo or 
GRF.  Because 0.05 for uncorrected p values is quite liberal, only the very 
large clusters survive the multiple comparisons correction.  So you can end up 
losing the smaller, but still significant clusters.  For very smooth data (e.g. 
dSPMs from MEG/EEG), you may just get one huge cluster if you use 0.05.



> Date: Fri, 29 Jan 2010 14:08:04 -0500
> From: gr...@nmr.mgh.harvard.edu
> To: dhagle...@hotmail.com
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] thickness maps: FDR versus Monte Carlo -
> different results
> 
> Don, why do you say that  .05 is too liberal? We use a simulation-based 
> test, not GRF, so we don't have to worry about the GRF assumptions 
> breaking down at higher p-values.
> 
> doug
> 
> Don Hagler wrote:
> > Who says FDR is more conservative?  It all depends on the thresholds 
> > you choose.
> >
> > Note that the FDR threshold is different from the cluster-based p 
> > threshold, and it isn't necessarily appropriate to use the same for both.
> >
> > The cluster-based p threshold controls the overall probability that 
> > you will get 1 or more false positives.  With p<0.05, the idea is that 
> > if you repeated your study 20 times, 19 times out of 20, you would 
> > have NO false positives.
> >
> > With an FDR threshold of 0.05, you are guaranteed that 5% of your 
> > "significant" vertices are false positives.  A more conservative 
> > threshold would be 0.01.
> >
> > By the way, for cluster thresholding, there are two p thresholds that 
> > are important.  The first is the p threshold applied to the z-stats or 
> > t-stats before finding clusters.  0.05 would usually be too liberal.  
> > 0.01 or 0.001 would be better.  The second is the multiple comparison 
> > corrected p value, for which you would usually use 0.05.
> >
> > 
> > Date: Fri, 29 Jan 2010 10:02:45 -0500
> > From: stefan.bra...@googlemail.com
> > To: Freesurfer@nmr.mgh.harvard.edu
> > Subject: [Freesurfer] thickness maps: FDR versus Monte Carlo - 
> > different results
> >
> > Hi there,
> >
> > we are struggling with one question and haven't yet heard back. We 
> > would be very grateful for any advice or recommendation.
> >
> > We were running an analysis (95 subjects) examining a group effect 
> > (two groups, controlling for the effects of a covariate and two 
> > cofactors, DODS model) on cortical thickness with mri_glmfit. We then 
> > corrected our results for multiple comparisons using two methods, FDR 
> > and Monte Carlo simulation with 4000 repeats. The threshold was set at 
> > p=0.05 respectively. Although examining the same population we got 
> > results in very different regions.
> >
> > command for the simulation:
> >
> > mri_glmfit-sim --glmdir .glmdir --sim mc-z 4000 1.301 mc-z 
> > abs.1.301 --sim-sign abs
> >
> > the fdr results were obtained setting the fdr-threshold at p=0.05 with 
> > the tksurfer script command (sclv_set current_threshold_using_fdr 0.05 0)
> >
> > With the fdr method we found a spot in the left supramarginal gyrus 
> > and with the clusterwise correction we got a cluster in the right 
> > middle temporal lobe (see pictures of corrected and uncorrected 
> > results attached). No other clusters/findings survived one of the 
> > correction methods.
> >
> > We are well aware of the fact that FDR and Monte Carlo simulation are 
> > very different statistical methods and that FDR is more conservative. 
> > Does that explain the discrepant results? Would you expect a highly 
> > robust FDR finding to not show up at all when using Monte Carlo? What 
> > additional information could be used to decide which method to use for 
> > the final models?  
> >  
> > Thank you,
> >
> > Stefan
> >
> >
> >
> >
> >
> > 
> > Hotmail: Free, trusted and rich email service. Get it now. 
> > <http://clk.atdmt.com/GBL/go/196390708/direct/01/>
> > 
> >
> > ___
> > Freesurfer ma

[Freesurfer] Postdoctoral Research Scholar Position, Multimodal Imaging Laboratory, University of California, San Diego

[Don Hagler]

Postdoctoral Research Scholar Position, Multimodal Imaging
Laboratory, University of California, San Diego

 

The Multimodal
Imaging Laboratory (MMIL) at the University of California, San Diego invites
applications for a postdoctoral research scholar position under the direction
of Drs. Donald Hagler and Anders Dale. The successful candidate will join a
multi-disciplinary team of scientists, programmers, and support staff
addressing a variety of neuroscience questions using multimodal brain imaging,
electrophysiology, behavior, and genetics. 


 

An important
component of the work done at MMIL, and an integral role of the currently
announced position, is the development and improvement of methods for the
analysis of neuroimaging data.  This
will include extending our recent work on a white matter fiber tract atlas
(Hagler et al., HBM 2009) to encompass a more diverse population of subjects,
additional fiber tracts, and a larger age range, including infants. The
postdoctoral researcher will receive training in brain imaging and methods
development, and will be encouraged to develop his or her own research
projects.

 

Applicants for the position must have completed relevant Ph.D. research 
activities within
the past five years. Applications from many disciplines may be considered, and
the position is open to qualified international applicants.

 

Experience or
expertise in the following areas is highly desired:

1. 
computer
programming (e.g. MATLAB, C/C++).

2. 
structural
MRI, diffusion MRI

3. 
neuroimaging
analysis software (e.g. FreeSurfer, FSL)

4. 
scientific
writing

 

This posting is
for a 2-year appointment beginning immediately. Salary will be consistent
with the NIH/NRSA levels in accordance with the University of California, San
Diego policies for Postdoctoral trainees. Compensation includes full staff
benefits, including health insurance, and vacation time. Review of applications
will begin immediately and will continue until the position is filled. To apply,
please send your CV, a brief statement of research
interests and goals, and any selected reprints to dhagle...@hotmail.com with
the subject line "MMIL
postdoctoral position".  Letters of
reference will be required before final approval of hiring. Informal inquiries
for more details are welcome.

  
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Re: [Freesurfer] retinotopy: MGH vs UCSD

[Don Hagler]

There is no version of freesurfer being distributed by Anders Dale at UCSD.


Marty Sereno does has a version of freesurfer branched from version 0.9.  His 
includes a gui called csurf that can launch the retinotopy analyses (among 
other things) for a single subject.  In general, it is somewhat dated.  For 
example, it does not use mgh/mgz format, but rather a mixture of BRIK and 
bfloat/bshort.  The cortical surface reconstruction stream also does not have 
many of the improvements made at MGH in the last several years (e.g. better 
topo fixing, aseg).

I've never used it, but an advantage of the MGH freesurfer retinotopy analysis 
stream is that it is documented, supported, and consistent with the latest 
cortical reconstruction stream distributed with MGH freesurfer.




> Date: Thu, 10 Jun 2010 05:59:58 -0400
> From: gr...@nmr.mgh.harvard.edu
> To: francescastrapp...@gmail.com
> CC: Freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] retinotopy: MGH vs UCSD
> 
> 
> What do you mean by the UCSD freesurfer? A long time ago I re-wrote
> a stream that Anders was using, and it gave similar results. I've just
> re-written it again and it will be released with version 5.
> 
> doug
> 
> 
> On Wed, 9 Jun 2010, francesca strappini wrote:
> 
> > Hi all,
> > I would ask you about freesurfer and retinotopy. I'm going to begin the
> > analysis of some retinotopic data. I would ask if you know if the
> > retinotopic analysis made by MGH freesurfer is qualitatively comparable to,
> > or it's good as, that made by USCD freesurfer (old freesurfer).
> > Thank you kindly in advance.
> >
> > Francesca
> >
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
> 
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> ___
> 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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[Freesurfer] MMIL postdoctoral position

[Don Hagler]

Postdoctoral Research Scholar Position, Multimodal Imaging
Laboratory, University of California, San Diego

 

The Multimodal
Imaging Laboratory (MMIL) at the University of California, San Diego invites
applications for a postdoctoral research scholar position under the direction
of Drs. Donald Hagler and Anders Dale. The successful candidate will join a
multi-disciplinary team of scientists, programmers, and support staff
addressing a variety of neuroscience questions using multimodal brain imaging,
electrophysiology, behavior, and genetics. 


 

An important
component of the work done at MMIL, and an integral role of the currently
announced position, is the development and improvement of methods for the
analysis of neuroimaging data.  This
will include extending our recent work on a white matter fiber tract atlas
(Hagler et al., HBM 2009) to encompass a more diverse population of subjects,
additional fiber tracts, and a larger age range, including infants. The
postdoctoral researcher will receive training in brain imaging and methods
development, and will be encouraged to develop his or her own research
projects.

 

Applicants for the position must have completed relevant Ph.D. research 
activities within
the past five years. Applications from many disciplines may be considered, and
the position is open to qualified international applicants.

 

Proficiency in
the following areas is required:

1. 
computer
programming (e.g. MATLAB, C/C++)

2. 
scientific
writing

 

Experience
and/or interest in the following areas is desired:

1. 
structural
MRI, diffusion MRI

2. 
neuroimaging
analysis software (e.g. FreeSurfer, FSL)

 

This posting is
for a 2-year appointment beginning immediately. Salary will be consistent
with the NIH/NRSA levels in accordance with the University of California, San
Diego policies for Postdoctoral trainees. Compensation includes full staff
benefits, including health insurance, and vacation time. Review of applications
will begin immediately and will continue until the position is filled. To apply,
please send your CV, a brief statement of research
interests and goals, and any selected reprints to dhagle...@hotmail.com with
the subject line "MMIL
postdoctoral position".  Letters of
reference will be required before final approval of hiring. Informal inquiries
for more details are welcome.

  
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Re: [Freesurfer] Replacing talairach.xfm

[Don Hagler]

The attached file can by copied over the existing talairach.xfm (you might want 
to make a backup copy).

To clarify for others reading this, you would only do this when you want to run 
make_average_subject on a single subject so as to resample a subject's surface 
to ico (useful for quantifying areal expansion/contraction, and for making 
MEG/EEG forward models with ico=4).


Date: Wed, 28 Jul 2010 01:27:52 +0100
From: lena.palaniyap...@nottingham.ac.uk
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] Replacing talairach.xfm





Message body


Hi all,

How do I replace talairach.xfm by an identity matrix to prevent reorienting of 
images when I make-average ?

Cheers

Lena



This message has been checked for viruses but the contents of an attachment
may still contain software viruses which could damage your computer system:
you are advised to perform your own checks. Email communications with the
University of Nottingham may be monitored as permitted by UK legislation.




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identity.xfm
Description: Binary data
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Re: [Freesurfer] keyboard problem in freesurfer

[Don Hagler]

We had exactly that problem on machines running RedHat 5, but it was solved by 
reinstalling with the latest CentOS.


From: kc...@bu.edu
Date: Wed, 4 Aug 2010 15:44:52 -0400
To: fis...@nmr.mgh.harvard.edu
CC: freesurfer@nmr.mgh.harvard.edu; ni...@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] keyboard problem in freesurfer

Nope, no errors when tksurfer starts, and I've tried running it with both my 
own data/folder and with the tutorial data/folders, and have the same problem.  
I don't currently have freesurfer installed on a laptop, and the only laptop I 
have access to is a mac (whereas I am using linux for most of my analysis).  I 
can see what happens if I try installing it on the mac and see if it has the 
same problem, but I assume it's somehow specific to my linux machine if others 
aren't having the same problem.


Katie

On Wed, Aug 4, 2010 at 3:19 PM, Bruce Fischl  wrote:


Hi Katie,

can you replicate this problem on a laptop? If so, maybe you want to swing by 
MGH with it and we can take a look? There are no errors when tksurfer starts?

Bruce

On Wed, 4 Aug 2010, Katie Bettencourt wrote:




Ok, I tried to unset the FSLTCLSH variable (which is the only one that came

up when I grep TCL) to see if that allowed me to use keyboard input with

tksurfer, but it didn't work.



I really need to be able to use the keyboard with tksurfer so that I can

save label files and rgbs, etc.  Is there any way I can get this fixed?

Please?



Katie








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Re: [Freesurfer] Red Hat vs. CentOs

[Don Hagler]

In my recent experience, no.  There were problems with entering text in 
tksurfer/tkmedit when running on the pre-installed RHEL that went away when 
CentOS was installed later.



