Freesurfer May 2011

freesurfer@nmr.mgh.harvard.edu

120 participants
155 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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rtview and color bar
by Michelle Umali 28 Jun '11

28 Jun '11

Hi Freesurfers! I ran rtview, and I couldn't find a color bar/legend. I'm just wondering how thow the colors get assigned. Is each color a position of wedge stimulus? I'm trying to define V1/V2/V3 boundaries and was wondering how to get the horizontal and vertical meridians. Any help would be most welcome. Thanks. Michelle

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display error
by Cris Lanting 20 Jun '11

20 Jun '11

Dear Freesurfer community, I have a display problem that affects especially tkmedit and tksurfer. We run freesurfer ( freesurfer-Linux-centos4_x86_64-stable-pub-v5.0.0) on a remote unix server and use Exceed (v. 14.0.0.376) to port the display to a local (windows) computer. At first we got a openGL error stating that OpenGL was not supported when calling e.g. tksurfer. Now we have installed Exceed 3D to support OpenGL it seems to continue beyond the previous error message but comes up with a different one (see snippet) <snippet> subject is js hemi is rh surface is pial surfer: current subjects dir: /home/cris/freesurfer/subjects surfer: not in "scripts" dir ==> using cwd for session root surfer: session root data dir ($session) set to: surfer: /home/cris Reading image info (/home/cris/freesurfer/subjects/js) Reading /home/cris/freesurfer/subjects/js/mri/orig.mgz surfer: Reading header info from /home/cris/freesurfer/subjects/js/mri/orig.mgz fsurfer: vertices=156376, faces=312748 surfer: single buffered window surfer: tkoInitWindow(js) Window type not found! surfer: failed, trying double buffered window Window type not found! surfer: failed, no suitable display found <end snippet> Any ideas? Note that other programs that do not use OpenGL seem to run fine (i.e. fslview and gedit) Kind regards, Cris Lanting Career Development Fellow MRC Institute of Hearing Research Science Road, University Park Nottingham NG7 2RD cris(a)ihr.mrc.ac.uk

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mri_ca_register error
by Vanessa Lim 14 Jun '11

14 Jun '11

Hi, I am getting the same error. I did set the environment to an external drive with LOTS of space. When I run it though I did notice it repeats the subject path which is the external drive but then says actual path ~/apps/freesurfer/subjects - this doesn't have much space cause it's a virtualbox and I don't know how to make it bigger. But the error below seems to be pointing to the right directory /home/...Desktop etc. > > GCAMwrite(transforms/talairach.m3z): gzip encountered error. > writing output transformation to transforms/talairach.m3z... > mri_ca_register: GCAMwrite(transforms/talairach.m3z) failed > ERROR: mri_ca_register with non-zero status 252 > but continuing despite the error > #-------------------------------------- > #@# CA Reg Inv Thu May 26 12:42:11 EDT 2011 > /home/virtualuser/Desktop/freeSurfer/CG2/mri > > mri_ca_register -invert-and-save transforms/talairach.m3z > > Loading, Inverting, Saving, Exiting ... > Reading transforms/talairach.m3z > ERROR: cannot find or read transforms/talairach.m3z > ERROR: mri_ca_register with non-zero status 0 > Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux > > Cheers, > Vanessa

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S_intraparietal-and_Parietal_transverse.label
by Esther Walton 03 Jun '11

03 Jun '11

Dear list, I am interested in the S_intraparietal-and_Parietal_transverse label from the Desitreux atlas using aparc.a2005s.annot. If I load this into fsaverage, it has three regions to it (see dark purple label in the attached screenshot): two big ones, very close to each other, connected by two narrow bridges, and another much smaller region more dorsally. Does this look fine to you?! Secondly, assuming this is ok, I created labels for each subject using mri_annotation2label and turned those labels into ROIs in standard space using mri_label2vol --label xx/label/lh.S_intraparietal-and_Parietal_transverse.label --temp xx/reg_standard/example_func.nii.gz --reg xx/reg/freesurfer/anat2std.register.dat --o xx/reg_standard/stats/lh.S_intraparietal-and_Parietal_transverse.nii.gz However, when I load this volume with: tksurfer fsaverage lh inflated -overlay lh.S_intraparietal-and_Parietal_transverse.nii.gz -mni152reg -fthresh 0.1 -fmax 1 it looks a bit off (see yellow label and red ROI in second screenshot). Would you think that's still ok taking into account the individual anatomy or did something go wrong somewhere? Thanks for your help, Esther

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freeview and wm-segmentation errors
by von Polier, Georg Ferdinand Anto 01 Jun '11

01 Jun '11

Hi, using FS 5.1 now, I encountered two problems: 1. when I try to start freeview on my personal laptop, this errors appears: [georg@localhost ~]$ freeview freeview.bin: error while loading shared libraries: libXss.so.1: cannot open shared object file: No such file or directory However, libXss.so.1 is installed on my system running linux (Fedora 15). Do you habe any idea? 2. Running recon-all with -all flag on a cluster (Linux CentOs 5.6) the stream finishes with errors repeatedly showing this message: #@# WM Segmentation Tue May 31 12:36:00 CEST 2011 mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt znzTAGskip: tag=544043625, failed to calloc 1952413696 bytes! $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /rwthfs/rz/cluster/work/gg855262/subjects_AN/4550/mri cmdline mri_binarize --i wm.mgz --min 255 --max 255 --o wm255.mgz --count wm255.txt sysname Linux input wm.mgz frame 0 nErode3d 0 nErode2d 0 output wm255.mgz Binarizing based on threshold min 255 max 255 binval 1 binvalnot 0 Cannot allocate memory recon-all -s 4550 exited with ERRORS at Tue May 31 12:36:01 CEST 2011 ------------------------------------------------------------------------------ | Execution of Batch-Request stopped at Tue May 31 12:36:01 CEST 2011 | peak memory value: 2.386G | real time used: 04:58:38 I did allocate 4 GB of memory and did not face this error when using FS 5.0 or FS 5.1-beta-release with same settings. Any recommendations? Thanks, Georg

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curvature of flattening
by Gabriel Go.Es. 31 May '11

31 May '11

Dear FS experts, I'm making some flattenings of one subject on FS and I'm wondering if it is possible to see the ?h.curv or the ?h.sulc on grayscale and not in red-green nor in the binary gray representations of tksurfer. Regards, Gabriel.

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Full-time Research Assistant position in Clinically-Oriented Cogn itive Neuroscience at Virginia Tech
by John Richey 31 May '11

31 May '11

Dear freesurfer users, The following advertisement is for a full-time research assistantship in cognitive neuroscience in the Department of Psychology at Virginia Tech. Please feel free to distribute to interested parties. **Full-Time Lab/Research Assistant Position: Social-Clinical-Affective Neuroscience Lab Description of Position & Duties: A full-time R.A. position is available in the lab of Dr. John Richey in the Department of Psychology at Virginia Tech. The Assistant will be involved in implementing and organizing studies that investigate brain function and structure in the context of autism and affective disorders. The central research program seeks to investigate and quantify in vivo the the relation between particular cortical regions and social-cognitive dysfunction across a range of pathological states. Ultimately, we aim to assess the impact of neurocognitive intervention on cortical function and behavioral/cognitive outcomes in patients. To investigate this, the laboratory utilizes several neuroimaging modalities, including functional magnetic resonance imaging (fMRI), high-resolution structural MRI and diffusion tensor imaging (DTI). The position involves data acquisition in human research subjects, data analysis and administrative tasks. It is expected that the candidate will be able to work collaboratively with an interdisciplinary group of clinicians, psychologists and cognitive neuroscientists to accomplish our research objectives.This is an excellent position for someone wishing to enter graduate or medical school. The start date is negotiable, but would be no earlier than August 1st 2011, and ideally no later than October 1st 2011. A one-year commitment is expected. Requirements: 1) Bachelor's degree in psychology, neuroscience, biomedical engineering, computer science or related field. 2) Strong organizational skills, including ability to prioritize tasks and make decisions independently. 3) Strong interpersonal skills and ability to work with patients. Although not required, experience in the technical aspects of fMRI, including Unix/Linux shell scripting and basic knowledge of common statistical software platforms (MATLAB, freesurfer, FSL) is desirable. The ideal candidate will also have a strong background in statistics, biology and/or neuroscience and a demonstrated interest in research Any interested candidates should provide a cover letter, a resume and the names and contact information of 2-3 references to Dr. John Richey (richey(a)vt.edu) Candidates are also welcome to contact with any questions about the position.

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Freesurfer May 2011