Freesurfer

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30086 discussions

How to compare conditions scanned within different runs?
by Shahin 15 Mar '10

15 Mar '10

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

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Re: [Freesurfer] optseq installation
by Florence POMARES 15 Mar '10

15 Mar '10

Dear Doug, Thank you for your answer. We run it from shell (a comand window of X11 because we are connected to the server by the way of a MacIntosh) but it isn't recognized. How can we make it executable ? We just upload optseq2 on the Linux server... Le 12 mars 10 à 20:30, Florence POMARES a écrit : > > > Début du message réexpédié : > >> De : Douglas N Greve <greve(a)nmr.mgh.harvard.edu> >> Date : 12 mars 2010 20:09:57 HNEC >> À : Florence POMARES <florence.borgetto(a)univ-st-etienne.fr> >> Cc : freesurfer(a)nmr.mgh.harvard.edu >> Objet : Rép : [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(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)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 >> >

2 1

Choroid plexus -filling
by Rajagopalan, Venkateswaran 15 Mar '10

15 Mar '10

Hi All, In my "filled.mgz" volume choroid plexus regions are left out in both right and left hemispheres, i am wondering whether i need to fill them or it is ok to leave them unfilled. Thanks venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

2 4

selxavg error
by Leila Reddy 15 Mar '10

15 Mar '10

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 2.0000 -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', '2.0000', '-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 TR 2.000000 TER 2.000000 Total Window 30 PreStim Window 6 Remove Baseline 1 Remove Trend 0 Remove QTrend 0 Rescale Target 1000 nSkip 0 InPlane Res 1.40625 FWHM 0 Hanning Radius 0 Time Offset 0 GammaFit 1 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

2 2

wm.mgz and wmparc.mgz
by Xiaoying Tang 15 Mar '10

15 Mar '10

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

3 2

Pial surface- clarification
by Rajagopalan, Venkateswaran 15 Mar '10

15 Mar '10

Hi All, I am working in ALS dementia patients where there is ventricle enlargement and more CSF filling when compared with controls. Since i am new to freesurfer and my knowledge of anatomy is limited i would like to clarify the following. Pial surface in right and left cerebral cortex looks suspicious to me, the brain extraction step left out some non brain regions, i tried to edit them but since some of the non brain regions are close to brain regions i didn't do too much editing for the fear of removing brain regions. I have attached a screen shot image in one of our subjects, kindly tell me whether the pial surface looks ok if not any suggestions to correct this problem. Thanks in advance venkat =================================== P Please consider the environment before printing this e-mail Cleveland Clinic is ranked one of the top hospitals in America by U.S.News & World Report (2009). Visit us online at http://www.clevelandclinic.org for a complete listing of our services, staff and locations. Confidentiality Note: This message is intended for use only by the individual or entity to which it is addressed and may contain information that is privileged, confidential, and exempt from disclosure under applicable law. If the reader of this message is not the intended recipient or the employee or agent responsible for delivering the message to the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please contact the sender immediately and destroy the material in its entirety, whether electronic or hard copy. Thank you.

2 2

rois based on mni coordinates
by Sharmili 57 14 Mar '10

14 Mar '10

Dear Freesurfer experts, i am trying to construct a roi based on some mni coordinates. I checked the coordinate in tkmedit, saved the point and opened it in tksurfer and transformed the selected vertices into labels. But the coordinates change as soon as I open the point in tksurfer. Is there a function like select_talairach_point for mni coordinates? Thanks a lot for your help! Sharmili _________________________________________________________________ http://redirect.gimas.net/?n=M1003xHM5Adressen2 Ein Postfach für Alles – bei Hotmail 5 E-Mail-Adressen online verwalten!

1 0

ERROR: comparison in expression (FS with SGE)
by Xue, Feng 13 Mar '10

13 Mar '10

Dear Bruce & FS experts, Please forgive my re-post, for I havn't got any response from last post. I do appreciate if anyone could give me a hint or suggestion. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ We are running freesurfer with Sun GridEngine. Currently, we repeatedly got this error in SGE's job error log file on some data when doing recon_all: $ cat recon_xf.e437 (standard_in) 2: Error: comparison in expression $ cat recon_xf.e431 (standard_in) 2: comparison in expression I also checked the recon-all-status.log file, but not error was found. Has anyone met this problem? Is it critical? Thanks in advance. -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org

2 1

Extracting ROIs from aparc.a2009s+aseg.mgz
by liang wang 12 Mar '10

12 Mar '10

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 -- 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: wanglbit(a)gmail.com

2 4

MNI-space label to dicom-space?
by Jesse Friedman 12 Mar '10

12 Mar '10

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 #1111 Charlestown, MA 02129 Phone: (617) 726-0307 Fax: (617) 726-4078 jessef(a)nmr.mgh.harvard.edu

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