Freesurfer December 2010

freesurfer@nmr.mgh.harvard.edu

92 participants
128 discussions

Re: [Freesurfer] ERROR: comparison in expression (FS with SGE)
by Xue, Feng 19 May '12

19 May '12

Sorry, I didn't notice that the reply address was not the list, I've done re-post it. Is there any method to check whether it is ok? For SGE, it might only write errors to dot e files instead of warnings. It seemed like a shell syntax error, however, I don't have that experience to check the recon-all script. On Sun, Mar 14, 2010 at 11:24 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > can you post this to the list? There are others better qualified to say > what's going on. But if everything finished ok is there really a problem? > Maybe this is just a warning? > On Sun, 14 Mar 2010, Xue, Feng wrote: > >> Hi Bruce, >> >> Thanks for your reply. The recon-all.log said it finished without >> error. please find the whole scripts root in the attachment. >> I'm also running a raw testing with one subject and without SGEяяMaybe >> I can report the result the day after tomorrow. >> >> BTW, I found in my 64bit Debian nodes, I repeated got the error as below >> (standard_in) 2: Error: comparison in expression >> but in 32bit, I met both. >> >> for the GMail security restriction, I changed recon-all.cmd in the >> attachment to recon-all.cmds. >> >> On Sat, Mar 13, 2010 at 11:58 PM, Bruce Fischl >> <fischl(a)nmr.mgh.harvard.edu> wrote: >>> >>> what does the recon-all.log say? Did the recon finish correctly? Does >>> this >>> happen if you just run it on the command line? >>> Bruce >>> >>> On Sat, 13 Mar 2010, Xue, Feng wrote: >>> >>>> Dear Bruce & FS experts, >>>> >>>> Please forgive my re-post, for I havn't got any response from last post. >>>> I do appreciate if anyone could give me a hint or suggestion. >>>> >>>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>>> >>>> We are running freesurfer with Sun GridEngine. Currently, we >>>> repeatedly got this error in SGE's job error log file on some data >>>> when doing recon_all: >>>> >>>> $ cat recon_xf.e437 >>>> (standard_in) 2: Error: comparison in expression >>>> $ cat recon_xf.e431 >>>> (standard_in) 2: comparison in expression >>>> >>>> I also checked the recon-all-status.log file, but not error was found. >>>> >>>> Has anyone met this problem? Is it critical? >>>> Thanks in advance. >>>> >>>> -- >>>> Best Regards >>>> >>>> Xue, Feng Phd. candidate >>>> Major in Developmental Cognitive Neuroscience >>>> >>>> National Key Laboratory of Cognitive Neuroscience and Learning >>>> Beijing Normal University >>>> Beijing, China. 100875 >>>> Tel: +86-13810154455 >>>> web: http://psychbrain.bnu.edu.cn >>>> ============================================== >>>> Welcome to MuDuo JinSheng BBS @ Beijing Normal University >>>> telnet://bbs.mdjs.org >>>> http://bbs.mdjs.org >>>> _______________________________________________ >>>> 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. >>> >>> >> >> >> > -- Best Regards Xue, Feng Phd. candidate Major in Developmental Cognitive Neuroscience National Key Laboratory of Cognitive Neuroscience and Learning Beijing Normal University Beijing, China. 100875 Tel: +86-13810154455 web: http://psychbrain.bnu.edu.cn ============================================== Welcome to MuDuo JinSheng BBS @ Beijing Normal University telnet://bbs.mdjs.org http://bbs.mdjs.org

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Re: [Freesurfer] Freesurfer Digest, Vol 75, Issue 15
by Sebastian Moeller 19 Jan '12

