Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30099 discussions

Freesurfer installation testing tksurfer error
by Octavian Lie 22 Dec '13

22 Dec '13

Dear All, I have recently upgraded freesurfer (dev version 12/19/2013 centos6, 86X64) on my ubuntu 12.04 box, I previously used v 5.1(centos 4). I fixed all other issues that I posted about (libnetcdf missing,.tcshrc editing), now all seems to go well, including testing, except when I load tksurfer bert rh pial, I see it well, and I can use tksurfer tools well, as expected; however, if I want to close the window displaying surfaces (either before or after closing tksurfer tools gui), I cannot; the only way to kill the process and exit tksurfer is to close the terminal. Also, if I try to maximize the same window, I get the following error: surfer: Error sending tcl command MoveToolWindow 65 656: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 65 1080: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 65 1080: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 65 1080: can't invoke "wm" command: application has been destroyed surfer: Error sending tcl command MoveToolWindow 65 1080: can't invoke "wm" command: application has been destroyed I loaded other subjects previously processed with v5.1 version, and I have the same issue. All other guis, including tkmedit, freeview and qdec work well. Please advise, Octavian

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tksurfer visualization and -aseg option in tkmedit
by Rujing Zha 21 Dec '13

21 Dec '13

Hi Doug, Bruce and others. Would you please help me deal with 2 problems? The 1st one is : There is a excellent segmentation in -surfs after editing the pial and running -autorecon-pial. Some voxels was removed from the brainmask.mgz(i.e. picture 2 in the attachment),but neither did -aseg image which had those voxels(i.e. picture 1 in the attachment) which I have removed from the brainmask.mgz when I ran "tkmedit subject brainmask.mgz -aux wm.mgz -surfs -aseg". Does this incorrect aseg image will influence my group thickness analysis? If so, what can I do to fix it? The 2nd one is : I could not visualize the inflated image properly in tksurfer by this command: tksurfer yizhihui rh inflated I could see little thing in the tksurfer after typing the command above. The result can be got in picture 3 of the attachment and the standard output message can be seen in the picture 4. I visualized the inflated image in the freeview tool by typing "freeview -f $SUBJETCS_DIR/yizhihui/surf/rh.inflated ". The result can be seen in picture 5. CentOS 5.8 is used in my server and I use "freesurfer-Linux-centos4-stable-pib-v5.3.0". Thanks in advance. All the best. 2013-12-17 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zharj(a)mail.ustc.edu.cn charujing(a)gmail.com charujing123(a)163.com 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 发送时间：2013-12-16 23:57 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人："Rujing Zha"<charujing123(a)163.com> 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> Hi Rujing you can use either our FTP site or our file drop. Info for this is at http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange and https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html cheers Bruce On Mon, 16 Dec 2013, Rujing Zha wrote: > Hi Bruce, > Maybe 163 email has some problems. I will try my gmail to send you and Louis > my data. But I donot know whether your email can get attachment size 289M? > Thanks. > All the best. > > 2013-12-16 > > ____________________________________________________________________________ > Rujing Zha > > ____________________________________________________________________________ > 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > 发送时间：2013-12-16 22:37 > 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the > command-line ERROR > 收件人："Rujing Zha"<charujing123(a)163.com> > 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> > > no, I didn't get it > On Mon, 16 Dec 2013, Rujing Zha wrote: > > > Dear Bruce, > > Thanks Bruce. That's all right. > > I want to know if I e-mail to you my subject's data successfully. The > > subject's image had a incorrect segmentation in surfs after recon-all. > > Thanks in advance. > > All the best. > > > > 2013-12-16 > > > > _________________________________________________________________________ > ___ > > Rujing Zha > > > > _________________________________________________________________________ > ___ > > 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > 发送时间：2013-12-16 22:24 > > 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the ?? ?> command-line ERROR > > 收件人："Rujing Zha"<charujing123(a)163.com> > > 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> > > > > sorry, I don't know that code very well. Doug is probably the right one t > o > ?? ? > > help you > > Bruce > > > > > > On Mon, 16 Dec 2013, Rujing Zha wrote: > > > > > Dear Bruce, > > > I did setup the "-run 015" not "013" in unpacksdcmdir as I told in prev > io > > us > > > message. But it generated the "013" folder automatically after running ?? ? > > > unpacksdcdir, which made me so confused. > > > As it created the "013" folder, I guess unpacksdcmdir didnot recognized > > > > structure image correctly which was in the "15th" line of the scan.info > . > ?? ?> Thanks Bruce. > > > All the best. > > > > > > 2013-12-16 > > > > > > _______________________________________________________________________ > __ > > ___ > > > Rujing Zha > > > > > > _______________________________________________________________________ > __ > > ___ > > > 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > > 发送时间：2013-12-16 22:12 > > > 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from th > e > ?? ?> command-line ERROR > > > 收件人："Rujing Zha"<charujing123(a)163.com> > > > 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> > > > > > > but why are you giving recon-all the path to run 013 instead of 015? I ?? ? > ?? ?> don't know the fsfast file structure, but your scan.info says that 01 > 3 is > > > > ?? ?an EPI fun and 015 is the mprage > > > > > > On Sat, > > > 14 Dec 2013, Rujing Zha wrote: > > > > > > > Hi Bruce, > > > > It generated a 013 subfolder in after running this code "unpacksdcmdi > r > ?? ? > > > > -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3dana > t > ?? ?mg > > > z > > > > 001.mgz". It is 15 that I can see the number of t1_mpr_ns_sag_iso_zh > an > > g > > ?? ?in > > > > the unpack.log. > > > > Then I ran "recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liuj > un > > ha > > > o", > > > > and it finished without error. > > > > "recon-all -s liujunhao -all" was run and ERROR would be displayed: ?? ? > > > > ERROR: input(s) cannot have multiple frames! > > > > The recon-all.log unpack.log and scan.info were unloaded in the attac > hm > > en > > > t. > > > > Thanks. > > > > All the best. > > > > > > > > 2013-12-14 > > > > > > > > _____________________________________________________________________ > __ > > __ > > > ___ > > > > Rujing Zha > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)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 > > i > > > s > > > addressed. If you believe this e-mail was sent to you in error and the ?? ?e- > > ma > > > il > > > contains patient information, please contact the Partners Compliance He > lp > > Li > > > ne at > > > http://www.partners.org/complianceline . If the e-mail was sent to you ?? ?in > > e > > > rror > > > but does not contain patient information, please contact the sender and > p > > ro > > > perly > > > dispose of the e-mail. > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 i > s > addressed. If you believe this e-mail was sent to you in error and the e-ma > il > contains patient information, please contact the Partners Compliance HelpLi > ne at > http://www.partners.org/complianceline . If the e-mail was sent to you in e > rror > but does not contain patient information, please contact the sender and pro > perly > dispose of the e-mail. > > >