> Date: Mon, 9 Aug 2010 15:42:57 -0400
> From: rai...@nmr.mgh.harvard.edu
> To: dah...@nmr.mgh.harvard.edu
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Red Hat vs. CentOs
> 
> 
> Yes, it should be almost no different.
> 
> On Mon, 9 Aug 2010 dah...@nmr.mgh.harvard.edu wrote:
> 
> > Hi,
> >
> > I'd like to make sure that a Dell desktop with pre-installed RHEL would
> > work seamlessly with Freesurfer, equivalent to CentOS. Is this correct?
> >
> > Thanks,
> > Dahlia.
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >
> >
> 
> -- 
> ---
> Paul Rainesemail: raines at nmr.mgh.harvard.edu
> MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging
> 149 (2301) 13th Street Charlestown, MA 02129  USA
> 
> 
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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 HelpLine 
> at
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Re: [Freesurfer] System requirements

[Don Hagler]

Is the 2.7GB RAM estimate new for v5?  For v3 and v4, 2GB seems to have been 
sufficient (using a hard limit on a cluster).  We haven't switched to v5 yet 
(waiting for 5.1 or 5.2), so would like to know what to expect when we do.

> From: ni...@nmr.mgh.harvard.edu
> To: daniel.geis...@gmail.com
> Date: Wed, 22 Sep 2010 16:50:59 -0400
> CC: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] System requirements
> 
> the second option is best because it uses the x86 processor (amd
> opteron), which is our common distribution.  the first option uses the
> Itanium processor which we dont actively support because we no longer
> have access to a build machine.
> 
> the recon-all stream is not parallelized so you wouldnt benefit from
> multi-cores or any special parallelization hardware.  runtime on the amd
> cluster would be about 25 hours per subject, and consume a peak of about
> 2.7GB of ram.  each subject consumes around 400MB of hard disk space
> (budget 500MB per subject).  negligible temporary hard disk space is
> used.
> 
> n.
> 
> On Wed, 2010-09-22 at 19:17 +0200, daniel geisler wrote:
> > Dear Freesurfers!
> > 
> > I am a new user of freesurfer and I intend to install it on a HPC
> > system. There are two different systems available (see end of
> > message). Could you please give me a hint which one is best suited wrt
> > hardware and software.
> > 
> > In order to use these systems one also has to state some estimations
> > of the needed resources. In detail, I have to estimate:
> > 
> >  * CPU time
> >  * maximal number of parallel used CPUs
> >  * size of used RAM
> >  * size of permanent HDD usage
> >  * size of temporary HDD usage
> > 
> > Could you share some experience how many resources are usually used
> > for the segmentation (recon-all) of a single subject?
> > 
> > Thank you & best wishes from Dresden,
> > Daniel
> > 
> > ---
> > 1.SGI Altix 4700 (Mars)
> > 
> >  * For highly parallel and memory-intensive applications
> >  * 2048 cores Intel Itanium II Montecito 1.6 GHz
> >  * 6,5 TB memory
> >  * One partition for interactive operation with 128 cores
> >  * 68 TB SAN disk storage
> >  * 1 PB SAN tape archive
> >  * SuSE Linux Enterprise Server 10, SGI ProPack 5, batch system LSF
> >  * 13,1 TFlop/s peak performance
> > 
> > 2. Linux Networx Evolocity II PC-Farm  (Deimos)
> > 
> >  * For capacity computing
> >  * 2576 cores AMD Opteron 2,6 GHz
> >  * 5,4 TB memory
> >  * 724 nodes with 1, 2, or 4 dual-core CPUs each
> >  * 68 TB SAN disk storage
> >  * SuSE Linux Enterprise Server 10, batch system LSF
> >  * 13,9 TFlop/s peak performance
> > 
> > For software specification please refer to:
> > http://tu-dresden.de/die_tu_dresden/zentrale_einrichtungen/zih/hpc/hochleistungsrechner/hpc_software?set_language=en&cl=en
> > ___
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> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
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Re: [Freesurfer] Surface Area and Cortical Volume

[Don Hagler]

The area maps do contain the actual surface area of each vertex with units of 
mm^2.  The problem is that the area at a given vertex depends on how many 
vertices a given patch of
 cortex was divided into, which is initially uniform but then varies 
arbitrarily due
 to topology correction, rendering it useless for making statistical maps.

If you are interested in making statistical maps of between-group differences 
in surface area, the best way to do that is by calculating the areal expansion 
measure.  This is not a normally used feature of freesurfer, but is possible by 
using make_average_subject separately for each subject.

If you use the area values in the aparc stats files, those are the sum of area 
for all vertices in each parcellation, and they have units of surface area 
(unlike measures of areal expansion).



> From: jsadino.que...@gmail.com
> Date: Wed, 29 Sep 2010 15:57:38 -1000
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] Surface Area and Cortical Volume
> 
> Hello,
> 
> As I understand it, the surface area measure is not a real surface
> area measure.  It is more a measure of how much the brain has to be
> stretched in order to get into a common space.  My question is that if
> the cortical volume is calculated by multiplying the thickness and the
> surface area (right?), then is it a real volume that can be compared
> between subjects?
> 
> Also, is it is more accurate to use the cortical volume measures from
> the aparc files rather than the aseg files, since the aseg files
> overestimate the white matter due to the manual tracing it is based
> on?
> 
> Thank you,
> Jeff
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> at
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> properly
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> 
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[Freesurfer] mri_vol2surf projfac-avg

[Don Hagler]

In the stable3 version of mri_vol2surf, there is an option listed 
"projfac-avg".  I can't tell if it is working or not.  In the output 
messages, it says that ProjFrac = 0.5 (or whatever value is given with 
-projfrac) but there is no mention of the projfrac-avg min and max.  Is the 
program doing what it is supposed to and not giving any relevant messages, 
or is the lack of messages an indicator that it is just doing the basic 
projfrac without averaging along the normal?



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Re: [Freesurfer] mri_vol2surf projfac-avg

[Don Hagler]

What's your cmd line? What's the output?


I've pasted the script I used and the output below.  You can see that there 
is no mention of projfract-avg in the output.


By the way, it seems that it is ignoring the voxel resolution in the 
registration file and instead using the (erroneous) resolution in the source 
volume.  That is, all of the activation is painted onto the midbrain.  I 
assume that it is related to this warning:


WARNING: the voxel resolution in the source volume (1,1,1) differs
from that listed in the registration file (3.125,3.125,3.5)

The bfloats and hdrs were generated with fourier, so there is no .bhdr file. 
 Anyway, it seems to me that it would be better to trust the voxel 
resolution in the registration file.




CMD LINE:
#! /bin/csh
source /space/monkeys/1/pubsw/packages/freesurfer/UCSDsurferenv-R302.csh
set curdir = `pwd`
set datadir = "/usr1"
set datadir = "/space/monkeys/1/home/dhagler/data"
set fspace = "$datadir/fspace"
set subj = 
set reg = register.dat
set pf_min = 0.1
set pf_max = 0.9
set pf_delta = 0.1
set session = 060312XX
set indir = avg-pol
set instem = pol-dfix-ccw-vreg-unwarp_fmri+orig
set newstem = test-polret
foreach hemi (rh lh)
 foreach infix (_r _i)
   set srcpath = "$fspace/$session/image/$indir/$instem$infix"
   set srcreg = "$fspace/$session/image/$indir/$reg"
   set outpath = $curdir/$newstem-mgh$infix-$hemi.w
   mri_vol2surf \
 --srcfmt bfloat --srcvol $srcpath --srcreg $srcreg \
 --srcoldreg --float2int tkreg \
 --hemi $hemi --surf white \
 --projfrac-avg $pf_min $pf_max $pf_delta \
 --trgsubject $subj \
 --o $outpath --ofmt paint
 end
end

OUTPUT:
CPU is x86_64
OS is RH4-x86_64-R302
afni,fsl,imagej  and spm5b are now  available.
Make sure you set SUBJECTS_DIR points to the subjects directory
-
Could not find the direction cosine information.
Will use the CORONAL orientation.
If not suitable, please provide the information in 
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/pol-dfix-ccw-vreg-unwarp_fmri+orig_r.bhdr 
file

-
INFO: output format is paint
srcvol = 
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/pol-dfix-ccw-vreg-unwarp_fmri+orig_r

srctype = bfloat
srcreg = 
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/register.dat

srcregold = 1
srcwarp unspecified
surf = white
hemi = rh
trgsubject = 
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
interp = nearest
float2int = tkreg
INFO: float2int code = 2
INFO: bvolumeRead: min = -33.9456, max = 35.5154
Done loading volume
WARNING: the voxel resolution in the source volume (1,1,1) differs
from that listed in the registration file (3.125,3.125,3.5)
Reading surface /home/dhagler/data/subjects//surf/rh.white
Done reading source surface
Reading thickness /home/dhagler/data/subjects//surf/rh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0.1 0.1 0.9
vol2surf_linear: nhits = 6675/127873
2 0.2 0.1 0.9
vol2surf_linear: nhits = 6602/127873
3 0.3 0.1 0.9
vol2surf_linear: nhits = 6551/127873
4 0.4 0.1 0.9
vol2surf_linear: nhits = 6534/127873
5 0.5 0.1 0.9
vol2surf_linear: nhits = 6483/127873
6 0.6 0.1 0.9
vol2surf_linear: nhits = 6435/127873
7 0.7 0.1 0.9
vol2surf_linear: nhits = 6419/127873
8 0.8 0.1 0.9
vol2surf_linear: nhits = 6353/127873
Done mapping volume to surface
Number of source voxels hit = 3362
avg = -0.601, stdev = 2.468, min = -29.056, max = 9.192
-
Could not find the direction cosine information.
Will use the CORONAL orientation.
If not suitable, please provide the information in 
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/pol-dfix-ccw-vreg-unwarp_fmri+orig_i.bhdr 
file

-
INFO: output format is paint
srcvol = 
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/pol-dfix-ccw-vreg-unwarp_fmri+orig_i

srctype = bfloat
srcreg = 
/space/monkeys/1/home/dhagler/data/fspace/060312XX/image/avg-pol/register.dat

srcregold = 1
srcwarp unspecified
surf = white
hemi = rh
trgsubject = 
surfreg = sphere.reg
ProjFrac = 0.5
thickness = thickness
interp = nearest
float2int = tkreg
INFO: float2int code = 2
INFO: bvolumeRead: min = -35.8874, max = 34.6494
Done loading volume
WARNING: the voxel resolution in the source volume (1,1,1) differs
from that listed in the registration file (3.125,3.125,3.5)
Reading surface /home/dhagler/data/subjects//surf/rh.white
Done reading source surface
Reading thickness /home/dhagler/data/subjects//surf/rh.thickness
Done
Mapping Source Volume onto Source Subject Surface
1 0.1 0.1 0.9
vol2surf_linear: nhits = 6675/127873
2 0.2 0.1 0.9
vol2surf_linear: nhits = 6602/127873
3 0.3 0.1 0.9
vol2surf_linear: nhits = 6551/127873
4 0.4 0.1 0.9
vol2su

[Freesurfer] memory limitations

[Don Hagler]

Running recon-all with the v3.0.2 release, I have noticed recently that the 
process will run into seg faults at various stages (e.g. topology 
correction, sphere reg, or cortical parcellation).  This seems somewhat 
random, but judging from some other posts, and the fact that it happenened 
when I was running multiple jobs at once but didn't (for the same subject) 
when it was the only job, it seems to be memory dependent.  That is, when 
there is not enough available memory, things crash without warning or 
relevant error messages (e.g. not enough memory).  Does that seem like an 
accurate assessment of things?


Aside from hardware solutions (e.g. more RAM or bigger swap space), is there 
anything that can be done to the software to allow the user to balance speed 
with memory usage?  And die in a less mysterious way?



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RE: [Freesurfer] neighborhood of a vertex

[Don Hagler]

From: "R. Chen" <[EMAIL PROTECTED]>
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] neighborhood of a vertex
Date: Mon, 12 Jun 2006 11:02:59 -0700 (PDT)

  I want to do some customrized smoothing and need to know the 
neighborhood of a vertex. I think FreeSurfer also uses this neighborhood 
information in random field modelling. Could you provide some information 
about how to get the neighborhood?


Take a look at $FREESURFER_HOME/matlab/read_surf.m.  Darren Webber at UCSF 
has something similar.


Moo Chung at UWisc has  a function called mni_getmesh.m that find the 
neighbors to enable smoothing and he has a function for heat kernel 
smoothing.


