Freesurfer

freesurfer@nmr.mgh.harvard.edu

12 participants
30060 discussions

Re: [Freesurfer] Help with Freesurfer Installation
by Binu Thomas 26 Apr '06

26 Apr '06

Thanks for the reply! Here is a detail of all that I did. I downloaded the RH9 version of the software to my /usr/local directory and installed it with the "tar xzvf" command. I then changed the shell to tcsh and then the rest of the output is as follows: [root@localhost ~]# set echo=1 [root@localhost ~]# setenv FREESURFER_HOME </usr/local>/freesurfer setenv FREESURFER_HOME [root@localhost ~]# source $FREESURFER_HOME/SetUpFreeSurfer.csh source /SetUpFreeSurfer.csh /SetUpFreeSurfer.csh: No such file or directory. [root@localhost ~]# I have followed all instructions provided on the freesurfer website. Thanks in advance for the help, Binu. Binu Thomas, M.S. Computer Programmer III Department of Psychiatry UT Southwestern Medical Center Phone: 214-645-2792 >>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 04/26/06 11:33 AM >>> Also, try enabling command echoing first, like this: set echo=1 source $FREESURFER_HOME/SetUpFreeSurfer.csh this will print-out details of the script as it runs. On Wed, 2006-04-26 at 12:27 -0400, Bruce Fischl wrote: > Hi Binu, > > can you send us the complete screen output from what you tried? > > thanks, > Bruce > On Wed, 26 > Apr 2006, Binu Thomas wrote: > > > Dear all, > > I posted a message yesterday regarding the same problem, > > didn't get much help, hoping to get some help today. I am running Red > > Hat Enterprise Linux 3, tried to install Freesurfer CentOS4, when I try > > to access the SetUpFreeSurfer.csh file with the "source" command, I get > > the error: File or Directory not found. I had the feeling that CentOS4 > > version of FreeSurfer might not be compatible with my OS, so I tried to > > configure the RH9 version of the software and ended up with the same > > error. I can see that the file exists in the "freesurfer" folder. I > > would greatly appreciate any help. > > > > Thanks in advance, > > Binu Thomas. > > Univ. of TX Southwestern Medical Center. > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

2 1

Help with Freesurfer Installation
by Binu Thomas 26 Apr '06

26 Apr '06

Dear all, I posted a message yesterday regarding the same problem, didn't get much help, hoping to get some help today. I am running Red Hat Enterprise Linux 3, tried to install Freesurfer CentOS4, when I try to access the SetUpFreeSurfer.csh file with the "source" command, I get the error: File or Directory not found. I had the feeling that CentOS4 version of FreeSurfer might not be compatible with my OS, so I tried to configure the RH9 version of the software and ended up with the same error. I can see that the file exists in the "freesurfer" folder. I would greatly appreciate any help. Thanks in advance, Binu Thomas. Univ. of TX Southwestern Medical Center.

3 2

Freesurfer on FC5
by Glenn Lawyer 26 Apr '06

26 Apr '06

Hi, Saw some discussion last week regarding problems with FreeSurfer on a 64 bit FC5 system. I am planning on upgrading from 32-bit FC4 to 64-bit FC5 at the end of this week, and am wondering if the problem was an isolated incident or if I am in for alot of work? Heck, I started my career in medical research as a test-rabbit, one more time shouldn't hurt that much, right? -------------------------------------- The zipper displaces the button and a man lacks just that much time to think while dressing at dawn, a philosophical hour, and thus a mechanical hour. > Glenn Lawyer < > +352 061 967 244 < > Instituttgruppe for psykiatri < > Postboks 1130 Blindern < > 0318 Oslo < < http://folk.uio.no/davidgl > <><><><><><><><><><><><><><><><><:)

