Freesurfer April 2009

freesurfer@nmr.mgh.harvard.edu

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Individual thickness data extraction from plot
by Marina.Lopez＠crccorp.es 22 Apr '09

22 Apr '09

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RES: [Freesurfer] Multiple Processors
by Pedro Paulo de Magalhaes Oliveira Junior 21 Apr '09

21 Apr '09

You can run 8 recon-all simultaneusly In bash recon-all -s subjid -all &> /dev/null & For each of the subjects. You should have at least one gigabyte per processor. The Darwin kernel (MacOs) will distribute the load. Sent from my Nokia phone @E71 -----Msg original----- De: Andrew Jahn Enviada: 21/04/2009 17:39:00 Para: Freesurfer(a)nmr.mgh.harvard.edu Assunto: [Freesurfer] Multiple Processors Hi, I am running Freesurfer on a Mac OS X 10.5 computer with a 2x2.8 GHz Quad-Core Intel Xeon processor. My question is, are there any subcommands to run recon-all assigning the processors to different jobs? Or is the speed of recon-all just dependent on pure processing power, no more? Thanks! -Andrew

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Multiple Processors
by Andrew Jahn 21 Apr '09

21 Apr '09

Hi, I am running Freesurfer on a Mac OS X 10.5 computer with a 2x2.8 GHz Quad-Core Intel Xeon processor. My question is, are there any subcommands to run recon-all assigning the processors to different jobs? Or is the speed of recon-all just dependent on pure processing power, no more? Thanks! -Andrew

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make_average_subject
by ata maroc 21 Apr '09

21 Apr '09

Dear freesurfer, i m running FS_v4.3.0 and i d like to create my own study group average subject. After finishing running make_average_subject, everything seems to work good except some files on my subjaverage/surf subdirectory that are not created at least not correctely. So instead of getting lh.curv or lh.pial all i get is a place holder indicating to or pointing to lh.avg_curv or in the other case pointing to lh.pial_avg which both files are in the same subdirectory. i ll be very gratefull for any hint _________________________________________________________________ http://redirect.gimas.net/?n=M0904xMSNMovies Filme.Gratis.Für alle. MSN Movies. Fehlt nur noch das Popcorn.

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--out_orientation question using mri_convert
by Dr.med. Johannes C. Klein 21 Apr '09

21 Apr '09

Dear all, I have acquired 4D data on a Siemens machine, and I'm using mri_convert to turn the DICOMs into NIFTI files. Now, I would like to "rectify" the 4D NIFTI volume, such that the principal axes display in a standard way in fslview. I can do this for 3D files like this is, and it works a charm for all sorts of original orientations: mri_convert --out_orientation LAS input.nii rectified_output.nii However, when I'm using a 4D NIFTi file as input, only the first volume is included in the rectified output and the rest is truncated. I was wondering if this is a known limitation, and if there is another tool I could use on 4D files which would save me having to split them up before reorientation? BTW, I've tried this on Freesurfer 4.3.0 and 4.0.5. Thanks in advance for your help, Johannes

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EM registration error?
by Wenger, Elisabeth 21 Apr '09