I've used those sources and made my own modifications that some might find 
useful.


Here is my modification of read_surf:
%
function [surf] = fs_read_surf(fname)
% fs_read_surf - read a freesurfer surface file
%
% [surf] = fs_read_surf(fname)
%
% Reads the vertex coordinates (mm) and face lists from a surface file
% Then finds neighbors for each vertex
%
% surf is a structure containg:
%   nverts: number of vertices
%   nfaces: number of faces (triangles)
%   faces:  vertex numbers for each face (3 corners)
%   coords: x,y,z coords for each vertex
%   nbrs:   vertex numbers of neighbors for each vertex
%
% created:    03/02/06 Don Hagler
% last modified:  05/09/06 Don Hagler
%
% code for reading surfaces taken from Darren Weber's freesurfer_read_surf
%
% see also: fs_read_trisurf, fs_find_neighbors, fs_calc_triarea
%

%%%

funcname = 'fs_read_surf';

%QUAD_FILE_MAGIC_NUMBER =  (-1 & 0x00ff) ;
%NEW_QUAD_FILE_MAGIC_NUMBER =  (-3 & 0x00ff) ;

TRIANGLE_FILE_MAGIC_NUMBER  =  16777214 ;
QUAD_FILE_MAGIC_NUMBER  =  16777215 ;

% open it as a big-endian file
fid = fopen(fname, 'rb', 'b') ;
if (fid < 0),
   str = sprintf('%s: could not open surface file %s.',funcname,fname) ;
   error(str) ;
end

magic = fs_fread3(fid) ;

if (magic == QUAD_FILE_MAGIC_NUMBER),
   surf.nverts = fs_fread3(fid) ;
   surf.nfaces = fs_fread3(fid) ;
   fprintf('%s: reading %d quad file vertices...',funcname,surf.nverts); 
tic;

   surf.coords = fread(fid, surf.nverts*3, 'int16') ./ 100 ;
   t=toc; fprintf('done (%0.2f sec)\n',t);
   fprintf('%s: reading %d quad file faces (please wait)...\n',...
 funcname,surf.nfaces); tic;
   surf.faces = zeros(surf.nfaces,4);
   for iface = 1:surf.nfaces,
 for n=1:4,
   surf.faces(iface,n) = fs_fread3(fid) ;
 end
 if(~rem(iface, 1)), fprintf(' %7.0f',iface); end
 if(~rem(iface,10)), fprintf('\n'); end
   end
   t=toc; fprintf('\ndone (%0.2f sec)\n',t);
elseif (magic == TRIANGLE_FILE_MAGIC_NUMBER),
   fprintf('%s: reading triangle file...',funcname); tic;
   tline = fgets(fid); % read creation date text line
   tline = fgets(fid); % read info text line

   surf.nverts = fread(fid, 1, 'int32') ; % number of vertices
   surf.nfaces = fread(fid, 1, 'int32') ; % number of faces

   % vertices are read in column format and reshaped below
   surf.coords = fread(fid, surf.nverts*3, 'float32');

   % faces are read in column format and reshaped
   surf.faces = fread(fid, surf.nfaces*3, 'int32') ;
   surf.faces = reshape(surf.faces, 3, surf.nfaces)' ;
   t=toc; fprintf('done (%0.2f sec)\n',t);
else
   str = sprintf('%s: unknown magic number in surface file 
%s.',funcname,fname) ;

   error(str) ;
end

surf.coords = reshape(surf.coords, 3, surf.nverts)' ;
fclose(fid) ;

%fprintf('...adding 1 to face indices for matlab compatibility.\n\n');
surf.faces = surf.faces + 1;

return
%

Here is my function for getting neighbors:
%
function [surf] = fs_find_neighbors(surf)
% fs_read_surf - find neighboring relations between vertices in a surface
%
% [surf] = fs_find_neighbors(surf)
%
% Input:
% surf is a structure containg:
%   nverts: number of vertices
%   nfaces: number of faces (triangles)
%   faces:  vertex numbers for each face (3 corners)
%   coords: x,y,z coords for each vertex
%
% Output:
% surf is a structure containg:
%   nverts: number of vertices
%   nfaces: number of faces (triangles)
%   faces:  vertex numbers for each face (3 corners)
%   coords: x,y,z coords for each vertex
%   nbrs:   vertex numbers of neighbors for each vertex
%
% created:05/09/06 Don Hagler
% last modified:  05/09/06 Don Hagler
%
% code for finding neighbors taken from Moo Chung's mni_getmesh
%
% see also: fs_read_surf, fs_read_trisurf, fs_calc_triarea
%

%%%

funcname = 'fs_find_neighbors';

if

RE: [Freesurfer] neighborhood of a vertex

[Don Hagler]

Hi Ron,

"fs_fread3" is actually just what I renamed the fread3.m found in 
$FREESURFER_HOME/matlab.
I actually made no changes; just wanted my own self-contained set of matlab 
scripts.  Anyway, here it is:


%
function [retval] = fs_fread3(fid)
% [retval] = fd3(fid)
% read a 3 byte integer out of a file
b1 = fread(fid, 1, 'uchar') ;
b2 = fread(fid, 1, 'uchar') ;
b3 = fread(fid, 1, 'uchar') ;
retval = bitshift(b1, 16) + bitshift(b2,8) + b3 ;
%



From: "R. Chen" <[EMAIL PROTECTED]>
To: Don Hagler <[EMAIL PROTECTED]>
CC: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] neighborhood of a vertex
Date: Tue, 13 Jun 2006 07:50:04 -0700 (PDT)

Thank you, Don.
 However, I try your code and matlab tells me 'Undefined function or 
variable 'fs_fread3''. Could you post other matlab function which are used 
by your 'fs_read_surf.m' and  ' fs_find_neighbors.m'?


 Ron

Don Hagler <[EMAIL PROTECTED]> wrote: >From: "R. Chen"
>To: freesurfer@nmr.mgh.harvard.edu
>Subject: [Freesurfer] neighborhood of a vertex
>Date: Mon, 12 Jun 2006 11:02:59 -0700 (PDT)
>
>   I want to do some customrized smoothing and need to know the
>neighborhood of a vertex. I think FreeSurfer also uses this neighborhood
>information in random field modelling. Could you provide some information
>about how to get the neighborhood?

Take a look at $FREESURFER_HOME/matlab/read_surf.m.  Darren Webber at UCSF
has something similar.

Moo Chung at UWisc has  a function called mni_getmesh.m that find the
neighbors to enable smoothing and he has a function for heat kernel
smoothing.

I've used those sources and made my own modifications that some might find
useful.

Here is my modification of read_surf:
%
function [surf] = fs_read_surf(fname)
% fs_read_surf - read a freesurfer surface file
%
% [surf] = fs_read_surf(fname)
%
% Reads the vertex coordinates (mm) and face lists from a surface file
% Then finds neighbors for each vertex
%
% surf is a structure containg:
%   nverts: number of vertices
%   nfaces: number of faces (triangles)
%   faces:  vertex numbers for each face (3 corners)
%   coords: x,y,z coords for each vertex
%   nbrs:   vertex numbers of neighbors for each vertex
%
% created:03/02/06 Don Hagler
% last modified:  05/09/06 Don Hagler
%
% code for reading surfaces taken from Darren Weber's freesurfer_read_surf
%
% see also: fs_read_trisurf, fs_find_neighbors, fs_calc_triarea
%

%%%

funcname = 'fs_read_surf';

%QUAD_FILE_MAGIC_NUMBER =  (-1 & 0x00ff) ;
%NEW_QUAD_FILE_MAGIC_NUMBER =  (-3 & 0x00ff) ;

TRIANGLE_FILE_MAGIC_NUMBER  =  16777214 ;
QUAD_FILE_MAGIC_NUMBER  =  16777215 ;

% open it as a big-endian file
fid = fopen(fname, 'rb', 'b') ;
if (fid < 0),
str = sprintf('%s: could not open surface file %s.',funcname,fname) ;
error(str) ;
end

magic = fs_fread3(fid) ;

if (magic == QUAD_FILE_MAGIC_NUMBER),
surf.nverts = fs_fread3(fid) ;
surf.nfaces = fs_fread3(fid) ;
fprintf('%s: reading %d quad file vertices...',funcname,surf.nverts);
tic;
surf.coords = fread(fid, surf.nverts*3, 'int16') ./ 100 ;
t=toc; fprintf('done (%0.2f sec)\n',t);
fprintf('%s: reading %d quad file faces (please wait)...\n',...
  funcname,surf.nfaces); tic;
surf.faces = zeros(surf.nfaces,4);
for iface = 1:surf.nfaces,
  for n=1:4,
surf.faces(iface,n) = fs_fread3(fid) ;
  end
  if(~rem(iface, 1)), fprintf(' %7.0f',iface); end
  if(~rem(iface,10)), fprintf('\n'); end
end
t=toc; fprintf('\ndone (%0.2f sec)\n',t);
elseif (magic == TRIANGLE_FILE_MAGIC_NUMBER),
fprintf('%s: reading triangle file...',funcname); tic;
tline = fgets(fid); % read creation date text line
tline = fgets(fid); % read info text line

surf.nverts = fread(fid, 1, 'int32') ; % number of vertices
surf.nfaces = fread(fid, 1, 'int32') ; % number of faces

% vertices are read in column format and reshaped below
surf.coords = fread(fid, surf.nverts*3, 'float32');

% faces are read in column format and reshaped
surf.faces = fread(fid, surf.nfaces*3, 'int32') ;
surf.faces = reshape(surf.faces, 3, surf.nfaces)' ;
t=toc; fprintf('done (%0.2f sec)\n',t);
else
str = sprintf('%s: unknown magic number in surface file
%s.',funcname,fname) ;
error(str) ;
end

surf.coords = reshape(surf.coords, 3, surf.nverts)' ;
fclose(fid) ;

%fprintf('...adding 1 to face indices for matlab compatibility.\n\n');
surf.faces = surf.faces + 1;

re

[Freesurfer] tksurfer rendering offscreen

[Don Hagler]

In older versions of tksurfer, it was possible to set a renderoffscreen flag 
(in a tcl script) that would make it possible to render images in the 
background.  I find this very valuable for rendering large batches of stats.


I would like to store surface-painted timeseries data in mgh format and 
render each frame in order to make a movie.  Since the old version of 
tksurfer will not read mgh files, I need to use the new one for this.  But 
rendering onscreen is very annoying because it means you can't use your 
computer for hours (if rendering lots of images).


The problem seems to be that tksurfer is opening a window and drawing it 
twice before the tcl script even begins to be interpreted.  Is this 
something that can be fixed?  Just in general, why should time be wasted 
drawing the surface twice upon opening?  And can the tcl script be 
interpreted *before* any open_window or redraw commands are given?



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Re: [Freesurfer] printing out from tksurfer and tkmedit

[Don Hagler]

If there is interest, I could post my shell script for generating a tcl 
script and running tksurfer (with an option to write to rgb).  I have 
another one that will render all w files in a particular directory (as 
rgb's) and another that will render all frames from an mgh (painted surface) 
file (as tif's).


With the older version of tksurfer, you can render offscreen, which is 
convenient for batches of files (because otherwise your monitor is unusable 
for a long time).




From: Bruce Fischl <[EMAIL PROTECTED]>
To: Kevin Teich <[EMAIL PROTECTED]>
CC: Chacko Cherian <[EMAIL PROTECTED]>, 
freesurfer@nmr.mgh.harvard.edu

Subject: Re: [Freesurfer] printing out from tksurfer and tkmedit
Date: Fri, 30 Jun 2006 11:39:03 -0400 (EDT)

but you could write a tcl script to do it automatically
On Fri, 30 Jun 2006, Kevin Teich wrote:


How can I can I print out the display images from tksurfer and
tkmedit other than manually saving them into tiff and then printing
them.IS there any way to print them directly?


No, sorry, saving TIFFs is the only output that tkmedit and tksurfer
do of that kind.



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Re: [Freesurfer] printing out from tksurfer and tkmedit

[Don Hagler]

Here you go.  No guarantees of usability or support.


From: Chacko Cherian <[EMAIL PROTECTED]>
To: Don Hagler <[EMAIL PROTECTED]>, [EMAIL PROTECTED],
[EMAIL PROTECTED]

CC: [EMAIL PROTECTED], freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] printing out from tksurfer and tkmedit
Date: Wed, 5 Jul 2006 16:15:05 -0700 (PDT)

Thanks Don.That would be really useful.

