Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30096 discussions

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 > >

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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

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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.

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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

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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.

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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.

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problems converting to nii
by Michele Perry 24 Apr '06

24 Apr '06

Hi, I am running FreeSurfer version 3.01 and am trying to convert some .mgz files to *.nii format. When I run >mri_convert in_vol.mgz out_vol.nii or >mri_convert -ot nii in_vol.mgz out_vol.nii mri_convert runs without errors but the resulting .nii file cannot be opened by AFNI. Do you know how I can create an nii file that will open in AFNI? ~Michele

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libs and APIs ??
by mweiss＠cbs.mpg.de 24 Apr '06

24 Apr '06

Are there libraries included in the freesurfer-download which contain the used algorithms an data-types? If so, where can I find the according APIs? greetings M.Weiß Leipzig University of Applied Sciences Max Planck Institute for Human Cognitive and Brain Sciences

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renaming
by Sasha Wolosin 23 Apr '06

23 Apr '06

Dear all, I am using freesurfer stable 3.0.1. If I want to rename a subject after the subject has been fully processed, are there any extra steps I would need to take to ensure that the subjects files are referenced correctly in group analysis/ future processing? Thanks, Sasha 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.

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FS on Fedore Core5
by Ryu-Ichiro Hashimoto 20 Apr '06

20 Apr '06

Hello, I have been using FreeSurfer on Dell Linux computer (64 bit) with Fedore Core 4 by downloading [freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.1-full] and had no problems. Recently our lab changed Linux distribution from Fedore Core 4 to 5 and I got the following message when I ran test commands. ---------------------------------- tksurfer test1 rh pial surfer: current subjects dir: /projects/fmri/fs_data surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /projects/fmri/fs surfer: Reading header info from /projects/fmri/fs_data/test1/mri/T1.mgz surfer: vertices=147407, faces=294810 surfer: single buffered window Received X error! Error code : 165 Request code : 145 Minor code : 2 Error text : 'GLXBadLargeRequest' (repeat) ----------------------------------- The other test commands for tkmedit (tkmedit test1 orig.mgz, tkmedit test1 norm.mgz -segmentation mri/aseg.mgz ...) displayed the results correctly. If you could give me any suggestion what to do (without going back to FC4 ... I have no control over it), it would be much appreciated. Thank you, Ryu Hashimoto

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