Freesurfer June 2006

freesurfer@nmr.mgh.harvard.edu

53 participants
107 discussions

Re: [Freesurfer] errors in library in new version of Freesurfer
by Joongnam Yang 06 Jun '06

06 Jun '06

Thanks for the question. Here is the info that I can provide. (1) When I did 'source' the *.csh, there was no error. here is the output -------- freesurfer-Linux-centos4_x86_64-stable-pub-v3.0.3 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer FSFAST_HOME /usr/local/freesurfer/fsfast SUBJECTS_DIR /usr/local/freesurfer/subjects FUNCTIONALS_DIR /usr/local/freesurfer/sessions MINC_BIN_DIR /usr/local/freesurfer/mni/bin MINC_LIB_DIR /usr/local/freesurfer/mni/lib PERL5LIB /usr/local/freesurfer/mni/lib/perl5/5.8.5 GSL_DIR /usr/local/freesurfer/lib/gsl QTDIR /usr/lib/qt3 TCLLIBPATH /usr/local/freesurfer/lib/tcltktixblt/lib FSL_DIR /usr/local/freesurfer/fsl (2) when I did, ldd 'which mri_convert', it gave me the following error message. ldd: ./which mri_convert: No such file or directory (3) When I did, however, just 'which mri_convert', it correctly points to its location, which is .........../freesurfer/bin/mri_convert. (4) Freesurfer is running on the latest version of SUSE on a 64-bit machine. I downloaded an appropriate version of Freesurfer. Nam. >>> Nick Schmansky <nicks(a)nmr.mgh.harvard.edu> 06/06/06 4:42 PM >>> What is the output when this is typed: source $FREESURFER_HOME/SetUpFreeSurfer.csh and this: ldd `which mri_convert` and what OS is this installed on? On Tue, 2006-06-06 at 15:24 -0400, Joongnam Yang wrote: > I installed the new version of Freesurfer by downloading from Freesurfer > Wiki website. > > Then, I ran recon-all -subjid subjectname -autorecon1, > and got the following library errors. > Would someone suggest a solution? > > Nam. > > mri_convert: error while loading shared libraries: libgsl.so.0: cannot open > shar ed object file: No such file or directory > mri_convert: error while loading shared libraries: libgsl.so.0: cannot open > shar ed object file: No such file or directory > strings: 'mritotal:': No such file > strings: 'Command': No such file > strings: 'not': No such file > strings: 'found.': No such file > nu_correct: Command not found. > ................. (and much more....) > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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errors in library in new version of Freesurfer
by Joongnam Yang 06 Jun '06

06 Jun '06

I installed the new version of Freesurfer by downloading from Freesurfer Wiki website. Then, I ran recon-all -subjid subjectname -autorecon1, and got the following library errors. Would someone suggest a solution? Nam. mri_convert: error while loading shared libraries: libgsl.so.0: cannot open shar ed object file: No such file or directory mri_convert: error while loading shared libraries: libgsl.so.0: cannot open shar ed object file: No such file or directory strings: 'mritotal:': No such file strings: 'Command': No such file strings: 'not': No such file strings: 'found.': No such file nu_correct: Command not found. ................. (and much more....)

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Re: freesurfer
by Nurunisa Neyzi 06 Jun '06

06 Jun '06

Hello, > I have whole brain T1 maps and the pseudo T1-weighted images that I > created out of them (so they are perfectly aligned). The are all brain > extracted using fsl and > I am doing my own tissue segmentation (again, using fsl), but in both > steps there is much optimization involved, because I want to do it very > carefully avoiding partial volume effects (I am looking at the cortical T1 > values). > I would like to look at the maps in the inflated and flattened spaces. > So I have been learning freesurfer over the past week but my problem is > with the surface reconstruction and that everything is automated. I don't > want freesurfer to do the segmentation for me. I was hoping it would work > well because the data is 1x1x1- but the segmentation is not nearly as > precise as I need it. > Is there a way that I give my already aligned T1 maps and structural > images and tissue segmentation and get out the surfaces with T1 values on > top of it? > > > >

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mri_volcluster example
by Paymon Hosseini 06 Jun '06

06 Jun '06

Hi Can you please post an example of "mri_volcluster" use with fsfast? more specifically, when i run : mri_volcluster \ --in /space/engram/12/users/pman/rk_fmri/Y15_111504/bold/rk_enc_sm5/RNeg_vs_Fix/sig \ --in_type bfloat \ --reg /space/engram/12/users/pman/rk_fmri/Y15_111504/bold/rk_enc_sm5/tal/register.dat \ --thmin 7 \ --minsize 640 \ --allowdiag i get the following error: NOT Adjusting threshold for 1-tailed test INFO: bvolumeRead: min = -16.6743, max = 25.5035 ERROR: Input volume voxel dimensions do not match those in the registration file. If the input volume is in bshort/bfloat format, check that there is an accompanying bhdr file. there are sig_xxx.bfloat and sig_xxx.hdr files in my "/space/engram/12/users/pman/rk_fmri/Y15_111504/bold/rk_enc_sm5/RNeg_vs_Fix/" directory. i am using "nmrenv" on engram.nmr.mgh any advice on how to resolve this? thanks a lot, paymon