Chacko.

--- Don Hagler <[EMAIL PROTECTED]> wrote:

> If there is interest, I could post my shell script
> for generating a tcl
> script and running tksurfer (with an option to write
> to rgb).  I have
> another one that will render all w files in a
> particular directory (as
> rgb's) and another that will render all frames from
> an mgh (painted surface)
> file (as tif's).
>
> With the older version of tksurfer, you can render
> offscreen, which is
> convenient for batches of files (because otherwise
> your monitor is unusable
> for a long time).
>
>
> >From: Bruce Fischl <[EMAIL PROTECTED]>
> >To: Kevin Teich <[EMAIL PROTECTED]>
> >CC: Chacko Cherian <[EMAIL PROTECTED]>,
> >freesurfer@nmr.mgh.harvard.edu
> >Subject: Re: [Freesurfer] printing out from
> tksurfer and tkmedit
> >Date: Fri, 30 Jun 2006 11:39:03 -0400 (EDT)
> >
> >but you could write a tcl script to do it
> automatically
> >On Fri, 30 Jun 2006, Kevin Teich wrote:
> >
> >>>How can I can I print out the display images from
> tksurfer and
> >>>tkmedit other than manually saving them into tiff
> and then printing
> >>>them.IS there any way to print them directly?
> >>
> >>No, sorry, saving TIFFs is the only output that
> tkmedit and tksurfer
> >>do of that kind.
> >>
> >>
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surfmgh
Description: Binary data


surfstats
Description: Binary data


rendall
Description: Binary data


rgbtojpg
Description: Binary data
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[Freesurfer] mri_normalize

[Don Hagler]

I am getting an error running mri_normalize (as part of recon-all) on a 
particular subject's volume.


Here is the command from recon-all:
mri_normalize -g 1 nu.mgz T1.mgz

Here is the output:
WM removal version
using max gradient = 1.000
reading from nu.mgz...
normalizing image...
talairach transform
0.860  -0.007  -0.123  -96.500;
-0.087   0.643  -0.647  -17.669;
0.096   0.653   0.636  -156.251;
0.000   0.000   0.000   1.000;
INFO: Modifying talairach volume c_(r,a,s) based on average_305
MRInormalize: could not find any valid peaks
mri_normalize: normalization failed



nu.mgz looks fine, so I wonder what could be the problem.  Any ideas?


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[Freesurfer] ca normalize

[Don Hagler]

I have a subject that has gotten stuck on the CA Normalize step.  I have 
tried running it several times and it always gets stuck in the same place, 
running away for days if I let it, using 99.9% of the CPU.  We are running 
RH4-x86_64-R302.


Is this something that has been observed / dealt with before?

This is the screen output for the CA Normalize step up to the point of 
getting stuck:

#--
[EMAIL PROTECTED] CA Normalize Fri Jan  5 11:02:19 PST 2007
/space/emc1/4/data/MMILDB/ADNI/Containers/FREESURFERRECON_005_S_0448_20060504.085355_1/mri

mri_ca_normalize -mask brainmask.mgz nu.mgz 
/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R302/average/RB_all_2006-02-15.gca 
transforms/talairach.lta norm.mgz


using MR volume brainmask.mgz to mask input volume...
reading 1 input volumes
reading atlas from 
'/space/monkeys/1/pubsw/packages/freesurfer/RH4-x86_64-R302/average/RB_all_2006-02-15.gca'...

setting gca type = Normal gca type
reading transform from 'transforms/talairach.lta'...
INFO: compute sample coordinates transform
1.405  -0.358   0.038   35.157;
0.193   0.687  -0.595   80.138;
0.176   0.895   1.062  -269.933;
0.000   0.000   0.000   1.000;
INFO: transform used

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[Freesurfer] aseg voxels

[Don Hagler]

Hi,

I've found that the number of voxels for a given aseg ROI in aseg.stats does 
not match exactly the number of voxels when I load the aseg.mgz in matlab 
and find the voxels of the corresponding ROI code.  e.g. 
vol=load_mgh('aseg.mgz'); length(find(vol==17)).


Is there a reason for this difference?

Don

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[Freesurfer] mri_convert -ait

[Don Hagler]

I was trying to warp a volume in atlas space (i.e. an ROI) to single subject 
space using mri_convert -ait ... (version = stable3) and ran into trouble.


I found that mri_convert will quit if the data type is int (type 1) and will 
give strange results if data type is float (type 3).  I was able to do what 
I needed by converting my input volume to uchar (type 0).


For what I want to do, uchar works just fine, but is there some reason why 
it fails for floats?


It might be helpful to include some kind of message in the help and maybe 
quit it the -ait option is used and the input datatype is not uchar.


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RE: [Freesurfer] importing EEG coordinates in free surfer

[Don Hagler]

To get your coordinates into freesurfer space, you need to register them 
with the T1 image.  You could in theory do this with tkmedit, but in my 
experience, the headpoints interface is broken.


I do the registration (manually) with a custom matlab program, but it 
requires that you have generated an outer scalp surface.  You could do this 
with watershed, although when I've tried running watershed, the output bem 
surfaces are not aligned with the input T1 image (with or without -useSRAS 
flag they come out with the axes mixed up).  I use another program for 
generating the bem surfaces, but it is not very user friendly and won't be 
released to the public.


If you want the matlab registration program, I can send it to you, but 
you'll have to find a way to generate the outer scalp surface for each 
subject.




From: abel cruz vadell <[EMAIL PROTECTED]>
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] importing EEG coordinates in free surfer
Date: Fri, 23 Feb 2007 10:27:49 +0100 (CET)

Hi everyone

I need to import EEG coordinates (obtained with
Polhemus system in ASCII format)
in the FreeSurfer workspace. My final aim is
characterize small areas of the cortical surface
(exactly the regions underlaying my sensors position)
with typical parameters of FreeSurfer (cortical
thikness,...) .

I have read some papers reporting partial solutions to
my needs. All of them used matlab with some exported
files of FreeSurfer and registered them with the
coordinates of the EEG or MEG analysis. I will like to
have an opposite solution: import the file with the
coordinates of the EEG into the FreeSufer workspace,
maybe using the Load/overlay /registration menu of
FreeSurfer or another that you can suggest me.

I guess my coordinates file needs some transformations
before import it to the FreeSurfer workspace

thanks in advance

abel



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RE: [Freesurfer] surface area

[Don Hagler]

Just a comment:  Surface area on a vertex-wise basis doesn't seem very 
informative.  Before topology fixing, the surface area should be about the 
same for all vertices (differences should be more or less random).  Topology 
fixing will add or remove vertices, so the surface area in a "fixed" region 
will go up or down depending on the type of defect.  So if you do a 
vertex-wise group average of surface area, you will possibly get a map of 
where you are most likely to get topological defects.  On the other hand, 
doing a group-level analysis of total surface areas within cortical 
parcellations is more likely to be meaningful.




From: "Goldman, Aaron (NIH/NIMH) [C]" <[EMAIL PROTECTED]>
To: 
Subject: [Freesurfer] surface area
Date: Thu, 22 Feb 2007 14:46:16 -0500

Hi, I was interested in comparing surface area between two groups on a
node-by-node basis (something like average area of the triangles
touching each node) and noticed there were automatically-generated files
named lh.area and lh.area.pial

I was wondering if these files contained the appropriate data for doing
something like that, and if so whether there's any documentation you can
recommend on how they are generated in Freesurfer.

Thanks,

-Aaron-

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[Freesurfer] talairach.lta

[Don Hagler]

Can someone please explain what transformation matrix is contained in 
talairach.lta?


Is this the registration matrix from atlas to subject or subject to atlas?

Also, is this matrix for rigid body registration only, or does it have the 
affine registration?


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Re: [Freesurfer] talairach.lta

[Don Hagler]

Hi Bruce,

I thought that the talairach.lta file was not actually registering to 
talairach, but instead to the atlas in advance of the nonlinear 
registration.


When I load the lta file in matlab (with read_lta.m) and then resample a 
volume using that registration matrix, the brain goes to a different place 
for each subject if I assume that the registration matrix is from subject to 
atlas.  If I assume that the matrix is instead from atlas to subject, then 
the resampled brain goes to roughly the same location for different 
subjects.


Don



From: Bruce Fischl <[EMAIL PROTECTED]>
To: Don Hagler <[EMAIL PROTECTED]>
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] talairach.lta
Date: Mon, 11 Jun 2007 23:44:20 -0400 (EDT)

Hi Don,

I believe it is from subject ras to talairach ras, and it is definitely 
affine (not just rigid). The .lta format is generic enough that it will 
list what type of transform it is (e.g. voxel or ras). Here are most of the 
relevant types:

#define LINEAR_VOX_TO_VOX   0
#define LINEAR_VOXEL_TO_VOXEL   LINEAR_VOX_TO_VOX
#define LINEAR_RAS_TO_RAS   1
#define LINEAR_PHYSVOX_TO_PHYSVOX 2
#define TRANSFORM_ARRAY_TYPE10
#define MORPH_3D_TYPE   11
#define MNI_TRANSFORM_TYPE  12
#define MATLAB_ASCII_TYPE   13
#define LINEAR_CORONAL_RAS_TO_CORONAL_RAS   21
#define LINEAR_COR_TO_COR   LINEAR_CORONAL_RAS_TO_CORONAL_RAS


cheers,
Bruce

On Mon, 11 Jun 2007, Don Hagler wrote:

Can someone please explain what transformation matrix is contained in 
talairach.lta?


Is this the registration matrix from atlas to subject or subject to atlas?

Also, is this matrix for rigid body registration only, or does it have the 
affine registration?


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[Freesurfer] control points

[Don Hagler]

In recon-all, it says you are supposed to use -autorecon2-cp if you use 
control points.  So I wonder why earlier normalization steps also use 
control points, such as Norm1 and CANormalize.  What effect do the control 
points have in those steps?


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Re: [Freesurfer] control points

[Don Hagler]

So then for redoing a recon with control points, it would be beneficial to 
start again at the mri_normalize step?



From: Nick Schmansky <[EMAIL PROTECTED]>
To: Bruce Fischl <[EMAIL PROTECTED]>
CC: Freesurfer Mailing List ,    Don 
Hagler <[EMAIL PROTECTED]>

Subject: Re: [Freesurfer] control points
Date: Thu, 12 Jul 2007 15:51:17 -0400

Don,

If the file $subjdir/tmp/control.dat exists, then it is automatically
added to the mri_normalize and mri_ca_normalize steps.  An explicit flag
is not needed.

Nick

On Wed, 2007-07-11 at 21:27 -0400, Bruce Fischl wrote:
> Hi Don,
>
> Nick actually just recently included something to allow you to pass the
> control points to mri_ca_normalize, so it can help the subcortical
> segmentation. Nick: what is the new flag?
>
> cheers,
> Bruce
>
> On Wed, 11 Jul 2007, Don Hagler
> wrote:
>
> > In recon-all, it says you are supposed to use -autorecon2-cp if you 
use
> > control points.  So I wonder why earlier normalization steps also use 
control
> > points, such as Norm1 and CANormalize.  What effect do the control 
points

> > have in those steps?
> >
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RE: [Freesurfer] writing surface file

[Don Hagler]

Hi Marie,

I think I had a similar problem with my script.  I believe the problem is 
with the two
lines of chars (the creation string).  For whatever reason, I think that it 
worked better

if the second line was empty.

This is the relevant section from my script:

fs_fwrite3(fid,TRIANGLE_FILE_MAGIC_NUMBER) ;
fprintf(fid,'created by %s on %s\n\n',user,datestr(now)); % creation date 
text line

fwrite(fid,nverts,'int32');
fwrite(fid,nfaces,'int32');
fwrite(fid,coords,'float32');
fwrite(fid,faces,'int32');

Comparing to the one you are using, only the creation string line is 
significantly different.


Don


From: Marie Schaer <[EMAIL PROTECTED]>
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] writing surface file
Date: Thu, 02 Aug 2007 16:39:31 +0200


Hello everybody,

I would like to write a surface in freesurfer format from a matlab  
triangular mesh (e.g. list of 67120 vertices associated with 134236  
faces). To read the freesurfer surfaces, I usually use the very  useful 
bioelectromagnetism toolbox by Darren Weber, but I am not able  to find out 
why the freesurfer_write_surface function (attached to  this mail) do not 
work with my mesh. It indeed seems to write a  surface of adequate size 
(2.3MB), but when I try to visualize it,  tkmedit respond:


"(null): vertex 0 x coordinate 282617032931096509022208.00 ! "

Does someone has any hints on that or an available matlab script to  write 
a freesurfer surface?


