[Freesurfer] Bad pial surface
Hi, Reviewing the results of recon-all I noticed that the segmentation of wm and gm was OK but that the computed pial surface chopped away an unacceptable amount of gm voxels, too many to manually edit. Is there a way to cure this problem by choosing some options? I used version 4.5.0 on a Mac Intel. Ed ___ 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.
[Freesurfer] Performance on brains with tumors
Hi, how does freesurfer perform on brains with tumor? Are the any specyfic options that could improve the results (like masking for example)? Cheers, Chris ___ 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.
Re: [Freesurfer] Performance on brains with tumors
I think the results may be quite unpredictable. It depends on the size of the tumor, the infiltration, the necrosis, etc. --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter SpeedComm Telecom --- Novo Netfilter 3.4 www.Netfilter.com.br --- Novo Netfilter Small Business 2010/3/12 Chris Filo Gorgolewski chris.gorgolew...@gmail.com Hi, how does freesurfer perform on brains with tumor? Are the any specyfic options that could improve the results (like masking for example)? Cheers, Chris ___ 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. ___ 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.
[Freesurfer] optseq installation
Dear Optseq Developpers, Few years ago we used to design our paradigm with optseq. We would like to use it again but we can't install it. We went on the web site : http://surfer.nmr.mgh.harvard.edu/optseq/ we download the linux version 2 we upload it to the our old linux server with matlab optseq and optseq2 aren't recognize as command. we also tried to install the cywin version on a PCwindows with cygwin and matlab. but when we execute the optseq2.exe it says that it doesn't find the input point of _isnand in the library of the dynmic links cywin1.ddl we don't know what to do. would you please help us ? thank you Isabelle Faillenot Ingénieur hospitalier service de neurologie - CM2R hôpital Nord 42055 Saint-Etienne cédex 2___ 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.
Re: [Freesurfer] Extracting ROIs from aparc.a2009s+aseg.mgz
Liang, We have a very good tutorial which takes you through what you would like to do. It's located here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual There is also some information on registration here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration Having the aparc divided up isn't necessary to do them though. Allison -- On Thu, 11 Mar 2010, liang wang wrote: Hi Allison, Thanks. I have used the command line below to separately create many label files, each of which include vertex number and XYZ coordinates. mri_annotation2label --subject BNC006 --hemi lh --labelbase aparc.a2009 Sorry for not declaring my intention previously. What I actually want to do is utilizing the gray ROIs recorded in aparc.a2009s+aseg.mgz to generate the average time courses of each ROI from BOLD fMRI scanned from the same subject. Can you give some advice how to accurately make it. Also, I am worried the registeration issues across different modality images. Best, Liang 2010/3/11 Allison Stevens astev...@nmr.mgh.harvard.edu Liang, mri_annotation2label will separate all the ROIs in the ?h.aparc.a2009s.annot - is this what you need? I'm not sure what you mean by mask image based on this image using 1, 2. You can merge or split labels as well. To display aparc.a2009s+aseg.mgz in tkmedit, you can do: tkmedit subjid orig.mgz -segmentation aparc.a2005s+aseg.mgz Allison -- On Wed, 10 Mar 2010, liang wang wrote: Hi FS experts, Does anyone know how to extract these ROIs (including all gyral and sulci) from the image aparc.a2009s+aseg.mgz. I just want to create a mask image based on this image by using 1, 2, .. to code different brain areas. Thanks for your solutions. Also, I can not display the image using the following command: tkmedit subjid orig -aux brain -aparc.a2009s+aseg.mgz, but can correctly display aparc+aseg.mgz. Any advise would be appreciated. Liang 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] problem on recon-all
Xiaoying, There are directions for how to do this located here: https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ?highlight=%28FAQ%29#SkullStrippingOptions Allison -- On Fri, 12 Mar 2010, Xiaoying Tang wrote: Hi all, When we do recon-all, we usually do autorecon1, autorecon2, and autorecon3 in sequence. But now suppose I have already have a very good skull-stripped subject. I mean I don't need to do skull-stripping with freesurfer. But I want to get greymatter and white matter, which are generated in autorecon2 and autorecon3. Is there any way to do this? Looking forward to your early reply. Best, Xiaoying ___ 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.