19 Jan '12

Hi Fred, yu probably checked the following already, but on the off chance you have not... Maybe you have set X11 to 256 color mode? Start X11.app (from /Applications/Utilities) go to the X11 menu, select Preferences..., switch to the tab called output and see what is selected for Colors. If it is set to 256 Colors you have your root cause, just switch to something higher and all should be fine. best Sebastian On May 9, 2010, at 9:00 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: > Send Freesurfer mailing list submissions to > freesurfer(a)nmr.mgh.harvard.edu > > To subscribe or unsubscribe via the World Wide Web, visit > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > or, via email, send a message with subject or body 'help' to > freesurfer-request(a)nmr.mgh.harvard.edu > > You can reach the person managing the list at > freesurfer-owner(a)nmr.mgh.harvard.edu > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > > 1. tksurfer/tkmedit display color fix in OSX 10.6? (Fred Dick) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Sun, 9 May 2010 15:34:35 +0100 > From: Fred Dick <fdick(a)crl.ucsd.edu> > Subject: [Freesurfer] tksurfer/tkmedit display color fix in OSX 10.6? > To: freesurfer(a)nmr.mgh.harvard.edu > Message-ID: <873B33F2-3339-4871-9395-1EFEEC1EFAAB(a)crl.ucsd.edu> > Content-Type: text/plain; charset="us-ascii" > > Dear all > > This is a pretty minor issue (except for figure making) - but has anyone experienced and then fixed a display problem in tksurfer/tkmedit in OSX 10.6 (possibly also 10.5) where graphics seem to be drawn only with 256 colors, thereby giving images a kind of contour-plot look? (See attached image below). [Running 10.6.3, i686-apple-darwin10-gcc-4.2.1, tksurfer 1.309 (yes, older), tkmedit v 1.330] > > I looked around the mail archives but didn't see anyone else commenting on this, but do know someone else having the same issue, so would be happy for any suggestions. > > Thanks, > Fred > > >

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downsampling 4D volume
by ythomas 10 Jan '12

10 Jan '12

Hi, I am trying to downsample a 4D volume using mri_convert. However, it seems to be killing the 4 dimension. For example, if I do mri_convert -voxsize 4 4 4 tmp.mgz tmp444.mgz The original volume which is 256 x 256 x 256 x 120 becomes 64 x 64 x 64. Thanks, Thomas

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Re: [Freesurfer] I/O performance mitigation
by Bruce Fischl 26 May '11

26 May '11

Hi David, I'm surprised you didn't have to do this in the past. We always space our jobs out. Glad there's an easy workaround cheers Bruce On Fri, 3 Sep 2010, David Mischel wrote: > We took the suggestion of staggering the launch of Freesurfer 5.0 recon-all > jobs. The attached Word doc (I don't know how to contribute this information > other than attaching the image and text using Word) shows a load graph on > our file server. When 20 FS jobs began at once (all processing servers using > a single file server) the load on the file server bulged up. When we spaced > out the launch of each job by 15 seconds the load hardly budged. > > > > We have not had to do this in the past with earlier versions of Freesurfer > but this is an obvious work around to the problem we encountered. > > > > < david > > > > > > David Mischel > > Manager of IT > > Center for Imaging of Neurodegenerative Diseases (CIND) > > <http://www.cind.research.va.gov/> http://www.cind.research.va.gov/ > > VA Medical Center > > 4150 Clement Street, 114M > > San Francisco, CA 94121 > > voice: 415-221-4810 x3864 > > fax: 415-668-2864 > >

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LGI error in make_outer_surface at 31
by Juranek, Jenifer 07 Apr '11

07 Apr '11

Hi, Encountering some difficulties with LGI on a RHEL4 box (64bit) with MATLAB v7.6.0.324 (R2008a) installed. Subject was processed under fsv405. Specific error is pasted below: Any suggestions to correct my error? Thanks, Jenifer >> reading filled volume... closing volume... ??? Undefined function or method 'fspecial' for input arguments of type 'char'. Error in ==> make_outer_surface at 31 Gaussian = fspecial('gaussian',[2 2],1); >> ERROR: make_outer_surface did not create output file 'tmp-mris_compute_lgi-lh.pial/lh.pial-outer'! Linux localhost.localdomain 2.6.9-5.ELsmp #1 SMP Wed Jan 5 19:29:47 EST 2005 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Wed Sep 24 11:51:01 CDT 2008 [jjuranek@localhost jjuranek_fsv405]$

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Recon-all Error: _FindFacePath
by Jennifer Addicks 18 Feb '11

18 Feb '11

Hello, I have completed cortical reconstructions for 79 of 80 scans without error. However, the recon for one participant exited during topology correction with the following error message: ERROR: _FindFacePath: could not find path! Darwin jennifer-phillipss-macbook-pro.local 9.8.0 Darwin Kernel Version 9.8.0: Wed Jul 15 16:55:01 PDT 2009; root:xnu-1228.15.4~1/RELEASE_I386 i386 recon-all exited with ERRORS at Sun Nov 28 19:32:14 EST 2010 This error has been posted to the archive previously but the solution does not seem to accompany it. Any help would be appreciated. Thanks, Jennifer

