Freesurfer May 2010

freesurfer@nmr.mgh.harvard.edu

98 participants
145 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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--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] 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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Methods for white matter hypointensities measure
by Laluz, Victor 30 Jul '10

30 Jul '10

Hello guys, I am curious as to how white matter hypointensities (on T1 mprage) are measured automatically for the aseg.stats file in FS? A group at UCSF is interested in using this measure for a study and would like to have a nice explanation or citation to describe how it is generated. I have looked through what I think the likely citations would be on the Freesurfer techniques article listing and came up empty. Thanks! Victor Victor Laluz : Imaging Coordinator : UCSF Memory and Aging Center

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Re: [Freesurfer] question about clustering simulation
by Michael Waskom 23 Jun '10

23 Jun '10

Hi Doug, This looks very helpful! Should we use the fwhm size corresponding to the argument of the --fwhm flag when recon-all runs mri_surf2surf (for anatomical stats), or round the measure found in the fwhm.dat of the glmfit dir? Thanks, Mike ---------- Forwarded message ---------- From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> To: porterj(a)umn.edu Date: Tue, 27 Apr 2010 11:17:24 -0400 Subject: Re: [Freesurfer] question about clustering simulation Yea, that was a bug in the simulation program I used. I did confirm that the simulations were done on the correct hemisphere. Feel free to edit the files. I'll fix the master when I get a chance. doug James Porter wrote: > Doug- > > Let me be the first to say thank you for saving me massive amounts of > simulation time. One bug though: the right hemisphere files say they were > created using the left hemisphere, and mri_surfcluster rejects them. Would > it be verboten to just alter the csd files, or do you have versions that > were created off of fsaverage's right hemisphere? > > matacao:mult-comp-cor porterj$ head > fsaverage/rh/cortex/fwhm19/abs/th33/mc-z.csd > # simtype null-z > # anattype surface fsaverage lh > # FixGroupSubjectArea 1 > # merged 0 > # contrast NA > # seed 1271355821 > # thresh 3.300000 > # threshsign 0.000000 > # searchspace 74490.928733 > # nullfwhm 19.000000 > > Jim Porter, M.A. > Graduate Student > Clinical Science& Psychopathology Research > University of Minnesota > > > On 7/22/64 1:59 PM, Douglas N Greve wrote: > >> 1. Correct on both counts. When I wrote the simulation, I was only trying >> to replicate the random fields analysis. But with a simulation, you have >> more freedom that I am not yet exploiting. >> 2. This is what we are already doing with mc-z >> 3. I'm working on this as well. It turns out that the random fields >> approximation works a lot better when using the number of vertices. >> >> Also, I've run mc-z simulations under a bunch of thresholding and FWHM >> conditions for whole-hemisphere cortex labels. These will be integrated in >> new version of FS, but I've put them here >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mult-comp-cor… well. There's a README file in there. This will make running your own >> time-consuming simulations unnecessary (when using the cortex mask at >> least). >> >> doug >> >> Anthony Dick wrote: >> >>> Hello all, >>> >>> I am interested in using the mri_glmfit simulation to control for >>> multiple comparisons in data I have run on the surface in AFNI. Before doing >>> this, I have a few questions: >>> >>> 1. What does the simulation with the mc-z flag do, exactly? It claims to >>> be comparable to AFNI's AlphaSim, but it takes a maximum cluster area for >>> each iteration, which is not exactly what AlphaSim does. Here is my guess: >>> >>> Given a surface, a given smoothness of the data, and a given per-vertex >>> threshold, for each iteration the simulation populates that surface with >>> random data taken from a normal distribution, thresholds the data, and >>> applies the smoothness of the actual data (supplied as an input parameter). >>> It then computes the maximum cluster size in area for that "image". Doing >>> this n iterations gives a distribution of maximum cluster sizes that occur >>> for random data of a given smoothness, and taking cluster sizes above a >>> certain percentile rank controls for the FWE at a level equal to that >>> percentile rank (e.g., 95th% controls for FWE = .05). AlphaSim does >>> something similar, although instead of taking maximum cluster sizes at each >>> iteration it computes all given cluster sizes. AlphaSim also allows for >>> different cluster connectivity radius, but it seems Freesurfer computes only >>> for neighboring vertices. All in all, if this is correct, it seems like a >>> good implementation. >>> >>> 2. It is my understanding that one could bypass running the glm in >>> Freesurfer and only compute the simulation, as the simulation only needs >>> information about the surface, and the smoothness of the data (which are >>> supplied by the user). To do so, you have to "fake out" Freesurfer to bypass >>> glm, but that turns out to be pretty painless. >>> >>> 3. In a future distribution, is it possible to modify this procedure to >>> also output maximum cluster sizes in terms of number of nodes, rather than >>> area? >>> >>> Can you please let me know if I am mistaken in any of these assumptions? >>> Thanks in advance. >>> >>> Anthony >>> >>> >> > > -- 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

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FDR correction in FS vs. SPM
by Jürgen Hänggi 04 Jun '10

04 Jun '10

Dear FS experts One of our reviewers would like to know whether the FDR procedures as implemented in FS on one hand and as implemented in SPM on the other hand are comparable. In FS, I think FDR is based on the height threshold (FDRp) and it is outside of the random Gaussian field theory framework, isn't it? For SPM, it has been shown that the FDR procedure based on height threshold (FDRp) is not appropriate in the random Gaussian field theory framework (Chumbley et al., 2010; Chumbley and Friston, 2009, both published in NeuroImage). Therefore, in SPM8 FDRc (based on the cluster volume) was implemented and should be preferred over FDRp, isn't it? Therefore, we conclude that it is not possible to use a comparable parametric multiple comparisons correction procedure in FS and SPM. Do the nonparametric procedures (SnPM for SPM and Monte Carlo simulations in FS) are comparable? Or is it impossible to get any comparable procedure due to the fact that a voxel is in 3D (as in SPM), whereas a vertex is on a 2D manifold (as in FS)? Thanks in advance Regards Jürgen Hänggi ---------------------------------------------------------------------------- Jürgen Hänggi, Ph.D. Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ----------------------------------------------------------------------------

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shared library error
by houman.ebrahimi 04 Jun '10

04 Jun '10

Hi, I am constantly getting the same error when running recon-all on different subjects: #@# Cortical ribbon mask Sat May 29 15:08:06 EST 2010 /home/houman/Desktop/freesurfer/subjects/PS2038/mri mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon --save_distance PS2038 mris_volmaskbin: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory Linux ubuntu 2.6.32-22-generic #33-Ubuntu SMP Wed Apr 28 13:28:05 UTC 2010 x86_64 GNU/Linux recon-all exited with ERRORS at Sat May 29 15:08:07 EST 2010 I am running: freesurfer-Linux-centos4_x86_64-stable-pub-v.4.5.0-full.tar.gz i7 processor - Ubuntu 10.04 (Kernel Linux 2.6.32-22-generic, GNOME 2.30.0) I have referred to the suggested solutions at the following post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07975.html but neither seem to correct the problem. I am interested mainly in the data in the stats/aseg.stats file (which is generate on the step before the error). Is this error likely to affect the data in that file? Thanks! Houman

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Freesurfer May 2010