Many thanks for your help,

Marie Schaer





<< freesurfer_write_surf.m >>




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RE: [Freesurfer] determining sizes of clusters at given CWP cutoff

[Don Hagler]

There is no reason why you shouldn't be able to get the cut-off size from 
monte carlo simulations.  It just depends on the program you use to do it.  
For example, AFNI's AlphaSim gives cluster sizes as  a function of corrected 
p-value.


By the way, monte carlo simulations are a waste of time.  Keith Worsley's 
"Random Field Theory" method 
(http://www.math.mcgill.ca/keith/fmristat/toolbox/stat_threshold.m) can be 
used to directly (in seconds) estimate the cluster size thresholds given:

total surface area
number of vertices
fwhm smoothness

I've found (Hagler et al., Smoothing and cluster thresholding for cortical 
surface-based group analysis of fMRI data, NeuroImage, 2006) that RFT and 
monte carlo simulations give practically identical results.


See the attached matlab script for a wrapper around Worsley's code to 
calculate the cluster size thresholds using RFT.




From: Robert Levy <[EMAIL PROTECTED]>
To: Freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] determining sizes of clusters at given CWP cutoff
Date: Fri, 03 Aug 2007 11:44:33 -0400

Hi,

I was trying to figure out if there is any way to determine the exact size 
at which clusters becomes significant given a specified significance, and 
it appeared from the mc-corrected overlay that in this overlay the clusters 
do not continously change in size but appear discretely at a given 
threshold and are the same size at higher thresholds in an all-or-nother 
sort of way.  I take this to mean that because the monte carlo simulation 
was performed at a given threshold, the clusters at that threshold size are 
corrected for mutiple comparisons based on the probability distribution of 
the chance data (though I don't know the details).  Because it is done in 
this way, it seems I would either have to run several monte carlo 
simulations, at successively higher minimum thresholds, in order to arrive 
at the critical cutoff sizes for significance.  This is impractical, so I 
guess my question is, does the way in which the monte carlo simulations are 
done preclude the possibility of getting the cluster sizes at which they 
will have a certain CWP value, or is there some way of doing this?


Thanks,
Rob

--

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Research Assistant, Manoach Lab
Massachusetts General Hospital
Charlestown Navy Yard
149 13th St., Room 2611
Charlestown, MA 02129
email: [EMAIL PROTECTED]
phone: 617-726-1908
fax: 617-726-4078

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function [cluster_threshold,peak_threshold] = 
fs_calc_cluster_thresh(nverts,area,fwhm,df,alpha,pval)
%function [cluster_threshold,peak_threshold] = 
fs_calc_cluster_thresh(nverts,area,fwhm,df,alpha,pval)

%
% Required Input:
%   nverts: number of vertices
%   area: total surface area across all vertices
%   fwhm: estimated full-width-half-max smoothness (mm)
%
% Optional Input:
%   df: degrees of freedom
% {default = 100}
%   alpha: corrected p-value
% {default = 0.05}
%   pval: uncorrected p-value
% {default = 0.001}
%
% Output:
%   cluster_threshold: spatial extent of cluster that can be used for
% cluster exclusion multiple comparison method
%
% NOTE: to get nverts and area run
%   fs_load_subj (or fs_read_surf) and fs_calc_triarea
%
% NOTE: this program uses Worsley's RFT method for t-stats
%
% NOTE: this code is provided with no warranty whatsoever,
%   no gaurantee of usefullness, and no offer of technical support.
%
% created:    07/06/07 Don Hagler
% last modified:  07/06/07 Don Hagler
%
% see also: fs_read_surf, fs_read_trisurf, fs_calc_triarea
%

cluster_threshold = NaN;
peak_threshold = NaN;

if nargin<3
 help(mfilename);
 return;
end;
if ~exist('df','var') | isempty(df), df=100; end;
if ~exist('alpha','var') | isempty(alpha), alpha=0.05; end;
if ~exist('pval','var') | isempty(pval), pval=0.001; end;

search_volume = [2 0 area];
[peak_threshold,cluster_threshold]=...
 stat_threshold(search_volume,nverts,fwhm,df,alpha,pval,alpha);

fprintf('%s: t-stat cluster_threshold = %0.4f 
mm^2\n',mfilename,cluster_threshold);

fprintf('%s: t-stat peak_threshold = %0.4f\n',mfilename,peak_threshold);

return;

%%


function [peak_threshold, extent_threshold, peak_threshold_1, 
extent_threshold_1] = ...

  stat_threshold(search_volume, num_voxels, fwhm, df, p_val_peak, ...
  cluster_threshold, p_val_extent, nconj, nvar, EC_file, expr)
%STAT_THRESHOLD finds thresholds and p-values of random fields 

RE: [Freesurfer] remote batch job?

[Don Hagler]

There is a renderoffscreen flag that can be used from a tcl script.

Unfortunately, this feature was broken when a particular section of the 
tksurfer code was commented out.  The problem was that the tclscriptflag 
used to determine whether to open a window was not getting set to true.  
Look for this:


 /* rkt: commented this part out. i'm not sure how it was accepting
any other command line options with it active. */

I think I emailed Kevin Teich about this some time ago.

Since then, I've made a modified version of tksurfer where this problem is 
fixed.  The solution is to actually replace tclscriptflag with the newer 
scriptok variable when it comes time to open a window only if not running 
from a script.  I can send that code to the mgh guys if desired, but as I 
said, the fix is easy (assuming you can compile the source code).


So anyway, this modified version can render offscreen (like the prehistoric 
versions of tksurfer).  This is very useful to me and probably to others who 
want to render in batches (e.g. making movies).  The only remaining problem, 
however, is that you still need a valid display.  So for example, you can't 
run these batch render jobs on a cluster.


I haven't yet tried to get tksurfer to render without any display, but I 
fear that it won't be possible for some OpenGL reason.  But if anyone can 
figure that one out, I would be very grateful.


Don




From: "Darren Weber" <[EMAIL PROTECTED]>
Reply-To: [EMAIL PROTECTED]
To: "freesurfer@nmr.mgh.harvard.edu" 
Subject: [Freesurfer] remote batch job?
Date: Thu, 16 Aug 2007 16:12:01 -0700

-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1


Hi Bruce et al.,

I want to run a batch job that will use tksurfer to display an inflated
surface, load some patches, and rotate and save images.  I have a .tcl
script to control the process in tksurfer and I have a shell script to
start the whole process off for a number of subjects.  My question now
is how to handle the case where I am working remotely and it is too slow
to have the display piped to the remote display, so I want to have
either (a) no visible display or (b) a display on the host machine.  If
I try the usual trick of setting DISPLAY env for the host machine, I'm
failing to open the display for any commands sent from the remote xterm.

Do you have a solution for this situation?

Take care, Darren

- --

Darren L. Weber, Ph.D.
Postdoctoral Scholar

Dynamic Neuroimaging Laboratory,
UCSF Department of Radiology,
185 Berry Street, Suite 350, Box 0946,
San Francisco, CA 94107, USA.

Tel: +1 415 353-9444
Fax: +1 415 353-9421
www: http://dnl.ucsf.edu/users/dweber
pgp: http://dnl.ucsf.edu/users/dweber/dweber_pgp.html

"To explicate the uses of the brain seems as difficult
a task as to paint the soul, of which it is commonly
said, that it understands all things but itself."
  Thomas Willis (The Anatomy of the Brain and Nerves, 1664)

"Fourteen billion nerve cells responding in complex ways
with multitudinous connections to each other give little
likelihood of providing a rational solution that would
allow prediction of mental process."
  Michael Posner (Chronometric Explorations of Mind, 1978)
-BEGIN PGP SIGNATURE-
Version: GnuPG v1.4.6 (GNU/Linux)
Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org

iD8DBQFGxNnBxaCYN7qs0v4RAiOOAJ48XbFN1UzICRYbe8yho2UIcMbm3ACfcp6Y
5GyJeS0o6a5L43pz74jeMyI=
=G5Ph
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[Freesurfer] version 4

[Don Hagler]

I processed some brains using version 4 and it seems that it took 
substantially longer than typical for version 3.  It took about 3 days for 
one subject with version 4, compared to 1.5 days for the same subject with 
version 3.0.5.  Is this on par with what others have experienced?


At least for this one subject, the inflated surface looks a bit strange for 
version 4 compared to version 3 (see attached).  I haven't yet done a 
side-by-side comparison for multiple subjects, so I don't know how 
reproducible this will be.


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[Freesurfer] thickness and curvature

[Don Hagler]

I see that mris_make_surfaces is normally used to generate thickness and 
curvature.  I would like to generate the ?h.thickness and ?h.curv files 
without running mris_make_surfaces (I already have white and pial surfaces).


Can mris_thickness and mris_curvature (or other programs) give the same 
results?  Those two programs are not heavily documented, so any help on 
which options to use (to give the same results as mris_make_surfaces) would 
be appreciated.


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Re: [Freesurfer] thickness and curvature

[Don Hagler]

Hi Bruce,

Thanks for the info.

mris_curvature gave me identical results as mris_make_surfaces with 10 
smoothing steps.


mris_thickness gave slightly different values compared to 
mris_make_surfaces.  Many vertices were identical, but many were not and 
some were off by as much as 0.2 mm.


Is there any reason to think that mris_make_surfaces and mris_thickness 
would have differences in how the thickness measurements are done?  I'm 
doing this with version 3.0.2 at present.


Don



From: Bruce Fischl <[EMAIL PROTECTED]>
To: Don Hagler <[EMAIL PROTECTED]>
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] thickness and curvature
Date: Sun, 16 Sep 2007 20:44:11 -0400 (EDT)

Hi Don,

I just added some help to these utilities:

./mris_curvature
usage: ./mris_curvature [options] 

This program will compute the second fundamental form of a cortical 
surface.
It will create two new files ..H and ..K with 
the

mean and Gaussian curvature respectively.
valid options are:

-w   save curvature files (will only generate screen 
output without this option)
-max save  1st (max) principal curvature in 
?h..max file
-min save  2nd (min) principal curvature in 
?h..min file
-a perform  iterative averages of curvature 
measure before saving



 ./mris_thickness
usage: ./mris_thickness [options]   

This program measures the thickness of the cortical surface and
writes the resulting scalar field into a 'curvature' file .

valid options are:

-maxuse  to threshold thickness (default=5mm)


is there anything else you need? This will be in the next release.

Bruce
On Sun, 16 Sep 2007, Don Hagler wrote:

I see that mris_make_surfaces is normally used to generate thickness and 
curvature.  I would like to generate the ?h.thickness and ?h.curv files 
without running mris_make_surfaces (I already have white and pial 
surfaces).


Can mris_thickness and mris_curvature (or other programs) give the same 
results?  Those two programs are not heavily documented, so any help on 
which options to use (to give the same results as mris_make_surfaces) 
would be appreciated.


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Re: [Freesurfer] thickness and curvature

[Don Hagler]

I looked at the code and found another option for mris_thickness: -N for 
neighborhood size.
For mris_make_surfaces, the default is 20, but for mris_thickness, the 
default is 2.  So setting it to 20 gave the correct result.



From: "Don Hagler" <[EMAIL PROTECTED]>
To: [EMAIL PROTECTED]
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] thickness and curvature
Date: Sun, 16 Sep 2007 23:23:50 -0700

Hi Bruce,

Thanks for the info.

mris_curvature gave me identical results as mris_make_surfaces with 10 
smoothing steps.


mris_thickness gave slightly different values compared to 
mris_make_surfaces.  Many vertices were identical, but many were not and 
some were off by as much as 0.2 mm.


Is there any reason to think that mris_make_surfaces and mris_thickness 
would have differences in how the thickness measurements are done?  I'm 
doing this with version 3.0.2 at present.


Don



From: Bruce Fischl <[EMAIL PROTECTED]>
To: Don Hagler <[EMAIL PROTECTED]>
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] thickness and curvature
Date: Sun, 16 Sep 2007 20:44:11 -0400 (EDT)

Hi Don,

I just added some help to these utilities:

./mris_curvature
usage: ./mris_curvature [options] 

This program will compute the second fundamental form of a cortical 
surface.
It will create two new files ..H and ..K 
with the

mean and Gaussian curvature respectively.
valid options are:

-w   save curvature files (will only generate screen 
output without this option)
-max save  1st (max) principal curvature in 
?h..max file
-min save  2nd (min) principal curvature in 
?h..min file
-a perform  iterative averages of curvature 
measure before saving



 ./mris_thickness
usage: ./mris_thickness [options]   

This program measures the thickness of the cortical surface and
writes the resulting scalar field into a 'curvature' file file>.


valid options are:

-maxuse  to threshold thickness (default=5mm)


is there anything else you need? This will be in the next release.

Bruce
On Sun, 16 Sep 2007, Don Hagler wrote:

I see that mris_make_surfaces is normally used to generate thickness and 
curvature.  I would like to generate the ?h.thickness and ?h.curv files 
without running mris_make_surfaces (I already have white and pial 
surfaces).


Can mris_thickness and mris_curvature (or other programs) give the same 
results?  Those two programs are not heavily documented, so any help on 
which options to use (to give the same results as mris_make_surfaces) 
would be appreciated.


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RE: [Freesurfer] t-value saved values

[Don Hagler]

Are you sure that it is saving t-values in F.mgh and not F-stats?



From: Glenn Lawyer <[EMAIL PROTECTED]>
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] t-value saved values
Date: Thu, 20 Sep 2007 15:00:44 +0200

Hi,

I asked about this last week, and had a nice discussion with Doug, but 
somehow in that we never got the answer to my original question.


When FreeSurfer saves t-values (in F.mgh), what is it actually saving? The 
numbers in the file do not have a t-distribution (even when the source data 
for the glm is random noise). Is a transform applied to the t-values before 
the write, as is done with the p-values?











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RE: [Freesurfer] activation patterns and par files

[Don Hagler]

Every time point not specified as a condition would be counted as baseline, 
right?  So does that mean then, that you have a different baseline for your 
3 and 5 condition analyses?




From: "Cameron Ellis" <[EMAIL PROTECTED]>
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] activation patterns and par files Date: Thu, 18 Oct 
2007 14:50:08 -0400 (EDT)


Hi all,
I have run two different group analyses in stable3. All of the analysis
parameters between the two are identical except that one uses a paradigm
file containing three conditions and the other uses a paradigm file
containing five conditions. The first three conditions in the analysis
using the five condition paradigm file are identical to those in the three
condition paradigm files, meaning the timing and definitions are exactly
the same. The five condition paradigm file just contains additional
conditions that were not originally defined, as additions to the three
condition paradigm files.

The problem is that the activation patterns I receive for contrasts using
only the first three conditions of the five condition paradigm files are
different from the activation patterns of contrasts using the three
condition paradigm files. I do not know why this would be. Is there
something about not defining all events that would lead to differences of
this sort? I have visually inspected all of my paradigm files so I am sure
the only diffences between them are the additional 2 conditions in the
five condition files. I have attached images of the differences and below
are the paths to both analyses as well as the commands run to produce the
5 condition results. The three condition commands were identical except
for calling the different analysis. Any help or insight would be much
appreciated!
Cameron

3condition:
/space/troy/3/users/retrievalnewest/Controlssh+smvsnh/bold/retrievalSPMHRF/sphsmooth-rfx/sh+smvsnh

5condition:
/space/troy/3/users/retrievalnewest/Controlssh+smvsnh/bold/retrievalSPMHRF_5cond/sphsmooth-rfx/sh+smvsnh


mkanalysis-sess.new -analysis retrievalSPMHRF_5cond -TR 2.5 -paradigm
paradigmmacro5 -designtype event_related -spmhrf 0 -nconditions 5
-timewindow 25 -prestim 5 -funcstem fmcsm -taumax
30 -polyfit 2 -inorm

selxavg-sess -sf sessidall -df sesspar -analysis retrievalSPMHRF_5cond

mkcontrast-sess -contrast -sh+smvsnh -analysis retrievalSPMHRF_5cond
-ncond 5 -a 1 -a 2 -c 3

func2sph-sess -sf sessidall -df sesspar -analysis retrievalSPMHRF_5cond

sphsmooth-sess -smoothsteps 20 -analysis retrievalSPMHRF_5cond -insphdir
sph -outsphdir sphsmooth -hemi rh -sf sessidall -df sesspar

isxavg-re-sess -analysis retrievalSPMHRF_5cond -contrast sh+smvsnh -group
Controlssh+smvsnh -space sph -spacedir sphsmooth -hemi rh -sf
sessidcontrolssh+smvsnh -df sesspar




<< 3cond.jpg >>




<< 5cond.jpg >>




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RE: [Freesurfer] Creating average overlays for time-varying data (MEG)

[Don Hagler]

If you have problems writing out mgh files with 14x1x1x500 volumes, maybe 
you need more memory (>=2GB?).  Or a 64 bit machine?  Or you could downsample 
your time courses if you haven't already.


I do use matlab to convert decimated source time course files (stc) to mgh.  
Before writing out the mgh file, I do sparse smoothing (10+ steps) followed by 
regular smoothing (10+ steps) on each frame.  It is slow, but works
fine on 64 bit machines with 2GB RAM.  It probably works on 32 bit machines 
too, but I haven't used one in awhile.  The largest number of frames I've tried 
is 450.

Resampling to ico7 for group averaging is straightforward with mri_surf2surf.  
I do group analysis one frame at time to conserve memory.

I don't think using mri_surf2surf to resample sparse data to ico4 (for example) 
would work well because of interpolation with neighboring zero values (but I 
haven't tried it).



An option that I am considering is to start with ico4 vertices and sample them 
to each subject in order to choose which vertices should be the set of 
"decimated" dipoles.  The complication here is that mri_surf2surf does not give 
a one-to-one mapping between ico vertices and single subject vertices.  I think 
it would be necessary to derive a look-up-table for each subject to provide 
such a one-to-one mapping.  Then the ico resampling would be done not with 
mri_surf2surf, but with a matlab script that consults the look-up-table.

For display purposes, I guess you would still need to create an ico4 average 
subject.



> Date: Mon, 21 Jan 2008 16:08:41 -0500
> From: [EMAIL PROTECTED]
> To: [EMAIL PROTECTED]
> Subject: Re: [Freesurfer] Creating average overlays for time-varying data 
> (MEG)
> CC: freesurfer@nmr.mgh.harvard.edu
> 
> 
> 
> Pádraig Kitterick wrote:
> 
> > Dear list,
> >
> > I am trying to use freesurfer to visualise MEG data (minimum norm) 
> > overlayed on the cortical surface, both at an individual and group 
> > level. I have successfully processed all of the participants MRIs 
> > using recon-all, and have decimated the cortical surface (white) to 
> > compute the MEG solution. I would be grateful if anyone could help 
> > with the following issues I have run into:
> >
> > 1) I would like to know how to view the time-varying solution over the 
> > cortex using tksurfer. I have successfully exported the overlay for a 
> > single sample to a .w file (using matlab), and then smoothed it 
> > (mri_surf2surf) and viewed it on the cortical surface, which works 
> > great. But I am aware that .w format only supports a single 'frame' of 
> > data. Some previous posts on the list suggest that exporting the data 
> > in .mgh format as a nverts x 1 x 1 x nsamples volume would allow 
> > visualisation of the timecourse in tksurfer.
> >
> > My question is: is there a way to only write out the data for the 
> > vertices with values (i.e. left after decimation) when using the mgh 
> > format, and not a matrix of the total vertices in the original cortex? 
> > For example, if the surface has N vertices, and after decimation I 
> > have M vertices left, using the .w format I only need to write out 
> > data for the M vertices, along with a list of the vertex numbers to 
> > place them on the original surface. Can I do this with .mgh? It is 
> > difficult to get matlab to write out an mgh file with a 14x1x1x500 
> > volume!
> 
> You can't do this with the mgh format. You can use compressed mgh (mgz), 
> and that will compress all the 0s, but that probably does not take you 
> where you need to be. How are you decimating your data? One way would be 
> to create a decimated average subject with a lower order icosahedron and 
> then use that as the target for mri_surf2surf.
> 
> >
> > 2) I wish to view the average data across several subjects, mapped 
> > onto the fsaverage subject template. I have seen that mris_preproc can 
> > warp one or more overlays onto a single subject. My question is: will 
> > mris_preproc work with the type of .mgh files I described above, i.e. 
> > containing multiple frames of data overlay? Or am I better trying to 
> > do the whole operation with .w files, with one per timepoint?
> 
> You can do it with multiple frame input (though the output frames will 
> be a stack of original frames from all the subjects).
> 
> doug
> 
> >
> > Many thanks in advance,
> >
> > Padraig
> 
> 
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> [EMAIL PROTECTED]
> Phone Number: 617-724-2358 
> Fax: 617-726-7422
> 
> In order to help us help you, please follow the steps in:
> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> 
> 
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RE: [Freesurfer] Creating average overlays for time-varying data (MEG)

[Don Hagler]

Hi Doug,

No, I haven't tried it for this, but I have read the help before.  It says this:
"If nnf is chosen, then the value at the target vertex is set to that of the 
closest source vertex."

If you wanted to go from a sparsely valued single subject surface (i.e. 
decimated dipoles) to ico4, it seems that you would probably miss many of your 
dipole vertices because they wouldn't necessarily be the ones closest to the 
ico4 vertices.  Going from decimated dipoles to ico7 may work ok, although you 
may still miss a few dipoles, which is why smoothing before sampling to ico 
seems to be a good idea.  And we have to smooth anyway before doing group 
analysis because the ico7 vertices that correspond to a single subject's 
decimated dipoles will vary from subject to subject.

If we chose our decimated dipoles based on ico4, we do could group analysis 
without any smoothing on a much smaller number of vertices.

Don

Date: Tue, 22 Jan 2008 17:01:45 -0500
From: [EMAIL PROTECTED]
To: [EMAIL PROTECTED]
Subject: Re: [Freesurfer] Creating average overlays for time-varying data (MEG)
CC: [EMAIL PROTECTED]; freesurfer@nmr.mgh.harvard.edu






  
  


Hi Don, have you tried using mri_surf2surf with  --mapmethod nnf ? That
will prevent the interpolation and map each ico4 to the nearest ico7.



doug



Don Hagler wrote:

  
  

If you have problems writing out mgh files with 14x1x1x500 volumes,
maybe you need more memory (>=2GB?).  Or a 64 bit machine?  Or you
could downsample your time courses if you haven't already.

  

I do use matlab to convert decimated source time course files (stc) to
mgh.  Before writing out the mgh file, I do sparse smoothing (10+
steps) followed by regular smoothing (10+ steps) on each frame.  It is
slow, but works
fine on 64 bit machines with 2GB RAM.  It probably works on 32 bit
machines too, but I haven't used one in awhile.  The largest number of
frames I've tried is 450.

  

Resampling to ico7 for group averaging is straightforward with
mri_surf2surf.  I do group analysis one frame at time to conserve
memory.

  

I don't think using mri_surf2surf to resample sparse data to ico4 (for
example) would work well because of interpolation with neighboring zero
values (but I haven't tried it).

  
  

An option that I am considering is to start with ico4 vertices and
sample them to each subject in order to choose which vertices should be
the set of "decimated" dipoles.  The complication here is that
mri_surf2surf does not give a one-to-one mapping between ico vertices
and single subject vertices.  I think it would be necessary to derive a
look-up-table for each subject to provide such a one-to-one mapping. 
Then the ico resampling would be done not with mri_surf2surf, but with
a matlab script that consults the look-up-table.

  

For display purposes, I guess you would still need to create an ico4
average subject.