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wm and pial edits
by Larissa Stanberry 09 Feb '11

09 Feb '11

Dear Freesurfers, Can I run recon-all -autorecon2-wm and recon-all -autorecon2-pial on the same subject at the same time? Or can I perhaps do smthg like recon-all -autorecon2-wm -autorecon2-pial? Many thanks Larissa

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New v5.0.0 release
by Nick Schmansky 26 Jan '11

26 Jan '11

Announcement! There is a new release of FreeSurfer, v5.0.0! Features and fixes are described in the ReleaseNotes page: http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes It is available for download at: http://surfer.nmr.mgh.harvard.edu/fswiki/DownloadAndInstall Please pose questions about the release to the freesurfer mailing list. The FreeSurfer Team

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asegstats2table in version 4.2.0 error?
by Jesse Bledsoe 24 Jan '11

24 Jan '11

Hello FreeSurfer group, I am unable to run asegstats2table and cannot view asegstats2table --help. I did some looking in the archives and it seems like there were bugs in previous versions that were fixed before version 4.2.0. Any ideas on how to fix this? At this point I have been creating my own tables and viewing each individual aseg.stats file for each participant. When I use the following: asegstats2table --subjects *subject1 subject 2* --meas volume --tablefile aseg_stats.txt I get the following error: 'import site' failed; use -v for traceback Traceback (most recent call last): File "/usr/local/freesurfer/bin/ > > asegstats2table", line 4, in ? > import os; > ImportError: No module named os > Thank you for your time, Jesse (Linux-centos4-stable-pub-v4.2.0) On Tue, Nov 30, 2010 at 3:43 PM, Jesse Bledsoe <bledsoej(a)msu.edu> wrote: > Hello, > > I am having difficulty generating an aseg_stats.txt table. > > When I use the following: > > asegstats2table --subjects *subject1 subject 2* --meas volume --tablefile > aseg_stats.txt > > I get the following error: > > 'import site' failed; use -v for traceback > Traceback (most recent call last): > File "/usr/local/freesurfer/bin/asegstats2table", line 4, in ? > import os; > ImportError: No module named os > > > I am on Linux-centos4-stable-pub-v4.2.0 > > Any suggestions are much appreciated, > Jesse > -- Jesse Bledsoe, M.A. Clinical Psychology Graduate Student Assistant Director, Consortium for Neurodevelopmental Study Department of Psychiatry Michigan State University 321 W. Fee Hall East Lansing, MI 48824 ______________________________________ Note: Information contained in this electronic message and any attachments to this message are intended for the exclusive use of the addressee(s) and may contain proprietary, confidential or privileged information. If you are not the intended recipient, you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately and destroy all copies of this message and any attachments.

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label2label error
by Lena Palaniyappan 07 Jan '11

07 Jan '11

For some of my data, label2label (one of the PALS labels from fsaverage being mapped on to a subject) gives this message Performing mapping from target back to the source label ERROR: srcvtxno = -1 < 0 trgvtxno = 140122, dmin = 1000 trgregxyz = 0, 0, 0 This means that a vertex in the target surface could not be mapped to a vertex in the source surface because the xyz of the target is outside of the range of the hash table Is there anything I can do to circumvent this? Cheers Lena _______________________________________________________ Lena Palaniyappan Clinical Lecturer & Honorary StR | Division of Psychiatry ( University of Nottingham) South Block 'A' floor| Queens Medical Centre | Nottingham | NG7 2UH This message and any attachment are intended solely for the addressee and may contain confidential information. If you have received this message in error, please send it back to me, and immediately delete it. Please do not use, copy or disclose the information contained in this message or in any attachment. Any views or opinions expressed by the author of this email do not necessarily reflect the views of the University of Nottingham. This message has been checked for viruses but the contents of an attachment may still contain software viruses which could damage your computer system: you are advised to perform your own checks. Email communications with the University of Nottingham may be monitored as permitted by UK legislation.

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Freesurfer December 2010