Freesurfer December 2013

freesurfer@nmr.mgh.harvard.edu

107 participants
197 discussions

Recon-all exits with errors for a patient with TBI
by Emad Ahmadi 23 Dec '13

23 Dec '13

Hello, I'm analyzing some images of patients with TBI. There's one of them having abnormalities in T1 images (skull fracture, epidural/intracranial hemorrhage, shifts) that can trouble image registration; when I run recon-all for this patient, it exits with errors. I wonder if it has anything to do with the abnormalities troubling the registration of T1 images. I've attached the log file, and some axial sections of the T1 images can be viewed here: https://drive.google.com/folderview?id=0B4AFmHFjy_bsbkotd2QyZjZ6dW8&usp=sha… Thank you and Merry Christmas! Emad

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Freesurfer installation error
by Octavian Lie 22 Dec '13

22 Dec '13

Dear All, I downloaded/installed freesurfer-Linux-centos6_x86_64-dev version (12/19/2013) on my ubuntu 12.04 using tcsh, also fixed missing libnetcdf libraries missing in my distro, here is fs home directory: 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 Testing using the commands on the testing page went OK, however, if I close the terminal, open another one, commands are not recognized, and I have to reset freesurfer home every time I open a terminal with setenv FREESURFER_HOME <freesurfer_installation_directory>/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh I thought this is a sudo issue, however if I use sudo setenv FREESURFER_HOME /usr/local/fs5.3/freesurfer, it tells me: sudo: setenv: command not found I mention I changed the default shell from bash to tcsh recently, Please advise, Octavian

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Freesurfer dev install/ testing error
by Octavian Lie 22 Dec '13

22 Dec '13

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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jpeg compressed dicom mri convert error
by Octavian Lie 22 Dec '13

22 Dec '13

Dear all, I tried to run a subject's T1 starting with the dicom convert step (until now, I used .nii volumes as imput, after dicom conversion in spm; I would like to be able to use the dicom convert in freesurfer, since I have a -T2pial step to refine pias afterwards, and it's easier this way). I get the following mri_convert error about jpeg compression (this is the only dicom output processed at our facility): recon-all -s subj -i /home/ovl/Desktop/freesurferdicom/subj/T1/51129 Subject Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217 Current Stamp: freesurfer-Linux-centos6_x86_64-dev-20131217 INFO: SUBJECTS_DIR is /usr/local/fs5.3/freesurfer/subjects Actual FREESURFER_HOME /usr/local/fs5.3/freesurfer Linux Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux /usr/local/fs5.3/freesurfer/subjects/subj mri_convert /home/ovl/Desktop/freesurferdicom/subj/T1/51129 /usr/local/fs5.3/freesurfer/subjects/subj/mri/orig/001.mgz mri_convert /home/ovl/Desktop/freesurferdicom/subj/T1/51129 /usr/local/fs5.3/freesurfer/subjects/subj/mri/orig/001.mgz $Id: mri_convert.c,v 1.206 2013/11/12 03:15:51 greve Exp $ reading from /home/ovl/Desktop/freesurferdicom/subj/T1/51129... Starting DICOMRead2() dcmfile = /home/ovl/Desktop/freesurferdicom/subj/T1/51129 dcmdir = /home/ovl/Desktop/freesurferdicom/subj/T1 Ref Series No = 302 Found 167 files, checking for dicoms Found 165 dicom files in series. First Sorting Computing Slice Direction Vs: -0.999557 0.0285859 -0.00787544 Vs: -0.99956 0.028586 -0.00787546 Second Sorting Counting frames nframes = 1 nslices = 165 ndcmfiles = 165 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.4.70-- ERROR: the pixel data cannot be loaded as it is JPEG compressed. (Transfer Syntax UID: 1.2.840.10008.1.2.4.70) jpegUID: --1.2.840.10008.1.2.4-- Linux ovl-Wild-Dog-Performance 3.2.0-56-generic #86-Ubuntu SMP Wed Oct 23 09:20:45 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj exited with ERRORS at Sun Dec 22 21:22:11 CST 2013 For more details, see the log file /usr/local/fs5.3/freesurfer/subjects/subj/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Is there a workaround in freesurfer? Thank you, Octavian

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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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Freesurfer December 2013