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Question regarding Outputs
by Goradia, Dhruman D 06 Jun '06

06 Jun '06

Hello all, The output of mris_anatomical_stats has a measurement called TotalWhiteMatterVolume for each hemisphere. From aseg.stat the measures for cerebellum-white volume and cerebral-white volume for each hemisphere can be obtain, but the sum of both the measures obtained from aseg is less than the total white matter volume obtained from the surface measures. Should they be different? If so what is the difference in measurement criteria? Thank you -Dhruman

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freesurfer and monkey (macaque) brain processing
by Istvan Akos Morocz 06 Jun '06

06 Jun '06

dear freesurfer group, is there anywhere some cookbook-like instruction for processing monkey (macaque) brain MRI data with FreeSurfer ? are there any normalized macaque brain templates needed for FreeSurfer ? thanks, bye, pisti ----- pisti(a)bwh.harvard.edu

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Problems runing a complete freesurfer analysis under Centos4 X86-64
by jorge luis 05 Jun '06

05 Jun '06

Hello all I have a Dual core Intel Pentium 3.0Gz machine with 2GB RAM and two SATA2 Hard Disks (300 GB and 80GB, respectively). I have successfully installed Linux Centos4 X86-64 (on the 80 GB disk) and the corresponding freesurfer version. I have run several freesurfer commands successfully (eg. tkmedit bert orig.mgz). The problem is when I try to run a complete analysis (recon-all - autorecon-all), the corresponding terminal gets stop undefinedly when it has to execute a copy operation (e.g. cp aseg.auto.mgz aseg.mgz). That is to say the problem get rise when freesurfer sends a copy order to the operating system. Manually I carry out the copy command and I don't have any problems. But when I reactivate freesurfer (eg. recon-all - autorecon2-cp) the terminal stops again when it has to carry out a copy operation again. I have another Intel Dual Xeon Dual Core 2.8Gz 5GB RAM machine with Linux Centos 4 X86-64 and the same configuration. No problem is there. Any tip to overcome this problem is welcome Thank you in advance Jorge ______________________________________________ LLama Gratis a cualquier PC del Mundo. Llamadas a fijos y móviles desde 1 céntimo por minuto. http://es.voice.yahoo.com

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problems with make_average_subject
by Lars M. Rimol 05 Jun '06

05 Jun '06

Hi, I am analysing a dataset with 180 subjects. When I run make_average_subjects it crashes, the error message usually being something like this: mghRead: encountered error executing: 'zcat /space/monkeys/1/home/lmr/subjects/VETSA_test/testAVG/tmp/make_average_vol-tmp/orig- 19963b.mgz',frame -1 I have tried running it with fewer subjects and it worked with 3, 10 and 73 subjects. Also, it crashes at different points in the processing stream, so once it crashed at subject # 130, which I removed from the list of subjects, and then next time it crashed at # 30. My frist guess was that it is a memory problem. I tried running the top command in a different terminal at the same time as running make_average_subject with 2 and 10 subjects, and it seemed to require up to 400m of virtual memory and 10% of memory, but I couldn't see any difference in memory demands between running 2 and 10 subjects. This was running with 4G of physical memory and 2G of swap. Is this a known issue? (Couldn't find anything in the mailing list archive..) Thank you! -- yours, LMR

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make_average_subject
by Lars M. Rimol 05 Jun '06

05 Jun '06

Hi, I have two questions on make_average_subject 1) Why are two sets of surfaces created by the make_average_subject script? What is the difference between e.g. inflated and inflated_avg? Which one(s) should be used for visualization? 2) As far as I understand, make_average_subject is run for visualization purposes only, and the output is not critical for the integrity of the statistical analyses (recon-all does the spherical warping and registration, and t he mris_preproc script makes sure the tesselation is uniform across the data set). So, does it matter if there are defects in the surfaces created by make_average_subject? I tend to get topological defects in the inflated_avg. Thank you! -- yours, LMR

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trouble importing SPM2/Analyze file with tkregister2 in order to create a register.dat file
by Istvan Akos Morocz 05 Jun '06

