Freesurfer August 2010

freesurfer@nmr.mgh.harvard.edu

102 participants
152 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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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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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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--fsl flag in bbregister
by Nasim Maleki 11 Dec '10

11 Dec '10

Hello Doug, I get an error message when using --fsl flag with bbregister: "ERROR: Flag --fsl unrecognized." I'm using: bbregister,v 1.14.2.12 2009/08/07 22:21:00 greve Is this version of the bbregister that I'm using the latest? Thank you, Nasim

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Re: [Freesurfer] Longitudinal processing
by Martin Reuter 27 Oct '10

27 Oct '10

Hi Sandra, (and the list, I think this might be interesting for others) 1. the longitudinal ?h.thickness files are in registration (within subject) so in order to compute the difference or the rate you can simply use: mris_calc -o lh.outdiff sdir2/surf/lh.thickness sdir1/surf/lh.thickness and for the rate, you can divide by time 1 thickness or by the average thickness. If the time points are not equally spaced across subjects, you can also divide by difference in time. It is best to smooth the thickness files before you do all this (i.e. within time point smooth the ?h.thickness files with mri_surf2surf). 2. then map everything to your template (e.g. fsaverage) with mri_surf2surf 3. there you can stack the thick-differences or thick-rates with mri_concat 4. do the glm Beste Gruesse, Martin On Tue, 2010-06-29 at 21:50 +0200, Sandra Duezel wrote: > Hi Martin > > I just have got your answer to the longitudinal processing question > from Michele and have some other questions regarding the output data > from the longitudinal stream. > Our study contains MRI scans of 45 elderly subjects from 2 timepoints. > I have done all steps from the longitudinal stream and it worked > without any problems. > > Now I would like calculate the thickness difference maps between the > prae and post scans, which are already longitudinally processed. > > I have tried the thickdiffmap-script using the <tp1>.long and > <tp2>.long data. It creates a .mgz file in each subject but also a new > folder "groupstudy" > with the prae/post data resampled to fsaverage (its an .mgh file) > > Is this the right way to calculate the difference for longitudinal data? > > Do I also need to proceed with GLM analysis as suggestet in http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis > or do I need to handle the longitudial data in a different way? > > Thank you very much for your help and answers! > > Best regards > > Sandra > > > > > > > > > Am 29.06.2010 um 17:24 schrieb Martin Reuter: > > > There is a step by step description on the longitudinal stream. > > It basically means: > > 1. to process your two time points individually through freesurfer > > (standard processing). > > 2. to create a template for each subjects from these processed time > > points > > 3. to run the two time points again (passing it the template) to > > compute > > better longitudinal results (less variability, more accuracy). > >

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Re: [Freesurfer] Retinotopic mapping of only polar data
by f.leone＠donders.ru.nl 04 Oct '10

04 Oct '10

Hi everyone, Doug: thanks a lot for the reply, that indeed worked, I now have a polar map overlayed on my inflated brain. But something seems to be amiss, because it plots it mainly on the temporal lobe, with nothing on the most dorsal slices, while actually I only scanned the 18 most dorsal (oriented along the occipital-parietal axis), sot here shouldn't be anything in the temporal or inferior frontal lobe. How can this be/where is it going wrong? Moreover, I'm not sure on the format used by the polar map: the scale bar states it ranges from 1.18 to 1.18, but I don't see the sense in that. What will come out? Radians I pressume? kind regards, thanks a lot in advance, Frank ----- Original Message ----- From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> To: "Frank Leoné" <f.leone(a)donders.ru.nl> Cc: freesurfer(a)nmr.mgh.harvard.edu Sent: Friday, January 8, 2010 4:26:21 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna Subject: Re: [Freesurfer] Retinotopic mapping of only polar data You can generate a register.dat with either fslregister-sess or spmregister-sess, or, if you have it in your version, use bbregister (note that there is not a -sess version for this yet). You can then use mri_vol2surf to resample the h.nii file to the surface, then view it in tksurfer. You can also extract certain frames with mri_convert with the --frame option. doug f.leone(a)donders.ru.nl wrote: > Hi everyone, > > Still not working fully, partly because I'm missing some info on the file formats. What I now did was a run of selfreqavg with four input polar sessions, which ran succesfully. This gives me the expected h.nii. Now I either want to > > - use this h file directly, using paint-sess (get message register.dat is missing) and sliceview-sess (get message it can't determine format h-offset, which makes sense, because it doesn't exist) > - or extract w files from the first three layers of the nii files and superimpose them in tksurfer. I don't know how I should extract them though. Can use the SPM surfrend functions, but I can't imagine that is the way, or is it? > > Hopefully someone can help me along either of the two paths, I'm really eager to see whether the retinotopic analysis worked. Thanks a lot in advance! > > kind regards, > > Frank > > ----- Original Message ----- > From: "f.leone(a)donders.ru.nl" <f.leone(a)fcdonders.ru.nl> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Monday, January 4, 2010 9:35:51 AM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna > Subject: Re: [Freesurfer] Retinotopic mapping of only polar data > > Hi everyone, > > I fixed it with the help of Jascha: when using the full path, e.g. /home/frank/etc.../007/f.nii it does find them. So it is now running. Thanks for the help! > > kind regards, > > Frank > > ----- Original Message ----- > From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> > To: "Frank Leoné" <f.leone(a)donders.ru.nl> > Cc: freesurfer(a)nmr.mgh.harvard.edu > Sent: Tuesday, December 22, 2009 7:58:23 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna > Subject: Re: [Freesurfer] Retinotopic mapping of only polar data > > Do you have read permissions to the file? If so, can you send the log > file created by sfa-sess? > > f.leone(a)donders.ru.nl wrote: > >> Thanks a lot for the reply. I now bump into different problems though: it doesn't understand my f.nii file, see below. I run: >> >> frank@frank-desktop:~/PhD/data/Exp1_Saccades_phase$ sfa-sess -a rtopy -s FSFAST_S1/ >> >> and I think the main error line is: >> >> ERROR: cannot determine format of 007/f >> >> >>>> ??? Attempt to reference field of non-structure array. >>>> >>>> >> 007 is my first session (is a dir) and in there is one f.nii, which includes all the scans of that run. . Previously I tried it with separate scan files, but that didn't work either. So what does it expect? And will it work with data preprocessed in SPM instead in FreeSurfer? The rest of the dir structure is setup as specified in the guide >> >> Hopefully someone can help me, thanks a lot in advance, >> >> kind regards, >> >> Frank >> >> frank@frank-desktop:~/PhD/data/Exp1_Saccades_phase$ mkanalysis-sess.new -force -a rtopy -TR 2.12 -designtype retinotopy -paradigm rtopy.par -funcstem f -ncycles 8 >> INFO: analysis rtopy exists, but overwrite forced by user. >> Completed successfully >> frank@frank-desktop:~/PhD/data/Exp1_Saccades_phase$ sfa-sess -a rtopy -s FSFAST_S1/ >> -------------------------------------------------------------- >> sfa-sess logfile is /home/frank/PhD/data/Exp1_Saccades_phase/log/sfa-sess-bold-rtopy-0912221252.log >> -------------------------------------------------------------- >> ------------------------------------------- >> /home/frank/PhD/data/Exp1_Saccades_phase/FSFAST_S1 >> Tue Dec 22 12:52:30 CET 2009 >> INFO (FSFAST_S1): RunList = 007 008 009 010 011 >> -------------------------------------------------- >> /home/frank/PhD/data/Exp1_Saccades_phase/FSFAST_S1/bold >> selfreqavg -TR 2.12 -o rtopy/polar/h -i 007/f -i 008/f -i 009/f -i 010/f -cfg /home/frank/PhD/data/Exp1_Saccades_phase/rtopy/analysis.cfg -parname rtopy.par >> -------------------------------------------------- >> --- Parsing Config File: /home/frank/PhD/data/Exp1_Saccades_phase/rtopy/analysis.cfg ---- >> -ncycles 8 -delay 0 -nskip 0 -fwhm 0 >> DirectionList: +1 +1 +1 -1 >> Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. >> >> < M A T L A B (R) > >> Copyright 1984-2009 The MathWorks, Inc. >> Version 7.8.0.347 (R2009a) 64-bit (glnxa64) >> February 12, 2009 >> >> >> To get started, type one of these: helpwin, helpdesk, or demo. >> For product information, visit www.mathworks.com. >> >> >> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> Extension format = nii >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> hanrad = 0 >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ERROR: cannot determine format of 007/f >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>> ??? Attempt to reference field of non-structure array. >>>> >>>> >> >> >> >>>> ??? Attempt to reference field of non-structure array. >>>> >>>> >> >> >> >>>> ??? Attempt to reference field of non-structure array. >>>> >>>> >> >> >> >>>>>> ??? Attempt to reference field of non-structure array. >>>>>> >>>>>> >> >> >> >>>>>> ??? Undefined function or variable 'lastslice'. >>>>>> >>>>>> >> >> >> >>>> ??? Attempt to reference field of non-structure array. >>>> >>>> >> >> >> >>>>>>>> ??? Attempt to reference field of non-structure array. >>>>>>>> >>>>>>>> >> >> >> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> ??? Index exceeds matrix dimensions. >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> >> >> >> >>>>>>>>>>>> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >>>>>>>>>>>> >>>>>>>>>>>> >> >> >> >>>> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >>>> >>>> >> >> >> >>>> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >>>> >>>> >> >> >> >>>> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >>>> >>>> >> >> >> >>>> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >>>> >>>> >> >> >> >>>> ??? Attempted to access tmp(NaN); index must be a positive integer or logical. >>>> >>>> >> >> >> >>>>>>>>>>>>>>>>>>>>>>>>>>>> Slice >> ??? Undefined function or variable 'lastslice'. >>>>>>>>>>>>>>>>>>>>>>>>>>>> >>>>>>>>>>>>>>>>>>>>>>>>>>>> >> >> >> >>>>>>>> ??? Attempt to reference field of non-structure array. >>>>>>>> >>>>>>>> >> Error in ==> MRIwrite at 94 >> hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3) mri.nframes]; >> >> >> >>>>>>>> ??? Attempt to reference field of non-structure array. >>>>>>>> >>>>>>>> >> Error in ==> MRIwrite at 94 >> hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3) mri.nframes]; >> >> >> >>>>>>>> ??? Attempt to reference field of non-structure array. >>>>>>>> >>>>>>>> >> Error in ==> MRIwrite at 94 >> hdr.dim = [mri.volsize(2) mri.volsize(1) mri.volsize(3) mri.nframes]; >> >> >> >>>>>>>>>> Saving header to rtopy/polar/h >>>>>>>>>> >>>>>>>>>> >>>> Could not open rtopy/polar/h.sfa for writing >>>> >>>> >> quiting matlab >> selfreqavg COMPLETED >> mri_convert rtopy/polar/h.nii -o rtopy/polar/h-offset.nii --frame 10 >> mri_convert rtopy/polar/h.nii -o rtopy/polar/h-offset.nii --frame 10 >> niiRead(): error opening file rtopy/polar/h.nii >> >> ----- Original Message ----- >> From: "Douglas N Greve" <greve(a)nmr.mgh.harvard.edu> >> To: "Frank Leoné" <f.leone(a)donders.ru.nl> >> Cc: freesurfer(a)nmr.mgh.harvard.edu >> Sent: Wednesday, December 16, 2009 5:12:41 PM GMT +01:00 Amsterdam / Berlin / Bern / Rome / Stockholm / Vienna >> Subject: Re: [Freesurfer] Retinotopic mapping of only polar data >> >> If you run the retinotopy analysis, it will expect eccen. If it stops >> without doing the polar analysis, you can "fool" it by copying the polar >> data into the eccen directory. >> >> doug >> >> f.leone(a)donders.ru.nl wrote: >> >> >>> Dear all, >>> >>> I just started using FreeSurfer, specifically for retinotopic data, on the moment only polar data. So I followed the guide as mentioned on http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis . This does seem to work to some extend, except that it complains that I don't have eccentricity data. He is right about that, but is the analysis also doable with the eccentricity data? I really hope so, thanks a lot in advance, >>> >>> kind regards, >>> >>> Frank >>> >>> >>> >>> >> >> > > -- 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Frank T.M. Leoné, MSc Graduate student | Donders Institute for Brain, Cognition and Behaviour f.leone(a)donders.ru.nl | +31 24 36 12542 / +31 24 36 68388 | Room B.1.31 / Room 1.34

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mris_anatomical_stats
by corinna bauer 02 Sep '10

02 Sep '10

I am trying to get an output with average gray/white ratio values for each segmentation. I tried using the gwratio.mgh file as the input for mris_anatomical_stats, but got the following error message: reading input surface /home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh... ERROR: MRISread: file '/home/freesurfer4.4.0/subjects/1057/surf/lh.gwratio.mgh' has 0 vertices! Any insight?

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base processing error
by Derin Cobia 01 Sep '10

01 Sep '10

In creating the base template for two of our subjects, the superior portion of the volume somehow got cut off (see attached). The original volumes for both time points are fine (i.e., do not display this problem), and completed the cross-sectional stream without problem. Is this an issue with aligning volumes from both time points, can it be fixed? Thanks. CentOS 5.2 FS v4.5.0 -Derin

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Freesurfer August 2010