2 1

Re: [Freesurfer] fsfast "selxavg-sess" error
by Jenn Segawa 26 Apr '06

26 Apr '06

Hello all, I had the same error as this previous post, but after the suggested fix, I'm getting the following matlab output/error messages. Does anyone know what I'm doing wrong? Thanks so much, Jenn %------------------------------------------------- Parsing Arguments RescaleTarget = 1000 Checking Parameters AutoStimDur: 0 StimDur: Number of Runs: 3 Input Volume List 1 014/fmc 2 016/fmc 3 017/fmc Input Pardigm File List 1 014/parfile.par 2 016/parfile.par 3 017/parfile.par Output Volume funcanal/h F Omnibus Volume funcanal/omnibus/f Sig Omnibus Volume funcanal/omnibus/fsig TR 2.870000 TER 2.870000 Total Window 0 PreStim Window 0 Remove Baseline 1 Remove Trend 0 Remove QTrend 0 Rescale Target 1000 nSkip 0 InPlane Res 3.125 FWHM 0 Hanning Radius 0 Time Offset 0 GammaFit 0 GammaFit Alpha: 2 SPM HRF: -1 Seg Brain/Air 1 SynthSeed 0 firstslice 0 nslices 27 nyqreg 0 SynthSeed = 0 Conditions Found (6): 1 2 3 4 5 6 Run 1: 72 72 72 72 36 36 Run 2: 72 72 72 72 36 36 Run 3: 72 72 72 72 36 36 Slice 0, 0.000159 -------------- First Pass (Accumulation), 0.024409 Run 1/3, 0.024782 Excluding 0 Points: Run 2/3, 5.67758 Excluding 0 Points: Run 3/3, 11.2836 Excluding 0 Points: Second Pass (Residual Error Estimation), 16.6096 Paradigm Condition: 33.8741 Var Reduction Range: 65.7977 85.9199 97.4559 Computing hhat Run 1/3, 16.6695 Excluding 0 Points: Run 2/3, 17.4337 Excluding 0 Points: Run 3/3, 18.1927 Excluding 0 Points: Saving data to funcanal/h_000.bfloat Saving offset to funcanal/h-offset_000.bfloat ??? Error using ==> .* Matrix dimensions must agree. Error in ==> /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m On line 657 ==> F = sign(qsum) .* Fnum ./ Fden; >> ??? Undefined function or variable 'r'. >> quiting matlab ------------------------------------------ ERROR: fast_selxavg() failed\n ERROR (<subject_dir>/<subject>): selxavg failed %---------------------------------------------------------- On 4/10/06, Doug Greve <greve(a)nmr.mgh.harvard.edu> wrote: > > Add the following lines to your startup.m file > > FSH = getenv('FREESURFER_HOME'); > fshmatlab = sprintf('%s/matlab',FSH); > path(path,fshmatlab); > clear fshmatlab; > > > Paymon Hosseini wrote: > > > hi > > > > i am going over the fsfast tutorial. i have completed all steps up to > > "FsFastTutorial/905 Average session-level data by condition" > > > > > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial_2f905_20Average_20…<https://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=https://surfer.nm…> on_2dlevel_20data_20by_20condition > > > > > > > > when i run "selxavg-sess -sf sessid -df sesspar -analysis sem_assoc", > > i get the following error: > > > > " > > ??? Undefined function or variable 'MRIread'. > > > > Error in ==> /usr/local/freesurfer/stable/fsfast/toolbox/fast_selxavg.m > > On line 160 ==> rstd = MRIread(instem,1); > > > >>> ??? Undefined function or variable 'r'. > >> > > > >>> quiting matlab > >> > > ------------------------------------------ > > ERROR: fast_selxavg() failed\n > > ERROR (/autofs/space/engram_012/users/pman/bert-functional): selxavg > > failed > > " > > > > can you please tell me why i am getting this error? > > > > thanks > > paymon hosseini > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=https://mail.nmr.…> > > > > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > 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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer<https://phsexchweb.partners.org/exchweb/bin/redir.asp?URL=https://mail.nmr.…> >

2 3

Re: [Freesurfer] Help with Freesurfer installation
by Binu Thomas 25 Apr '06

25 Apr '06

Yes FREESURFER_HOME was set to the installed directory with the etenv command. The CentOS4 version of the software was installed on Red Hat Linux Enterprise Edition WS 3. >>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 04/25/06 3:18 PM >>> Is FREESURFER_HOME set to where the tarball was installed? What OS is this installed on? On Tue, 2006-04-25 at 15:16 -0500, Binu Thomas wrote: > Dear Listserv, > I am trying to install the freesurfer > "CentOS4 v.3.0.2" stable release on Red Hat Linux Enterprise Edition > WS3, and I am having problems. I am not sure if I am using the worng > version of the software on my OS. When I use the command: "source > $FREESURFER_HOME/SetUpFreeSurfer.csh", I get the error message: "No such > File or Directory". > Am I using the wrong version of the software, do I have to upgrade my OS > to Linux Enterprise Edition WS4? Hoping to hear from you soon. > > Thanks in advance, > > Binu Thomas, M.S. > Computer Programmer III > Department of Psychiatry > UT Southwestern Medical Center > Phone: 214-645-2792 > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