  

  

  

  > Date: Mon, 21 Jan 2008 16:08:41 -0500

> From: [EMAIL PROTECTED]

> To: [EMAIL PROTECTED]

> Subject: Re: [Freesurfer] Creating average overlays for
time-varying data (MEG)

> CC: freesurfer@nmr.mgh.harvard.edu

> 

> 

> 

> Pádraig Kitterick wrote:

> 

> > Dear list,

> >

> > I am trying to use freesurfer to visualise MEG data (minimum
norm) 

> > overlayed on the cortical surface, both at an individual and
group 

> > level. I have successfully processed all of the participants
MRIs 

> > using recon-all, and have decimated the cortical surface
(white) to 

> > compute the MEG solution. I would be grateful if anyone could
help 

> > with the following issues I have run into:

> >

> > 1) I would like to know how to view the time-varying solution
over the 

> > cortex using tksurfer. I have successfully exported the
overlay for a 

> > single sample to a .w file (using matlab), and then smoothed
it 

> > (mri_surf2surf) and viewed it on the cortical surface, which
works 

> > great. But I am aware that .w format only supports a single
'frame' of 

> > data. Some previous posts on the list suggest that exporting
the data 

> > in .mgh format as a nverts x 1 x 1 x nsamples volume would
allow 

> > visualisation of the timecourse in tksurfer.

> >

> > My question is: is there a way to only write out the data for
the 

> > vertices with values (i.e. left after decimation) when using
the mgh 

> > format, and not a matrix of the total vertices in the
original cortex? 

> > For example, if the surface has N vertices, and after
decimation I 

> > have M vertices left, using the .w format I only need to
write out 

> > data for the M vertices, along with a list of the vertex
numbers to 

> > place them on the original surface. Can I do this with .mgh?
It is 

> > difficult to get matlab to write out an mgh 

RE: [Freesurfer] vertex neighbourhood

[Don Hagler]

It is easier to find the neighborhood for a given number of steps away from the 
vertex of interest.  One easy way is to set the value of a single vertex, 
smooth for a particular number of iterations, and then select the non-zero 
vertices.  If you smooth 5 times, you will get 5 steps away.  The number of 
vertices in that neighborhood will vary from vertex to vertex.



> Date: Thu, 24 Jan 2008 16:02:14 -0500
> From: [EMAIL PROTECTED]
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] vertex neighbourhood
> 
> hi surfers,
> Imagine that I need to know what are the closest N vertices (let's say
> n=100) to a given vertex (i mean two dimentionsal neighourhood on
> surfaces) . Any idea how to do that? anybody has a written code for this?
> cheers
> nima
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RE: [Freesurfer] Creating average overlays for time-varying data (MEG)

[Don Hagler]

To resample from ico4, use --srcsubject ico --srcicoorder 4

If you use nnf, some of the source vertices may not get sampled.  If you use 
nnfr, you should get clusters of vertices for every ico4 vertex.  You should be 
able to find the clusters and then pick the vertex with max intensity for each 
cluster.  That set of max intensity vertices defines the mapping between ico 4 
and the single subject.

If you do this, you can use the mgh format and then display directly on an ico4 
surface.  Doug mentioned that you could somehow create a downsampled average 
subject.

If you get this working, please let me know.

> Date: Tue, 29 Jan 2008 00:25:08 +
> From: [EMAIL PROTECTED]
> To: [EMAIL PROTECTED]
> Subject: Re: [Freesurfer] Creating average overlays for time-varying data 
> (MEG)
> CC: freesurfer@nmr.mgh.harvard.edu
> 
> A question related to this: is it possible to take a surface overlay (.w 
> format) containing a set number of vertices, all with the same value, in 
> one subject space and warp it to another subject while keeping the same 
> number of vertices? I would like to try to define a set of source points 
> on an average surface, and then warp those points back to each 
> individual subject for source analysis. Perhaps the 'ico' option of 
> mri_surf2surf solves this problem, but I am not fully clear on how that 
> works. Any pointers to documentation on this would be most appreciated.
> 
> I have tried using mri_surf2surf to achieve this, but I either end up 
> with too little (nnf) or too many vertices (nnfr) on the target surface. 
> I have had some problems with resampling a sparse set of individual data 
> points to an average surface and smoothing (on source or target 
> surfaces), as the smoothing seems to introduce entirely new foci of 
> activity, particularly around the insula. Therefore, I am trying to find 
> a way to have a set of common source points so that smoothing can be 
> avoided until the final step to display the data.
> 
> Thanks in advance,
> 
> P.
> 
> Don Hagler wrote:
> > If you wanted to go from a sparsely valued single subject surface (i.e. 
> > decimated dipoles) to ico4, it seems that you would probably miss many 
> > of your dipole vertices because they wouldn't necessarily be the ones 
> > closest to the ico4 vertices.  Going from decimated dipoles to ico7 may 
> > work ok, although you may still miss a few dipoles, which is why 
> > smoothing before sampling to ico seems to be a good idea.  And we have 
> > to smooth anyway before doing group analysis because the ico7 vertices 
> > that correspond to a single subject's decimated dipoles will vary from 
> > subject to subject.
> 
> -- 
> Pádraig Kitterick
> Graduate Student
> Department of Psychology
> University of York
> Heslington
> York YO10 5DD
> UK
> 
> Tel: +44 (0) 1904 43 3170
> Email: [EMAIL PROTECTED]
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RE: [Freesurfer] mri_watershed -> BEM surfaces problem

[Don Hagler]

matlab's reducepatch
Date: Thu, 10 Apr 2008 10:39:37 -0700
From: [EMAIL PROTECTED]
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_watershed -> BEM surfaces problem

P.S.  Also, I was wondering if there is a utility to reduce the number
of vertices of a given surface (i.e. to make a less precise
triangulation) at will. I
 thought I may use the pial left and right 
halves greatly reduced (from about 140k vertices to 10k or less) for
the brain surface instead of the mri_watershed output. 

  
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RE: [Freesurfer] LGI

[Don Hagler]

You can see that it is running matlab just before the error.  So it must be 
using the matlab load_mgh function, which does convert from mgz to mgh and then 
deletes the tmp file when it is done.  Maybe you are setting rm as an alias for 
'rm -i' in your .cshrc.  



> Subject: Re: [Freesurfer] LGI
> From: [EMAIL PROTECTED]
> To: [EMAIL PROTECTED]
> Date: Tue, 15 Apr 2008 13:04:13 -0400
> CC: freesurfer@nmr.mgh.harvard.edu
> 
> Leila,
> 
> This is a strange error.  The LGI utility doesnt work with .mgh files
> (it uses .mgz), so I am not sure where or how the 'rm: remove regular
> file `/tmp/tmp8147237.mgh'? ' message originates.
> 
> I would try deleting all the .mgh files in the /tmp directory, and try
> again.  And if the message repeats, try using mri_info on the file to
> determine its origin.  Or you can try responding with 'y' to the prompt
> and see if it continues.
> 
> Nick
> 
> 
> On Tue, 2008-04-15 at 18:29 +0200, Leila BH wrote:
> > Hi 
> > 
> > I am trying to launch the LGI option, but the program seems to wait
> > for a response, here is the complete output,. Even if I type yes it
> > doesn’t seems to continue.
> > 
> > Do you know how to solve this?
> > 
> >  
> > 
> > Thanks in advance
> > 
> > Leila
> > 
> >  
> > 
> >  
> > 
> > [EMAIL PROTECTED] ~/freesurfer]# recon-all -lgi -sid chuv60
> > 
> > INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects
> > 
> > Actual FREESURFER_HOME /home/cammoun/freesurfer
> > 
> > -rwxrwxrwx 1 root root 569567 Apr 15
> > 18:20 /usr/local/freesurfer/subjects/chuv60/scripts/recon-all.log
> > 
> > Linux lts1pc72.epfl.ch 2.6.20-1.2944.fc6 #1 SMP Tue Apr 10 17:46:00
> > EDT 2007 x86_64 x86_64 x86_64 GNU/Linux
> > 
> > INFO: current FREESURFER_HOME does not match that of previous
> > processing.
> > 
> > Current: /home/cammoun/freesurfer
> > 
> > Previous: /usr/local/freesurfer
> > 
> > /usr/local/freesurfer/subjects/chuv60/surf
> > 
> > #
> > 
> > [EMAIL PROTECTED] Local Gyrification Index lh Tue Apr 15 18:21:04 CEST 2008
> > 
> >  
> > 
> >  mris_compute_lgi --i lh.pial 
> > 
> >  
> > 
> > =
> > 
> > rm -Rf tmp-mris_compute_lgi
> > 
> > =
> > 
> > =
> > 
> > mkdir -p tmp-mris_compute_lgi
> > 
> > =
> > 
> > =
> > 
> > mris_fill -c -r 1 lh.pial tmp-mris_compute_lgi/lh.pial.filled.mgz
> > 
> > =
> > 
> > reading surface from lh.pial...
> > 
> > writing filled volume to tmp-mris_compute_lgi/lh.pial.filled.mgz...
> > 
> > conforming output volume
> > 
> > setting resolution for intermediate calculations to 1.
> > 
> > =
> > 
> > make_outer_surface('tmp-mris_compute_lgi/lh.pial.filled.mgz',15,'tmp-
> > mris_compute_lgi/lh.pial-outer')
> > 
> > =
> > 
> > Warning: Unable to open display 'iconic'.  You will not be able to
> > display graphics on the screen.
> > 
> >  
> > 
> >   < M A T L A B >
> > 
> >   Copyright 1984-2007 The MathWorks, Inc.
> > 
> >  Version 7.5.0.338 (R2007b)
> > 
> >August 9, 2007
> > 
> >  
> > 
> >  
> > 
> >   To get started, type one of these: helpwin, helpdesk, or demo.
> > 
> >   For product information, visit www.mathworks.com.
> > 
> >  
> > 
> > >> reading filled volume...
> > 
> > rm: remove regular file `/tmp/tmp8147237.mgh'? 
> > 
> >  
> > 
> >  
> > 
> > 
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> 
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[Freesurfer] flattening full patch

[Don Hagler]

When I try to do a full flattening of a surface I often get areas with 
extreme squishing, looking like wrinkles.  Usually if I redo the cuts in 
slightly different ways (e.g. adjust the spacing between cuts, extend the 
cuts farther onto the lateral surface, etc) I can get the flattened surface 
to come out looking smooth.  Sometimes it takes several attempts (with 
several hours of computation for each attempt) to get it right.  Has anyone 
else noticed this, and has anyone attempted to improve the flattening 
algorithm?



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[Freesurfer] head points

[Don Hagler]

Can anyone supply an example head points file for use with tkmedit?


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[Freesurfer] keeping wm edits

[Don Hagler]

When I run recon-all with the -autorecon2-wm flag, my white matter edits get 
overwritten, presumably by aseg, even if I use the -keepwmedits flag.  Is 
that the correct behavior or is this a bug?


If instead of -autorecon2-wm I use -stage2, then the wm is untouched (as 
desired).  For some reason though, it was then unable to find the pons and I 
had to use the -pons-xyz option to get it to work.  Any idea why using 
-stage2 would produce this problem with finding the pons?



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Re: [Freesurfer] keeping wm edits

[Don Hagler]

Here is the version info for recon-all:

$Id: recon-all-nmr,v 1.107 2005/09/12 17:36:59 greve Exp $



From: Doug Greve <[EMAIL PROTECTED]>
To: Don Hagler <[EMAIL PROTECTED]>
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] keeping wm edits
Date: Mon, 07 Nov 2005 16:08:02 -0500

what version of recon-all do you have?



Don Hagler wrote:

When I run recon-all with the -autorecon2-wm flag, my white matter edits 
get overwritten, presumably by aseg, even if I use the -keepwmedits flag.  
Is that the correct behavior or is this a bug?


If instead of -autorecon2-wm I use -stage2, then the wm is untouched (as 
desired).  For some reason though, it was then unable to find the pons and 
I had to use the -pons-xyz option to get it to work.  Any idea why using 
-stage2 would produce this problem with finding the pons?



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




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[Freesurfer] freesurfer + fsl

[Don Hagler]

I had a similar problem running Linux RedHat E4.  It seems that fsl and 
freesurfer have incompatible versions of tcltktix.  One solution is to 
always run freesurfer and fsl from different terminal windows.



Peter Soros wrote:
Wed, 02 Nov 2005 15:19:19 -0800

Hi All,


I have installed Freesurfer for Mac OS X (2 Oct 2005) on my system (running 
10.4.2) - thanks for the OS X release!


Unfortunately, fsl doesn't work after the installation of Freesurfer.