21 Apr '09

Dear freesurfer specialists, we just ran a sample of subjects, and in a few of them the following problem occured: freesurfer exited with error during em registration, telling us that the wm peak could not be found. The protocol looks like this: #@# EM Registration Tue Mar 24 18:47:53 CET 2009 /Applications/freesurfer/subjects/hu66B/mri \n mri_em_register -mask brainmask.mgz nu.mgz /Applications/freesurfer/average/RB_all_2008-03-26.gca transforms/talairach.lta \n using MR volume brainmask.mgz to mask input volume... reading 1 input volumes... logging results to talairach.log reading '/Applications/freesurfer/average/RB_all_2008-03-26.gca'... average std = 6.9 using min determinant for regularization = 4.7 0 singular and 1812 ill-conditioned covariance matrices regularized reading 'nu.mgz'... freeing gibbs priors...done. bounding unknown intensity as < 14.9 or > 790.2 total sample mean = 84.0 (478 zeros) ************************************************ spacing=8, using 2185 sample points, tol=1.00e-05... ************************************************ register_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 102 --> 107 resetting gm mean[0]: 64 --> 64 input volume #1 is the most T1-like using real data threshold=12.9 skull bounding box = (61, 32, 28) --> (196, 145, 201) using (106, 70, 115) as brain centroid... mean wm in atlas = 107, using box (89,56,94) --> (122, 83,136) to find MRI wm before smoothing, mri peak at 0 after smoothing, mri peak at 0, scaling input intensities by inf Darwin mpib4003.mpib-berlin.mpg.de 9.6.0 Darwin Kernel Version 9.6.0: Mon Nov 24 17:37:00 PST 2008; root:xnu-1228.9.59~1/RELEASE_I386 i386 recon-all exited with ERRORS at Tue Mar 24 18:48:48 CET 2009 We are freesurfer beginners and don't have a clue what kind of mistake this could be. We couldn't find any obvious differnces to our other subjects which ran fine. I also attach the whole recon-all.log file, just in case a problem occured on a previous stage we didn't recognize. Thank you for your help! Best, Elisabeth and Shireen

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Re: [Freesurfer] t4_read error (fwd)
by Zhen Zonglei 21 Apr '09