Re: [Freesurfer] Bad pial surface
Ed, Usually a problem with the pial surface indicates a problem with the white surface and fixing the wm.mgz will fix the pial. But you said the wm segmentation is okay in the areas where the pial is a problem? What area of the brain are you finding this problem? Allison -- On Fri, 12 Mar 2010, Ed Gronenschild wrote: Hi, Reviewing the results of recon-all I noticed that the segmentation of wm and gm was OK but that the computed pial surface chopped away an unacceptable amount of gm voxels, too many to manually edit. Is there a way to cure this problem by choosing some options? I used version 4.5.0 on a Mac Intel. Ed ___ 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.
Re: [Freesurfer] Bad pial surface
Hi Ed, we can't possibly diagnose this without seeing some images. cheers Bruce On Fri, 12 Mar 2010, Ed Gronenschild wrote: Hi, Reviewing the results of recon-all I noticed that the segmentation of wm and gm was OK but that the computed pial surface chopped away an unacceptable amount of gm voxels, too many to manually edit. Is there a way to cure this problem by choosing some options? I used version 4.5.0 on a Mac Intel. Ed ___ 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.
Re: [Freesurfer] Performance on brains with tumors
Hi Chris, it depends on where the tumor is and how big it is. It it's within the wm you could certainly just fill it as a wm edit and things should work. cheers Bruce On Fri, 12 Mar 2010, Chris Filo Gorgolewski wrote: Hi, how does freesurfer perform on brains with tumor? Are the any specyfic options that could improve the results (like masking for example)? Cheers, Chris ___ 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.
Re: [Freesurfer] problem on recon-all
Hi Allison, You are so helpful. Thanks a lot. Best, Xiaoying - Original Message - From: Allison Stevens astev...@nmr.mgh.harvard.edu Date: Friday, March 12, 2010 7:43 am Subject: Re: [Freesurfer] problem on recon-all To: Xiaoying Tang xta...@jhu.edu Cc: freesurfer@nmr.mgh.harvard.edu Xiaoying, There are directions for how to do this located here: Allison -- On Fri, 12 Mar 2010, Xiaoying Tang wrote: Hi all, When we do recon-all, we usually do autorecon1, autorecon2, and autorecon3 in sequence. But now suppose I have already have a very good skull-stripped subject. I mean I don't need to do skull-stripping with freesurfer. But I want to get greymatter and white matter, which are generated in autorecon2 and autorecon3. Is there any way to do this? Looking forward to your early reply. Best, Xiaoying ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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 . 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. ___ 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.
[Freesurfer] selxavg error
Hi,
I'm running into an error with selxavg ('Input to SVD must not contain NaN or
Inf') that has been posted before on the mailing list but I couldn't find a
solution to it.
The command was selxavg-sess -sf sessid -df sessdir -analysis loc-sm3.
The output of the log file is:
selxavg-sess log file
$Id: selxavg-sess,v 1.15 2006/01/06 02:37:22 greve Exp $
uid=502(lreddy) gid=502(lreddy) groups=502(lreddy), 81(appserveradm),
79(appserverusr), 80(admin)
/Volumes/donnees/GR/gr_analysis/kan_gr_006
/Applications/freesurfer/fsfast/bin/selxavg-sess
-sf sessid -df sessdir -analysis loc-sm3
Darwin g5-leila.local 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10 18:23:28
PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386
Fri Mar 12 17:07:53 CET 2010
selxavg: Command not found.