This is the error message I get when I try to open the fsl GUI:

Error in startup script: no suitable image found.  Did find:

/Applications/freesurfer/lib/tcltktixblt/lib/ libtix8.1.8.4.a: unknown fi

le type, first eight bytes: 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A
   while executing
"load /Applications/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix"
   ("package ifneeded" script)
   invoked from within
"package require Tix"
   invoked from within

"if { [ string first tclsh [ file tail [ info nameofexecutable ] ] ] ! = 0 } 
{


   package require Tix
   tix configure -scheme TixGray
   option add ..."
   (file "/usr/local/fsl/tcl/fslstart.tcl" line 3)
   invoked from within
"source [ file dirname [ info script ] ]/fslstart.tcl"
   (file "/usr/local/fsl/tcl/fsl.tcl" line 71)
   invoked from within
"source ${FSLDIR}/tcl/${origname}.tcl"
   (file "/usr/local/fsl/bin/fsl" line 19)


FSL was installed in the recommended directory /usr/local/fsl/ and worked 
well before.


Any help to get FSL working again is highly appreciated!!

Peter


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RE: [Freesurfer] freesurfer + fsl

[Don Hagler]

I forgot to mention that your .cshrc or .bashrc should not automatically 
initialize freesurfer or fsl.  You would want to set up an alias to do that 
selectively per terminal window.


Don Hagler wrote:


I had a similar problem running Linux RedHat E4.  It seems that fsl and 
freesurfer have incompatible versions of tcltktix.  One solution is to 
always run freesurfer and fsl from different terminal windows.



Peter Soros wrote:
Wed, 02 Nov 2005 15:19:19 -0800

Hi All,


I have installed Freesurfer for Mac OS X (2 Oct 2005) on my system (running 
10.4.2) - thanks for the OS X release!


Unfortunately, fsl doesn't work after the installation of Freesurfer.

This is the error message I get when I try to open the fsl GUI:

Error in startup script: no suitable image found.  Did find:

/Applications/freesurfer/lib/tcltktixblt/lib/ libtix8.1.8.4.a: unknown fi

le type, first eight bytes: 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A
   while executing
"load /Applications/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix"
   ("package ifneeded" script)
   invoked from within
"package require Tix"
   invoked from within

"if { [ string first tclsh [ file tail [ info nameofexecutable ] ] ] ! = 0 
} {


   package require Tix
   tix configure -scheme TixGray
   option add ..."
   (file "/usr/local/fsl/tcl/fslstart.tcl" line 3)
   invoked from within
"source [ file dirname [ info script ] ]/fslstart.tcl"
   (file "/usr/local/fsl/tcl/fsl.tcl" line 71)
   invoked from within
"source ${FSLDIR}/tcl/${origname}.tcl"
   (file "/usr/local/fsl/bin/fsl" line 19)


FSL was installed in the recommended directory /usr/local/fsl/ and worked 
well before.


Any help to get FSL working again is highly appreciated!!

Peter


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RE: [Freesurfer] freesurfer + fsl

[Don Hagler]

The problem does occur when fsl is initialized after freesurfer, but it may 
be possible to comment out certain lines from the freesurfer setup script.  
I haven't tried that.




From: Stephen Smith <[EMAIL PROTECTED]>
To: Don Hagler <[EMAIL PROTECTED]>
CC: freesurfer@nmr.mgh.harvard.edu, [EMAIL PROTECTED]
Subject: RE: [Freesurfer] freesurfer + fsl
Date: Wed, 9 Nov 2005 18:33:55 + (GMT)


Right - but does FreeSurfer actually use those environment variables or
does it just set them up because it's own bundled version of FSL needs
them? If it's the latter it may just be enough to initialise FreeSurfer
first and FSL second, and then all may be well?

Cheers.



On Tue, 8 Nov 2005, Don Hagler wrote:

> I forgot to mention that your .cshrc or .bashrc should not automatically
> initialize freesurfer or fsl.  You would want to set up an alias to do 
that

> selectively per terminal window.
>
> Don Hagler wrote:
> >
> >I had a similar problem running Linux RedHat E4.  It seems that fsl and
> >freesurfer have incompatible versions of tcltktix.  One solution is to
> >always run freesurfer and fsl from different terminal windows.
> >
> >
> >Peter Soros wrote:
> >Wed, 02 Nov 2005 15:19:19 -0800
> >
> >Hi All,
> >
> >
> >I have installed Freesurfer for Mac OS X (2 Oct 2005) on my system 
(running

> >10.4.2) - thanks for the OS X release!
> >
> >Unfortunately, fsl doesn't work after the installation of Freesurfer.
> >
> >This is the error message I get when I try to open the fsl GUI:
> >
> >Error in startup script: no suitable image found.  Did find:
> >
> >/Applications/freesurfer/lib/tcltktixblt/lib/ libtix8.1.8.4.a: unknown 
fi

> >
> >le type, first eight bytes: 0x21 0x3C 0x61 0x72 0x63 0x68 0x3E 0x0A
> >while executing
> >"load /Applications/freesurfer/lib/tcltktixblt/lib/libtix8.1.8.4.a Tix"
> >("package ifneeded" script)
> >invoked from within
> >"package require Tix"
> >invoked from within
> >
> >"if { [ string first tclsh [ file tail [ info nameofexecutable ] ] ] ! 
= 0

> >} {
> >
> >package require Tix
> >tix configure -scheme TixGray
> >option add ..."
> >(file "/usr/local/fsl/tcl/fslstart.tcl" line 3)
> >invoked from within
> >"source [ file dirname [ info script ] ]/fslstart.tcl"
> >(file "/usr/local/fsl/tcl/fsl.tcl" line 71)
> >invoked from within
> >"source ${FSLDIR}/tcl/${origname}.tcl"
> >(file "/usr/local/fsl/bin/fsl" line 19)
> >
> >
> >FSL was installed in the recommended directory /usr/local/fsl/ and 
worked

> >well before.
> >
> >Any help to get FSL working again is highly appreciated!!
> >
> >Peter
> >
> >
> >___
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 John Radcliffe Hospital, Headington, Oxford OX3 9DU, UK
 +44 (0) 1865 222726  (fax 222717)

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[Freesurfer] motion correction during recon-all

[Don Hagler]

I want to average multiple structural scans for input into the surface 
recon.  Two are axial and one is sagittal.  (I plan to correct for the 
gradient inhomogeneities in the sagittal images, so that shouldn't be an 
issue.)


Anyway, the problem comes when recon-all does "motion correction" to align 
the scans.  For some strange reason, the axial and sagittal scan protocols 
use slightly different TRs and TEs (e.g. TR=7.996 vs. 8.012).  For some even 
stranger reason, this brings recon-all to a screaching halt.  I'm guessing 
that this is actually a MINC problem but I wonder if there is a way to make 
it ignore the TR and TE when aligning two structural scans.


My work around is to explicitly set the TR and TE for the sagittal scan when 
running mri_convert:

mri_convert -tr 8.012 -te 3.136 -it dicom i\*.1 $destdir/$mgzname.mgz


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Re: [Freesurfer] motion correction during recon-all

[Don Hagler]

Sorry for being overly dramatic.  recon-all just quits with error messages:

ERROR: TRs are inconsistent 8.012 7.996
ERROR: mri_motion_correct exited with non-zero status



From: Doug Greve <[EMAIL PROTECTED]>
To: Don Hagler <[EMAIL PROTECTED]>
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] motion correction during recon-all
Date: Mon, 28 Nov 2005 17:08:37 -0500


Can you elaborate on what "brings to a screetching halt means"? Is there an 
error msg or does it just hang?


doug



Don Hagler wrote:

I want to average multiple structural scans for input into the surface 
recon.  Two are axial and one is sagittal.  (I plan to correct for the 
gradient inhomogeneities in the sagittal images, so that shouldn't be an 
issue.)


Anyway, the problem comes when recon-all does "motion correction" to align 
the scans.  For some strange reason, the axial and sagittal scan protocols 
use slightly different TRs and TEs (e.g. TR=7.996 vs. 8.012).  For some 
even stranger reason, this brings recon-all to a screaching halt.  I'm 
guessing that this is actually a MINC problem but I wonder if there is a 
way to make it ignore the TR and TE when aligning two structural scans.


My work around is to explicitly set the TR and TE for the sagittal scan 
when running mri_convert:

mri_convert -tr 8.012 -te 3.136 -it dicom i\*.1 $destdir/$mgzname.mgz


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




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[Freesurfer] fieldsign broken with new surfaces

[Don Hagler]

I tried to run fieldsign calculation using surfaces created with the new 
recon-all but the results look wrong, with some vertices that have a 
salt-and-peppery look to them.  The code I'm using is ripped out of an older 
version of tksurfer and works fine on old surfaces.


It seems that there is a lack of correspondence between vertex numbers in 
the flattened surface and orig or something.  Another odd thing is that the 
ripflag is set for all vertices in the flat patch, but that is probably 
unrelated.  We noticed that the file size of the different surfaces (e.g. 
orig, smoothwm, inflated) varies.  In the older version, the surfaces all 
had an identical size.  This suggests that the different surfaces have 
different number of vertices now, or you've changed the file format 
somewhat.  Can you tell me what's going on there?


My current work-around is to use recon-all up to the point of fill, taking 
advantage of the new aseg, but then I'm using the old programs to generate 
surfaces compatible with my fieldsign code.



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[Freesurfer] mri_surf2surf

[Don Hagler]

Hi guys,

There seems to be a minor bug in mri_surf2surf when trg_type = w.  If 
trgsurfval is given as a relative path name (e.g. no directory sepcified 
with intention to create in current working directory), the output file name 
can be prefixed by" lh."  or "rh." and it can be put in the subjects surf 
directory.  Being put in that directory only happens when trgsubject is not 
ico.


Don


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RE: [Freesurfer] mri_surf2surf

[Don Hagler]

I should have mentioned that a simple workaround is to precede the 
trgsurfval with "./" to explicitly specify that it should be created in the 
current working directory.




From: "Don Hagler" <[EMAIL PROTECTED]>
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] mri_surf2surf
Date: Thu, 09 Feb 2006 14:35:38 -0800

Hi guys,

There seems to be a minor bug in mri_surf2surf when trg_type = w.  If 
trgsurfval is given as a relative path name (e.g. no directory sepcified 
with intention to create in current working directory), the output file 
name can be prefixed by" lh."  or "rh." and it can be put in the subjects 
surf directory.  Being put in that directory only happens when trgsubject 
is not ico.


Don


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[Freesurfer] paint, mri_vol2surf, paint-sess

[Don Hagler]

I tried painting to a surface created with the new recon-all (using paint or 
mri_vol2surf (version 1.22 2005/07/05)), and it seems that the surrfaces are 
not being read correctly (the data in the w file has the speckled appearance 
you get when the vertex numbers are wrong).


I posted a message before about my fieldsign code not working on the new 
surfaces and Bruce Fischl said this about the different surfaces (i.e. orig, 
smoothwm, inflated, etc.):
"check the # of vertices etc... with mris_euler_number (or mris_info). Make 
sure they all are the same. The file sizes aren't necessarily the same any 
more as they contain additional info, but the # of vertices etc. should be 
invariant."


So are paint and mri_vol2surf still supported under the current distribution 
of MGH FreeSurfer?  Are there newer versions out there?  Or is everyone 
using paint-sess these days?


By the way, what was done to the format of the surfaces?  What additional 
info do they contain?  Is there documentation or posted code on how to read 
the new surfaces?



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RE: [Freesurfer] paint, mri_vol2surf, paint-sess

[Don Hagler]

oops, my dumb mistake.  I forgot to change the subjet name in the 
register.dat.




From: "Don Hagler" <[EMAIL PROTECTED]>
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] paint, mri_vol2surf, paint-sess
Date: Thu, 23 Feb 2006 14:26:14 -0800

I tried painting to a surface created with the new recon-all (using paint 
or mri_vol2surf (version 1.22 2005/07/05)), and it seems that the surrfaces 
are not being read correctly (the data in the w file has the speckled 
appearance you get when the vertex numbers are wrong).


I posted a message before about my fieldsign code not working on the new 
surfaces and Bruce Fischl said this about the different surfaces (i.e. 
orig, smoothwm, inflated, etc.):
"check the # of vertices etc... with mris_euler_number (or mris_info). Make 
sure they all are the same. The file sizes aren't necessarily the same any 
more as they contain additional info, but the # of vertices etc. should be 
invariant."


So are paint and mri_vol2surf still supported under the current 
distribution of MGH FreeSurfer?  Are there newer versions out there?  Or is 
everyone using paint-sess these days?


By the way, what was done to the format of the surfaces?  What additional 
info do they contain?  Is there documentation or posted code on how to read 
the new surfaces?



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