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Re: [Freesurfer] 3 groups and one covariate
by yashin7020＠libero.it 21 Dec '13

21 Dec '13

I'm sorry, but my difficult is due to lacking of an example with three levels/groups and one covariates. I have found a lot of example in the guide but they are referred to two levels with covariate or three levels is without covariates. Please can you check these mtx? 3 classes 1 variable contrast 1.mtx - diff A vs B 1 -1 0 0 0 0 contrast 2.mtx - slope for A and B 0 0 0 1 -1 0 contrast 3.mtx - diff A vs C 1 0 -1 0 0 0 contrast 4.mtx - slope for A and C 0 0 0 1 0 -1 contrast 5.mtx - diff B vs C 0 1 -1 0 0 0 contrast 6.mtx - slope for B and C 0 0 0 0 1 -1 groups effect.mtx 1 -1 0 0 0 0 1 0 -1 0 0 0 groups effect covariate slope.mtx 0 0 0 1 -1 0 0 0 0 1 0 -1 A+B vs C.mtx 0.5 0.5 -1 0 0 0 A+B vs C covariate slope.mtx 0 0 0 0.5 0.5 -1 Thank you very much, Stefania ----Messaggio originale---- Da: greve(a)nmr.mgh.harvard.edu Data: 20-dic-2013 16.47 A: <freesurfer(a)nmr.mgh.harvard.edu> Ogg: Re: [Freesurfer] 3 groups and one covariate Hi Stef, there are examples there with covariates. Can you follow those? doug On 12/19/2013 05:56 PM, yashin7020(a)libero.it wrote: > Hi experts, > I'd like to find group difference (thickness) among 3 groups taking in account > one covariate. > I'd like to use DOSS. Is correct? I have read the guide and I have carried out > fsgd file as suggest for Three Groups (One Factor/Three Levels), No Covariates. > Now, my problem is "which are the .mtx that I should add?" > Thanks a lot. > > Stef > > _______________________________________________ > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)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.