---
/Volumes/donnees/GR/gr_data/kan_gr_006
Fri Mar 12 17:07:53 CET 2010
/Volumes/donnees/GR/gr_data/kan_gr_006/bold
selxavg2 -TR 2. -parname loc.para -o loc-sm3/h -i 018/fmc-sm3 -i
019/fmc-sm3 -i 020/fmc-sm3 -cfg
/Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg -ipr 1.40625
-pomnibus loc-sm3/omnibus/fsig -fomnibus loc-sm3/omnibus/f
cat: /Applications/freesurfer/fsfast/docs/version: No such file or directory
--- Parsing Config File:
/Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg
-gammafit 2.25 1.25 -timewindow 30 -prestim 6 -polyfit 1 -TER 2 -nskip 0 -fwhm
0 -extreg mcextreg -nextreg 3 -rescale 1000
Logfile is loc-sm3/h_sxa.log
matlab file is /tmp/sxa_5739.m
--- Matlab file --
% Matlab file for selxavg2 Fri Mar 12 17:07:53 CET 2010
% This file may be deleted
% /tmp/sxa_5739.m
global QuitOnError;
QuitOnError = 1;
r = fast_selxavg( '-TR', '2.', '-parname', 'loc.para', '-o', 'loc-sm3/h',
'-i', '018/fmc-sm3', '-i', '019/fmc-sm3', '-i', '020/fmc-sm3', '-cfg',
'/Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg', '-ipr',
'1.40625', '-pomnibus', 'loc-sm3/omnibus/fsig', '-fomnibus',
'loc-sm3/omnibus/f');
if(r==0)
fmri_touch('/Volumes/donnees/GR/gr_data/kan_gr_006/bold/loc-sm3/selxavg.ok.5739');
end
qoe;
---
--
--- matlab output
Warning: Unable to open display iconic, MATLAB is starting without a display.
You will not be able to display graphics on the screen.
M A T L A B
Copyright 1984-2007 The MathWorks, Inc.
Version 7.4.0.287 (R2007a)
January 29, 2007
Warning: Duplicate directory name: /Users/lreddy/matlab.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com.
$Id: fast_selxavg.m,v 1.22.2.2 2006/09/29 21:54:40 greve Exp $
Parsing Arguments
RescaleTarget = 1000
Checking Parameters
AutoStimDur: 0
StimDur: Number of Runs: 3
Input Volume List
1 018/fmc-sm3
2 019/fmc-sm3
3 020/fmc-sm3
Input Pardigm File List
1 018/loc.para
2 019/loc.para
3 020/loc.para
Output Volume loc-sm3/h
F Omnibus Volume loc-sm3/omnibus/f
Sig Omnibus Volume loc-sm3/omnibus/fsig
TR2.00
TER 2.00
Total Window 30
PreStim Window 6
Remove Baseline 1
Remove Trend0
Remove QTrend 0
Rescale Target 1000
nSkip 0
InPlane Res 1.40625
FWHM0
Hanning Radius 0
Time Offset 0
GammaFit1
1 2.25 1.25
GammaFit Alpha: 2
SPM HRF: -1
Seg Brain/Air 1
SynthSeed 0
ExtReg File mcextreg
NExtReg 3
ExtRegOrthog 0
firstslice 0
nslices 17
nyqreg 0
SynthSeed = 0
Conditions Found (4): 1 2 3 4
Run 1: 32 32 32 32
Run 2: 32 32 32 32
Run 3: 32 32 32 32
Slice 0, 9.3119e-05 --
First Pass (Accumulation), 0.000414148
Run 1/3, 0.000853017
Excluding 0 Points:
Run 2/3, 0.622743
Excluding 0 Points:
Run 3/3, 1.0841
Excluding 0 Points:
Second Pass (Residual Error Estimation), 1.52296
??? Error using == svd
Input to SVD must not contain NaN or Inf.
Error in == cond at 40
s = svd(A);
Error in == fast_selxavg at 193
c = cond(SumXtWX);
??? Undefined function or variable 'r'.
quiting matlab
2010-03-12 17:08:05.047 MATLAB[5789] Process manager already initialized --
can't fully enable headless mode.
--
ERROR: fast_selxavg() failed\n
The output of bugr is
FREESURFER_HOME: /Applications/freesurfer
Build stamp: freesurfer-Darwin-tiger-i686-stable-pub-v3.0.5
Kernel info: Darwin 8.11.1 i386
Thanks in advance,
Leila
___
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
[Freesurfer] wm.mgz and wmparc.mgz
Hi all, After autorecon3, there are two files named wm.mgz and wmparc.mgz. What's the difference between this two? If I just want the white matter, should I use wm.mgz or wmparc.mgz? The corresponding grey matter is aparc+aseg.mgz. Looking forward to your early reply. Best, Xiaoying ___ 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.