21 Apr '09

Hi avi: Thanks for your help. Still have two questions. 1) How to determine whether the Talairach transform is reasonable based on recon-all.log? 2) As you mentioned, we can make a suitable 3T atlas-representative target to resolve the Talairach transform problem. Now, we have several dozens of adult Chinese 3T MPRAGE data. Would you please give us some cues how to generate the 3T atlas target with FreeSurfer? Anyone has ideas on this issue,please let me know. Thanks again. Zonglei 2009/4/20 Avi Snyder <avi(a)npg.wustl.edu> > Zonglei, > > The log files contain the string "t4_read:..... read error" > This is a benign message indicating the the affine transform > file was not found. This always occurs at the start of the > affine transform sequence and carries no significance. > > Review of the log file indicates that in the case of subjA39 > Talairach atlas transform achieved a reasonable numeric result. > > In the case of subjA06 the Talairach transform did not achieve > a good result. This is an algorithmic issue. It appears that > the talairah_avi module was initiated twice, I assume, in an attmept > to improve the result, but the result did not improve. In this > log file the "read error" message occurs twice but it simply > means that the transform sequence was initiated twice. > > So, there is a problem but the the "read error" message has nothing > to do with it. Poor MP-RAGE to atlas representative target results > most likely are attributable to use of a 1.5T target with 3T input. > It this is correct, then a permanent solution to the problem could > be achieved by selecting the > atlas-representative target according to the MP-RAGE source. > Generation of a suitable 3T target would not be difficult. > > Avi > ------------------------------------------------------ > Date: Sun, 19 Apr 2009 22:52:35 +0800 > Subject: Re: [Freesurfer] t4_read error (fwd) > From: Zhen Zonglei <zonglei.fsl(a)gmail.com> > To: Avi Snyder <avi(a)npg.wustl.edu> > Cc: fischl(a)nmr.mgh.harvard.edu, nicks(a)nmr.mgh.harvard.edu, > freesurfer(a)nmr.mgh.harvard.edu > > Hi avi: > > Thanks for your response, attachments are my recon-all.logs. > If you have any ideas,please let me know. > > Thanks again. > > 2009/4/17 Avi Snyder <avi(a)npg.wustl.edu> > ----------------------------------------------- > > Zonglei, > > > > Send the log file to > > > > avi(a)npg.wustl.edu > > ---------------------------------------- > > >Date: Fri, 17 Apr 2009 11:15:19 -0400 (EDT) > > >From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > >To: Avi Snyder <avi(a)npg.wustl.edu> > > >cc: nicks(a)nmr.mgh.harvard.edu > > > > > >do you want to contact him directly? > > > > > >On Fri, 17 Apr 2009, Avi Snyder wrote: > > > > > >> Most likely the MPRAGE->atlas computation aborted without creating > > >> the relevant t4 file (ASCII representation of the affine transform). > > >> This could occur if the images were somehow corrupted. > > >> > > >> Alternatively, the t4 file is present but a recent OS upgrade has > caused > > >> the previously compiled t4_read FORTRAN function to bomb. I have seen > this > case > > >> once before and have therefore created an all-C t4 i/o module. > > >> > > >> We can distinguish these cases by asking if you got a core dump, of if > > >> a t4 file is still present. The complete tal transform log file would > > >> be diagnostically very helpful. > > >> > > >> Avi > > >> ------------------------------------------ > > >>> Date: Fri, 17 Apr 2009 07:58:36 -0400 (EDT) > > >>> From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > >>> To: Avi Snyder <avi(a)npg.wustl.edu> > > >>> cc: Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> > > >>> Subject: [Freesurfer] t4_read error (fwd) > > >>> > > >>> Hi Avi, > > >>> > > >>> do you know what this message means? > > >>> > > >>> thanks > > >>> Bruce > > >>> ---------- Forwarded message ---------- > > >>> Date: Fri, 17 Apr 2009 19:32:05 +0800 > > >>> From: Zhen Zonglei <zonglei.fsl(a)gmail.com> > > >>> To: freesurfer(a)nmr.mgh.harvard.edu > > >>> Subject: [Freesurfer] t4_read error > > >>> > > >>> Dear all: > > >>> Recon-all has finished without error in my reconstruction. However, > when I > > >>> checked recon-all.log, I found three was a error “t4_read: > > >>> talsrcimg_to_711-2C_as_mni_average_305_t4 read error”. > > >>> > > >>> What's this error mean? Does it have some effects on my > reconstruction? > > >>> > > >>> Thanks > > >>> > > >>> -- > > >>> Zonglei Zhen, PhD > > >>> Assistant Professor of Cognitive Neuroscience > > >>> BNU Imaging Center for Brain Research, State Key Laboratory of > > Cognitive > > >>> Neuroscience and Learning, P.R. China > -- > Zonglei Zhen, PhD > Assistant Professor of Cognitive Neuroscience > BNU Imaging Center for Brain Research, State Key Laboratory of Cognitive > Neuroscience and Learning, P.R. China > > > -- Zonglei Zhen, PhD Assistant Professor of Cognitive Neuroscience BNU Imaging Center for Brain Research, State Key Laboratory of Cognitive Neuroscience and Learning, P.R. China

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Re: [Freesurfer] t4_read error
by Allison Stevens 21 Apr '09

21 Apr '09

This message appears in the recon-all.log for several data sets I have here and all that data looks good. The most important thing is how your data looks. Does it look okay? I'm not sure why this message is there (Nick?) but I think you can ignore it. Allison On Sat, 18 Apr 2009, Zhen Zonglei wrote: > The log files from both version 4.03 and version 4.30 report this error( > t4_read: talsrcimg_to_711-2C_as_mni_average_305_t4 read error ). It occurs > in imgreg_4dfp. > > attachment is my logfile,please check it. > > 2009/4/17 Allison Stevens <astevens(a)nmr.mgh.harvard.edu> > >> What version of FreeSurfer are you using and what step of the process does >> that error appear in? >> Allison >> >> -- >> >> On Fri, 17 Apr 2009, Zhen Zonglei wrote: >> >> Dear all: >>> Recon-all has finished without error in my reconstruction. However, when I >>> checked recon-all.log, I found three was a error ?t4_read: >>> talsrcimg_to_711-2C_as_mni_average_305_t4 read error?. >>> >>> What?s this error mean? Does it have some effects on my reconstruction? >>> >>> >>> >>> Thanks >>> >>> >>> > > >