1 0

Help with Freesurfer installation
by Binu Thomas 25 Apr '06

25 Apr '06

Dear Listserv, I am trying to install the freesurfer "CentOS4 v.3.0.2" stable release on Red Hat Linux Enterprise Edition WS3, and I am having problems. I am not sure if I am using the worng version of the software on my OS. When I use the command: "source $FREESURFER_HOME/SetUpFreeSurfer.csh", I get the error message: "No such File or Directory". Am I using the wrong version of the software, do I have to upgrade my OS to Linux Enterprise Edition WS4? Hoping to hear from you soon. Thanks in advance, Binu Thomas, M.S. Computer Programmer III Department of Psychiatry UT Southwestern Medical Center Phone: 214-645-2792

2 1

interaction effects
by Sasha Wolosin 25 Apr '06

25 Apr '06

Dear FreeSurfers, I am interested in examining interaction effects between two sets of classes where each covers all the data, let's say Male/Female and Treatment/Control. I know mri_glmfit can be used to run t-test comparisons between groups (e.g. All Treatment vs. All Control , or Male & Control vs. Male & Treatment), but can mri_glmfit be used to examine interaction effects between these two sets of classes (for surface data)? my FSGD file looks like this: GroupDescriptorFile 1 Class MaleTreatment Class MaleControl Class FemaleTreatment Class FemaleControl Input subjid1a MaleTreatment Input subjid1b FemaleTreatment Input subjid2a FemaleControl Input subjid2b MaleControl etc... Thanks, Sasha Sasha Wolosin Research Assistant Developmental Cognitive Neurology Kennedy Krieger Institute 707 N. Broadway Baltimore, MD 21205 ph: (443) 923-9270 wolosin(a)kennedykrieger.org Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

3 7

Troubleshooting
by Lee HL 25 Apr '06

25 Apr '06

Hi, I'm a freesurfer newbie. I was wondering what constitutes a good grey-white matter segmentation and a good pial surface outline? I've been trying to follow the exercise from the website with respect to the manual intervention, using my own data as an experience, but I don't know how best to decide what is good or bad. Are there any more detailed documentation with respect to troubleshooting? Pardon my ignorance. Thanks! -- Best regards, HweeLing Research Scientist Cognitive Neuroscience Laboratory Singapore Health Services

3 4

question about tksurfer
by adam walczak 25 Apr '06

25 Apr '06

Hello, I am testing the output of some data I ran through the reconstruction process. While attempting to view the rh.sphere volume with the rh.curv overlay, I only could see the red lines, not the green lines. I noticed that I had to adjust the settings (view--configure--curvature display). I had to change the value of the threshold midpoint to .2 and the threshold slope to 3.5. Only then could I see both. Is this normal, or maybe is something wrong...all of the processes said they finished without error. Thanks. Adam adam --------------------------------- Love cheap thrills? Enjoy PC-to-Phone calls to 30+ countries for just 2¢/min with Yahoo! Messenger with Voice.

2 1

physical sizes too big
by Sasha Wolosin 25 Apr '06

25 Apr '06

Dear FreeSurfer, During mri_convert, I get the following warning, and then an error during mri_em_register in -autorecon2. Would greatly appreciate any help, Thanks, Sasha WARNING ==================++++++++++++++++++++++++======================================= The physical sizes are (307.20 mm, 307.20 mm, 186.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 308 slices. The freesurfer tools should be able to handle more than 256 slices. If you find problems, please let us know (freesurfer(a)nmr.mgh.harvard.edu) ========================== #@# EM Registration Fri Apr 7 15:08:40 EDT 2006 /data/subjects/2154/mri mri_em_register -mask brainmask.mgz nu.mgz /freesurfer/average/RB_all_2006-02-15.gca transforms/talairach.lta using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/freesurfer/average/RB_all_2006-02-15.gca'... setting gca type = Normal gca type average std = 7.4 using min determinant for regularization = 5.5 0 singular and 1662 ill-conditioned covariance matrices regularized reading 'nu.mgz'... Segmentation fault Linux localhost.localdomain 2.6.9-22.0.2.ELsmp #1 SMP Tue Jan 17 06:12:06 CST 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri Apr 7 15:08:49 EDT 2006 Disclaimer: The materials in this e-mail are private and may contain Protected Health Information. Please note that e-mail is not necessarily confidential or secure. Your use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer