Freesurfer March 2010

freesurfer@nmr.mgh.harvard.edu

101 participants
153 discussions

optseq2 installation
by Florence POMARES 16 Mar '10

16 Mar '10

Dear Doug, The command is still not known. I think that our linux platform is too old... Just to be sure : - optseq2 need matlab ? - optseq2 can be run even if Freesurfer and FS-FAST are not installed ? thank you. other wise, do you know another program doing similar things than optseq ? regards De : Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Date : 15 mars 2010 18:51:19 HNEC À : Florence POMARES <florence.borgetto(a)univ-st-etienne.fr> Cc : freesurfer(a)nmr.mgh.harvard.edu Objet : Rép : [Freesurfer] optseq installation what do you mean it is not recognized? To make it executable, you need to run chmod a+x optseq2 to run it, either put it into your PATH, or cd to where it is located and run ./optseq2 the "./" is necessary if it is not in the PATH doug Florence POMARES wrote: 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 <mailto:greve@nmr.mgh.harvard.edu >> *Date : *12 mars 2010 20:09:57 HNEC *À : *Florence POMARES <florence.borgetto(a)univ-st-etienne.fr <mailto:florence.borgetto@univ-st-etienne.fr >> *Cc : *freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@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

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How to transform brain.mgz back to native space
by liang wang 16 Mar '10

16 Mar '10

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: wanglbit(a)gmail.com

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Clusterwise Correction for Multiple Comparisons
by liyari5018 16 Mar '10

16 Mar '10

Hi all, I used QDEC compare differences between normal subjects and patients, the activation can be seen without correction, after correction by FDR ,all disappeared.I read about the Clusterwise Correction for Multiple Comparisons of the manual. I am confused about the meaning of Correction. I use the simulation when an error is as follows: ############################################################################################# ERROR: dimension mismatch between X and contrast /usr/local/freesurfer/subjects/sad/qdec/Untitled/tmp.mri_glmfit-sim-2797/lh-Avg-Intercept-area.mtx X has 8 cols, C has 2 cols ############################################################################################# Why is that? Also could you please give some recommendations on the correction. Thanks for your reply, i 'll be very grateful to you for your help. LJ

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modification made to longitudinal results
by Guang Zeng 16 Mar '10

16 Mar '10

Hi, there, I need add some control points to the longitudinal results. After adding control points, I need rerun it. which command should I use? recon-all -s subj.long.baseid .... or recon-all -long subj baseid .... Thanks! Guang _________________________________________________________________ Your E-mail and More On-the-Go. Get Windows Live Hotmail Free. http://clk.atdmt.com/GBL/go/201469229/direct/01/

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gaussian and mean curvature in qdec
by Ana Catarino 16 Mar '10

16 Mar '10

Hello, I have 2 groups, normal and patients, and was using qdec to compare groups for several measures (thickness, curv, sulc, etc), but couldn't do it for Gaussian (white.K) and mean curvature (white.H). I get the following error: Error in Analyze: Couldn't open file $SUBJECTS_DIR/AS1/surf/lh.white.K.fwhm10.avgsubject.mgh How can I create the ?h.white.K.fwhm??.avgsubject.mgh file for every subject? Many Thanks, Ana Catarino

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recon-all fails because of mri_label error
by Guang Zeng 15 Mar '10

15 Mar '10

Hi, there, recon-all fails because of mri_label error , I copied the last few lines of recon-all.log. Any suggestions? gca peak Unknown = 0.94427 ( 0) gca peak Left_Inf_Lat_Vent = 0.26806 (38) gca peak CSF = 0.21047 (24) gca peak Left_Accumbens_area = 0.37761 (71) gca peak Left_VentralDC = 0.15788 (92) gca peak Left_undetermined = 1.00000 (35) gca peak Left_vessel = 0.65148 (62) gca peak Left_choroid_plexus = 0.09084 (48) gca peak Right_Inf_Lat_Vent = 0.30889 (34) gca peak Right_Accumbens_area = 0.44316 (77) gca peak Right_vessel = 0.83418 (60) gca peak Right_choroid_plexus = 0.10189 (48) gca peak Fifth_Ventricle = 0.54604 (27) gca peak WM_hypointensities = 0.14831 (83) gca peak non_WM_hypointensities = 0.09346 (54) gca peak Optic_Chiasm = 0.34849 (76) mri_ca_label GCA sequential renormalization: label 28 not consistently computed. not using caudate to estimate GM means setting label Right_VentralDC based on Left_VentralDC = 1.15 x + 0 estimating mean gm scale to be 1.01 x + 0.0 estimating mean wm scale to be 1.00 x + 0.0 estimating mean csf scale to be 1.04 x + 0.0 Left_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) Right_Pallidum too bright - rescaling by 0.914 (from 1.075) to 101.2 (was 110.7) saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux dnode26.mayo.edu 2.6.18-92.1.6.el5 #1 SMP Wed Jun 25 13:45:47 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Mar 12 19:55:35 CST 2010 _________________________________________________________________ The New Busy is not the old busy. Search, chat and e-mail from your inbox. http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:…

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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 >> >

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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.

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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

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Freesurfer March 2010