05 Jun '06

dear freesurfer team, i experience trouble to compute the register.dat file when using tkregister2 to import an SPM2 BOLD brain volume f.img together with an 001.mgz structural file. segmentation and flattening worked flawlessly for that 001.mgz file (imported initially from an SPM2 anatomical data). here some examples of my desperate attempts: tkregister2 --mov ANALYZE/f.img --s fs1 --regheader --noedit --reg register.dat tkregister2 --mov ANALYZE/f.img --targ ANALYZE/cor.img --s fs1 --regheader --noedit --reg register.dat tkregister2 --mov ANALYZE/f.img --targ ANALYZE/cfs1/mri/orig/001.mgz --s fs1 --regheader --noedit --reg register.dat tkregister2 --mov ANALYZE/f.img --targ fs1/mri/orig/001.mgz --s fs1 --regheader --noedit --reg register.dat tkregister2 --mov ANALYZE/f.mat --targ fs1/mri/orig/001.mgz --s fs1 --regheader --noedit --reg register.dat tkregister2 --mov ANALYZE/f.hdr --targ fs1/mri/orig/001.mgz --s fs1 --regheader --noedit --reg register.dat please, see error messages below. something seems to run wrongly when reading the f.mat file. i use matlab v7.1 with SPM2. the mat file initially was created as compressed mat file (v7 style), but then i converted the f.mat alsoto a v6 style = non-compressed, but no difference. content of the f.mat file is, after doing: 'load f.mat' mat = 3.7499 -0.0312 0.0122 -128.3677 0.0325 3.6227 -1.2914 -110.0712 -0.0008 0.9686 4.8303 -86.1374 0 0 0 1.0000 ==> are there somewhere out there clear instructions how to make SPM2 and freesurfer coexist ? thanks, bye, pisti ---------------------------------------------------------------------- error messages: - 1 ------------------------------------------------------------------ tkregister2 --mov ANALYZE/f.img --s fs1 --regheader --reg register.dat INFO: no target volume specified, assuming FreeSurfer orig volume. target volume orig movable volume ANALYZE/f.img reg file register.dat LoadVol 1 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 matfile: only read 423 bytes of name (1768711468 specified) MatlabRead: readHeader returned NULL WARNING: analyzeRead(): matfile ANALYZE/f.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. ----------------------------------------------------------------- INFO: could not find ANALYZE/f.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in ANALYZE/f.mat file ----------------------------------------------------------------- INFO: loading target /data/kodaly/r/pisti/numerals/fMRI_LM_060427/fs1/mri/orig.mgz INFO: changing target type to float Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable ANALYZE/f.img matReadHeader: couldn't allocate 1768711469 bytes for name Cannot allocate memory - 2 ------------------------------------------------------------------ tkregister2 --mov ANALYZE/f.img --targ fs1/mri/orig/001.mgz --s fs1 --regheader --noedit --reg register.dat target volume fs1/mri/orig/001.mgz movable volume ANALYZE/f.img reg file register.dat LoadVol 0 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 matfile: only read 423 bytes of name (1768711468 specified) MatlabRead: readHeader returned NULL WARNING: analyzeRead(): matfile ANALYZE/f.mat exists but could not read ... may not be matlab4 mat file ... proceeding without it. ----------------------------------------------------------------- INFO: could not find ANALYZE/f.mat file for direction cosine info. INFO: use Analyze 7.5 hdr->hist.orient value: 0, transverse unflipped (default). INFO: if not valid, please provide the information in ANALYZE/f.mat file ----------------------------------------------------------------- INFO: loading target fs1/mri/orig/001.mgz INFO: target does not conform to COR format, so I'm going to reslice to COR. This will not affect the final registration. Ttarg: -------------------- -1.000 0.000 0.000 128.000; 0.000 0.000 1.000 -128.000; 0.000 -1.000 0.000 128.000; 0.000 0.000 0.000 1.000; INFO: loading movable ANALYZE/f.img matReadHeader: couldn't allocate 1768711469 bytes for name Cannot allocate memory - 3 ------------------------------------------------------------------ tkregister2 --mov ANALYZE/f.hdr --targ fs1/mri/orig/001.mgz --s fs1 --regheader --noedit --reg register.dat target volume fs1/mri/orig/001.mgz movable volume ANALYZE/f.hdr reg file register.dat LoadVol 0 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 ERROR: cannot determine type of ANALYZE/f.hdr - 4 ------------------------------------------------------------------ tkregister2 --mov ANALYZE/f.mat --targ fs1/mri/orig/001.mgz --s fs1 --regheader --noedit --reg register.dat target volume fs1/mri/orig/001.mgz movable volume ANALYZE/f.mat reg file register.dat LoadVol 0 $Id: tkregister2.c,v 1.49.2.4 2006/03/27 21:48:16 greve Exp $ Diagnostic Level -1 matfile: only read 423 bytes of name (1768711468 specified) MatlabRead: readHeader returned NULL ImageRead(ANALYZE/f.mat) failed Segmentation fault and so on... ----- pisti(a)bwh.harvard.edu

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Freesurfer June 2006