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Re: [Freesurfer] Freesurfer dev install/ testing error
by Octavian Lie 20 Dec '13

20 Dec '13

I forgot to mention that I downloaded the freesurfer-Linux-centos6_x86_64-dev version (again 12/19/2013), and that other lib files, such as libjpeg.so files (related to install issues on some ubuntu systems according to the release notes) are stored in /usr/lib/x86_64-linux-gnu/ on my computer Thank you, Octavian On Fri, Dec 20, 2013 at 2:44 PM, Octavian Lie <octavian.lie(a)gmail.com>wrote: > Dear All, > > I have ubuntu 12.4, and downloaded/installed the dev (12/19/2013) version > of Freesurfer (I used previously version 5.1). Installation was uneventful, > including getting the return to command > > > source $FREESURFER_HOME/SetUpFreeSurfer.csh > > FREESURFER_HOME /usr/local/fs5.3/freesurfer > FSFAST_HOME /usr/local/fs5.3/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /usr/local/fs5.3/freesurfer/subjects > MNI_DIR /usr/local/fs5.3/freesurfer/mni > > When testing Freesurfer with freeview or tkmedit bert commands, I get > invariably the following error > > 'error while loading shared libraries: libnetcdf.so.6: cannot open shared > object file: No such file or directory' > > Can you advise what I should do, including syntax (Gari has a similar > problem, and he solved it "after reinstalling netCDF and updating the links > (and some 64 bit packages missing too)"). > > Please let me know what else I should add/ modify after > > sudo apt-get install libnetcdf6 > > and what other packages and links have to be installed/ fixed > > Many thanks, > > Octavian > > > >

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vertex-wise threshold and cluster-wise p values
by Rujing Zha 20 Dec '13

20 Dec '13

Hi all, I want to know difference between vertex-wise and cluster-wise in Groupanalysis. Can I just think vertex-wise are uncorrected P-value(which is the same as voxel-wise value) and cluster-wise value are the vertex population which are survived after a specific threshold correction? Thanks. All the best. 2013-12-21 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zharj(a)mail.ustc.edu.cn charujing(a)gmail.com charujing123(a)163.com

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p value in CWP colume
by Rujing Zha 20 Dec '13

20 Dec '13

Hi all, I just study group analysis tutorial and I am confused with how to find cluster-wise probability in CWP colume(i.e 0.20000 in clusterno 1). Did I need to process additinoally? Thanks. All the best. 2013-12-21 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zharj(a)mail.ustc.edu.cn charujing(a)gmail.com charujing123(a)163.com

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3 groups and one covariate
by yashin7020＠libero.it 20 Dec '13

20 Dec '13

Hi experts, I'd like to find group difference (thickness) among 3 groups taking in account one covariate. I'd like to use DOSS. Is correct? I have read the guide and I have carried out fsgd file as suggest for Three Groups (One Factor/Three Levels), No Covariates. Now, my problem is "which are the .mtx that I should add?" Thanks a lot. Stef

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trac-all -path Help needed
by Francesco Baldacchini 20 Dec '13

20 Dec '13

Hi everybody, I'm having problems running the trac-all -path command. It's giving me this error: *Segmentation fault (core dumped) Linux opbg 3.11.0-15-generic #23-Ubuntu SMP Mon Dec 9 18:17:04 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux trac-paths exited with ERRORS at mar 17 dic 2013, 16.09.33, CET* I searched but it seems I'm the only one getting this error. To give you more information I can show you how the trac-all -bedp command ended, to me it seems without error: *59 slices processed61 slices processedQueuing post processing stage/usr/local/freesurfer/bin/bedpostx_mgh: line 439: 5294 Terminated ${subjdir}.bedpostX/monitor* In attachment I loaded my drirc.tutorial configuration file. Thanks, Francesco Baldacchini

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mri_glmfit error
by Rujing Zha 19 Dec '13

19 Dec '13

Hi all, I try to run mri_glmfit, but it export "ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08 -------------------------------- Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class.". I upload the data in the attachment, and the glmfit_output is the standard output of the "mri_glmfit". Thanks. All the best. 2013-12-19 Rujing Zha

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Surface ROIs
by Danielle Sliva 19 Dec '13

19 Dec '13

Dear FreeSurfer Experts, I have defined an ROI as a FreeSurfer label on the pial surface of a single subject. Could someone recommend the best way to determine the corresponding ROIs for other subjects in my study? Thanks in advance, Danielle -- Danielle Sliva, MA Boston Children's Hospital Division of Developmental Medicine Laboratories of Cognitive Neuroscience, Gaab Lab Fetal-Neonatal Neuroimaging & Developmental Science Center

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