Re: [Freesurfer] optseq installation
Did you make it executable? They are run from the shell, not matlab. doug Florence POMARES wrote: Dear Optseq Developpers, Few years ago we used to design our paradigm with optseq. We would like to use it again but we can't install it. We went on the web site : http://surfer.nmr.mgh.harvard.edu/optseq/ we download the linux version 2 we upload it to the our old linux server with matlab optseq and optseq2 aren't recognize as command. we also tried to install the cywin version on a PCwindows with cygwin and matlab. but when we execute the optseq2.exe it says that it doesn't find the input point of _isnand in the library of the dynmic links cywin1.ddl we don't know what to do. would you please help us ? thank you Isabelle Faillenot Ingénieur hospitalier service de neurologie - CM2R hôpital Nord 42055 Saint-Etienne cédex 2 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
Re: [Freesurfer] selxavg error
hmmm, something is going wrong with the whitening. Can you try it
without whitening? Also, look in the 4d volume for some artifact (eg, a
spike). This might account for it.
doug
Leila Reddy wrote:
Hi,
I'm running into an error with selxavg ('Input to SVD must not contain
NaN or Inf') that has been posted before on the mailing list but I
couldn't find a solution to it.
The command was selxavg-sess -sf sessid -df sessdir -analysis loc-sm3.
The output of the log file is:
selxavg-sess log file
$Id: selxavg-sess,v 1.15 2006/01/06 02:37:22 greve Exp $
uid=502(lreddy) gid=502(lreddy) groups=502(lreddy), 81(appserveradm),
79(appserverusr), 80(admin)
/Volumes/donnees/GR/gr_analysis/kan_gr_006
/Applications/freesurfer/fsfast/bin/selxavg-sess
-sf sessid -df sessdir -analysis loc-sm3
Darwin g5-leila.local 8.11.1 Darwin Kernel Version 8.11.1: Wed Oct 10
18:23:28 PDT 2007; root:xnu-792.25.20~1/RELEASE_I386 i386 i386
Fri Mar 12 17:07:53 CET 2010
selxavg: Command not found.
---
/Volumes/donnees/GR/gr_data/kan_gr_006
Fri Mar 12 17:07:53 CET 2010
/Volumes/donnees/GR/gr_data/kan_gr_006/bold
selxavg2 -TR 2. -parname loc.para -o loc-sm3/h -i 018/fmc-sm3 -i
019/fmc-sm3 -i 020/fmc-sm3 -cfg
/Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg -ipr
1.40625 -pomnibus loc-sm3/omnibus/fsig -fomnibus loc-sm3/omnibus/f
cat: /Applications/freesurfer/fsfast/docs/version: No such file or
directory
--- Parsing Config File:
/Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg
-gammafit 2.25 1.25 -timewindow 30 -prestim 6 -polyfit 1 -TER 2 -nskip
0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000
Logfile is loc-sm3/h_sxa.log
matlab file is /tmp/sxa_5739.m
--- Matlab file --
% Matlab file for selxavg2 Fri Mar 12 17:07:53 CET 2010
% This file may be deleted
% /tmp/sxa_5739.m
global QuitOnError;
QuitOnError = 1;
r = fast_selxavg( '-TR', '2.', '-parname', 'loc.para', '-o',
'loc-sm3/h', '-i', '018/fmc-sm3', '-i', '019/fmc-sm3', '-i',
'020/fmc-sm3', '-cfg',
'/Volumes/donnees/GR/gr_analysis/kan_gr_006/loc-sm3/analysis.cfg',
'-ipr', '1.40625', '-pomnibus', 'loc-sm3/omnibus/fsig', '-fomnibus',
'loc-sm3/omnibus/f');
if(r==0)
fmri_touch('/Volumes/donnees/GR/gr_data/kan_gr_006/bold/loc-sm3/selxavg.ok.5739');
end
qoe;
---
--
--- matlab output
Warning: Unable to open display iconic, MATLAB is starting without a
display.
You will not be able to display graphics on the screen.
M A T L A B
Copyright 1984-2007 The MathWorks, Inc.
Version 7.4.0.287 (R2007a)
January 29, 2007
Warning: Duplicate directory name: /Users/lreddy/matlab.
To get started, type one of these: helpwin, helpdesk, or demo.
For product information, visit www.mathworks.com
http://www.mathworks.com.
$Id: fast_selxavg.m,v 1.22.2.2 2006/09/29 21:54:40
greve Exp $
Parsing Arguments
RescaleTarget = 1000
Checking Parameters
AutoStimDur: 0
StimDur: Number of Runs: 3
Input Volume List
1 018/fmc-sm3
2 019/fmc-sm3
3 020/fmc-sm3
Input Pardigm File List
1 018/loc.para
2 019/loc.para
3 020/loc.para
Output Volume loc-sm3/h
F Omnibus Volume loc-sm3/omnibus/f
Sig Omnibus Volume loc-sm3/omnibus/fsig
TR2.00
TER 2.00
Total Window 30
PreStim Window 6
Remove Baseline 1
Remove Trend0
Remove QTrend 0
Rescale Target 1000
nSkip 0
InPlane Res 1.40625
FWHM0
Hanning Radius 0
Time Offset 0
GammaFit1
1 2.25 1.25
GammaFit Alpha: 2
SPM HRF: -1
Seg Brain/Air 1
SynthSeed 0
ExtReg File mcextreg
NExtReg 3
ExtRegOrthog 0
firstslice 0
nslices 17
nyqreg 0
SynthSeed = 0
Conditions Found (4): 1 2 3 4
Run 1: 32 32 32 32
Run 2: 32 32 32 32
Run 3: 32 32 32 32
Slice 0, 9.3119e-05 --
First Pass (Accumulation), 0.000414148
Run 1/3, 0.000853017
Excluding 0 Points:
Run 2/3, 0.622743
Excluding 0 Points:
Run 3/3, 1.0841
Excluding 0 Points:
Second Pass (Residual Error Estimation), 1.52296
??? Error using == svd
Input to SVD must not contain NaN or Inf.
Error in == cond at 40
s = svd(A);
Error in == fast_selxavg at 193
c = cond(SumXtWX);
??? Undefined function or variable 'r'.
quiting matlab
2010-03-12 17:08:05.047 MATLAB[5789] Process manager already
initialized -- can't fully enable headless mode.
--
ERROR: fast_selxavg() failed\n
The output of bugr is
FREESURFER_HOME: /Applications/freesurfer
Build
Re: [Freesurfer] wm.mgz and wmparc.mgz
Hi Xiaoying, the wm.mgz is our preliminary estimate of the white matter (a binary segmentation). The wmparc.mgz is the labeling of the interior of the white matter by proximity to cortical folds (and it occurs much later in the analysis) cheers Bruce On Fri, 12 Mar 2010, Xiaoying Tang wrote: Hi all, After autorecon3, there are two files named wm.mgz and wmparc.mgz. What's the difference between this two? If I just want the white matter, should I use wm.mgz or wmparc.mgz? The corresponding grey matter is aparc+aseg.mgz. Looking forward to your early reply. Best, Xiaoying ___ 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.
[Freesurfer] How to compare conditions scanned within different runs?
I want to compare 2 different experimental conditions that were scanned within different runs. For example assume that, in ten runs I have had conditions 1 and 2 and in another ten runs I have had condition 3 and 4. Now I want to compare condition 1 and 3. Is it possible? Regards Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard University ___ 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.
[Freesurfer] freesurfer and DTI
Hello everyone, I have a colleague (cc'd) who is interested in using FreeSurfer's segmentation with DTI results he obtained with TBSS. I am not sure how he should go about this. Any advice is appreciated. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2...@med.cornell.edu ___ 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.
Re: [Freesurfer] freesurfer and DTI
Hi Dana, I guess the easiest thing to do would be to pool FA values by wmparc region. I'm not sure that using tbss is needed for that though. Did you have something else in mind? cheers, Bruce On Fri, 12 Mar 2010, Dana W. Moore wrote: Hello everyone, I have a colleague (cc'd) who is interested in using FreeSurfer's segmentation with DTI results he obtained with TBSS. I am not sure how he should go about this. Any advice is appreciated. Thanks, Dana Dana W. Moore, Ph.D. Neuropsychology Fellow Cornell Neuropsychology Service Weill Medical College of Cornell University New York Presbyterian Hospital Department of Neurology Neuroscience 428 East 72nd Street, Suite 500 New York, NY 10021 Phone: 212-746-2441 Fax: 212-746-5584 Email: dwm2...@med.cornell.edu ___ 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.
[Freesurfer] MNI-space label to dicom-space?
Hi, I'd like to convert a label from fsaverage/MNI-space to the space of a subject's unpacked, unreconstructed, dicom-format scan. Will this be possible? Thank you, Jesse -- Jesse Friedman Martinos Center for Biomedical Imaging, Manoach Lab Massachusetts General Hospital 149 13th Street # Charlestown, MA 02129 Phone: (617) 726-0307 Fax: (617) 726-4078 jes...@nmr.mgh.harvard.edu ___ 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.
Re: [Freesurfer] Extracting ROIs from aparc.a2009s+aseg.mgz
Hi Allison, Thanks for the website you provide me. Through reading, I understand how to averaged extract contrast effect size in each ROI generated by FreeSurfer (e.g. aparc.a2009s+aseg.mgz). You know, the contrast image is a 3D file for each subject. However, BOLD data usually is a 4D image (i.e. 3D + time course). I try to use the following commands to carry out what I need (Let me say *BNC006 *is a subject ID, *example_func.nii.gz* a motion correction template and *filtered_func.nii.gz* a 4D BOLD data with realigment to example.nii.gz). Note that The below id is just to test whether there is a correct output. $ bbregister --mov example_func.nii.gz --bold --s BNC006 --init-fsl --reg register.dat $ mri_vol2vol --mov filtered_func.nii.gz --reg register.dat --fstarg --interp nearnest --o filtered_func.anat.mgh $ mri_segstats --seg $SUBJECTS_DIR/BNC006/mri/aparc.a2009s+aseg.mgz --ctab $FREESURFER/FreeSurferColorLUT.txt --id \ 11101 --id 11105 --i fitered_fun.anat.mgh --sum filter.stats The fist two lines run fine, but the last one seems stop after displaying loading filter_fun.anat.mgh. Your any suggests will be appreciated. Best, Liang 2010/3/12 Allison Stevens astev...@nmr.mgh.harvard.edu Liang, We have a very good tutorial which takes you through what you would like to do. It's located here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual There is also some information on registration here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalRegistration Having the aparc divided up isn't necessary to do them though. Allison -- On Thu, 11 Mar 2010, liang wang wrote: Hi Allison, Thanks. I have used the command line below to separately create many label files, each of which include vertex number and XYZ coordinates. mri_annotation2label --subject BNC006 --hemi lh --labelbase aparc.a2009 Sorry for not declaring my intention previously. What I actually want to do is utilizing the gray ROIs recorded in aparc.a2009s+aseg.mgz to generate the average time courses of each ROI from BOLD fMRI scanned from the same subject. Can you give some advice how to accurately make it. Also, I am worried the registeration issues across different modality images. Best, Liang 2010/3/11 Allison Stevens astev...@nmr.mgh.harvard.edu Liang, mri_annotation2label will separate all the ROIs in the ?h.aparc.a2009s.annot - is this what you need? I'm not sure what you mean by mask image based on this image using 1, 2. You can merge or split labels as well. To display aparc.a2009s+aseg.mgz in tkmedit, you can do: tkmedit subjid orig.mgz -segmentation aparc.a2005s+aseg.mgz Allison -- On Wed, 10 Mar 2010, liang wang wrote: Hi FS experts, Does anyone know how to extract these ROIs (including all gyral and sulci) from the image aparc.a2009s+aseg.mgz. I just want to create a mask image based on this image by using 1, 2, .. to code different brain areas. Thanks for your solutions. Also, I can not display the image using the following command: tkmedit subjid orig -aux brain -aparc.a2009s+aseg.mgz, but can correctly display aparc+aseg.mgz. Any advise would be appreciated. Liang 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. -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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.
[Freesurfer] How to transform brain.mgz back to native space
Hi FS experts, I find that FS does make a great skullstrip and extract a perfect brain (ie. brain.mgz). I am thinking to register this brain to MNI152 standard space using FSL. Does anyone know how to transfer the brain (256.^3, 1mm ) to subject-specific native space (224*256*176, 1mm). Thanks in advance. Liang -- Liang Wang, PhD Postdoctoral Fellow Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: wangl...@gmail.com ___ 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.