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selxavg3/fast_selxavg3, error saving matrix when Gamma/SPM-HRF
by N. Eiji Nawa 20 Apr '09

20 Apr '09

Hi: I am trying to perform a first-level analysis using mkanalysis-sess and selxavg3-sess using data from one of my experiments and the steps described in the FsFastTutorial (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorial ). I am able to complete the analysis using the tutorial data but on my data selxavg3 returns the following error: ... ... > In fast_selxavg3 at 212 Warning: Matrix is singular, close to singular or badly scaled. Results may be inaccurate. RCOND = NaN. > In fast_selxavg3 at 212 ntptot = 740, nX = 32, DOF = 708 Saving X matrix to /Users/eiji/exp/ FS_classic_oddball_2009/090407_Kitamichi/bold/classodd-gamma-fwhm8/ Xtmp.mat ??? Error using ==> svd Input to SVD must not contain NaN or Inf. Error in ==> cond at 40 s = svd(A); Error in ==> fast_selxavg3 at 248 XCond = cond(XtX); >> 2009-04-20 13:47:07.771 MATLAB[82205:60b] Process manager already initialized -- can't fully enable headless mode. ------------------------------------------ ERROR: fast_selxavg3() failed\n This only happens when I choose the Gamma function or the SPM hemodynamic response function in mkanalysis-sess. If the chosen function is the finite-impulse response, selxavg3 finishes with no major problems. I am clueless about what could be causing this error. If you have any ideas or need more detailed information, please, let me know! Thanks very much. Eiji -- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.3.0 Kernel info: Darwin 9.6.0 i386 (Mac OS X 10.5.6 Intel)

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slice time correction in preproc-sess, stc.fsl and Analyze
by N. Eiji Nawa 19 Apr '09

19 Apr '09

Hi, I was trying to preprocess some data with the option of slice time correction but preproc-sess exited with the following error: preproc-sess -sf sessid -df sesspar -rlf runlistfile -sliceorder odd - fwhm 8 -update ... ... -------------------- INFO: set hdr.hist.orient to -1 /Users/eiji/exp/myFS slicetimer -i /Users/eiji/exp/FS_classic_oddball_2009/090407_K/bold/ 004/tmp.76874/in.img -o /Users/eiji/exp/ FS_classic_oddball_2009/090407_K/bold/004/tmp.76874/out.img --ocustom=/ Users/eiji/exp/FS_classic_oddball_2009/090407_K/bold/004/tmp.76874/ saof.dat ERROR:: Unrecognised value (ANALYZE) of environment variable FSLOUTPUTTYPE Legal values are: NIFTI, NIFTI_PAIR, NIFTI_GZ, NIFTI_PAIR_GZ ERROR: mc-sess failed It turns out that I have FSL 4.1 installed on my system and FSL 4.1 does not support outputting of Analyze files anymore (http://www.fmrib.ox.ac.uk/fsl/fsl/whatsnew.html ). I suppose this error will not occur if one sticks with the FSL package (3.2?) that comes bundled with freesurfer. So I thought the "least effort" solution would be to prevent preproc- sess from trying to output in Analyze. Below are 3 changes I had to do in fsfast/bin/stc.fsl to make it work: 1) Comment out line #158 in stc.fsl #setenv FSLOUTPUTTYPE ANALYZE 2) Edit line #159 from set outtmp = $tmpdir/out.img to set outtmp = $tmpdir/out.nii.gz 3) Edit line #176 from set cmd = (mri_convert -it analyze4d $outtmp $outfunc) to set cmd = (mri_convert -it nii $outtmp $outfunc) I want to make sure I am not unknowingly messing up with some later stage in preproc-ses, if you find something like that, please let me know! Thanks a lot! Eiji -- FREESURFER_HOME: /Applications/freesurfer Build stamp: freesurfer-Darwin-leopard-i686-stable-pub-v4.3.0 Kernel info: Darwin 9.6.0 i386 (Mac OS X 10.5.6 Intel)

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Freesurfer April 2009