Red Hat Enterprise Linux Server release 5.9 (Tikanga) freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0
Caspar 2015-11-23 14:37 GMT-05:00 <zkauf...@nmr.mgh.harvard.edu>: > What system are you running on? Also, what are the contents of your > build-stamp.txt file (in your FREESURFER_HOME directory)? > > -Zeke > > > > Hi Zeke, > > I tried the is new version. Now I am getting: > > > > mri_coreg: /lib64/libuuid.so.1: no version information available > (required > > by mri_coreg) > > mri_coreg: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found > > (required by mri_coreg) > > mri_coreg: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.9' not found > > (required by mri_coreg) > > mri_coreg: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > > mri_coreg) > > > > Caspar > > > > > > 2015-11-23 14:20 GMT-05:00 <zkauf...@nmr.mgh.harvard.edu>: > > > >> There were some recent changes in the build that eliminated the > >> necessity > >> for that library. Casper, can you try using this most recent version and > >> let me know if it works? > >> > >> > >> > ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_x86_64/mri_coreg > >> > >> Thanks, > >> > >> -Zeke > >> > >> > >> > Zeke, is this a new library that we need for v6? > >> > doug > >> > > >> > On 11/20/2015 09:42 AM, Caspar M. Schwiedrzik wrote: > >> >> Hi Doug, > >> >> when I try to execute mri_coreg, I get the following error message: > >> >> > >> >> error while loading shared libraries: libnetcdf.so.6: cannot open > >> >> shared object file: no such file or directory > >> >> > >> >> Caspar > >> >> > >> >> > >> >> 2015-11-19 18:49 GMT-05:00 Douglas Greve <gr...@nmr.mgh.harvard.edu > >> >> <mailto:gr...@nmr.mgh.harvard.edu>>: > >> >> > >> >> > >> >> Can you try mri_coreg instead of fsl? > >> >> > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg > >> >> > >> >> > >> >> > >> >> > >> >> On 11/19/15 5:25 PM, Caspar M. Schwiedrzik wrote: > >> >>> Hi! > >> >>> I am trying to align a mean EPI volume and a Bruker magnitude > >> map > >> >>> from a fieldmap measurement using tkregister2, > >> fsl_rigid_register > >> >>> and mri_vol2vol. Unfortunately, it seems that somewhere, most > >> >>> likely during fsl_rigid_register, the image orientation get > >> >>> scrambled, and the output has the wrong orientation. > >> >>> > >> >>> Here is what I get from*tkregister2:* > >> >>> > >> >>> target volume epi.nii > >> >>> movable volume fieldmap0001.nii > >> >>> reg file mag_2_mocovol.register.dat > >> >>> LoadVol 0 > >> >>> ZeroCRAS 0 > >> >>> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ > >> >>> Diagnostic Level -1 > >> >>> INFO: loading target epi.nii > >> >>> Setting targ orientation to RIA > >> >>> 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 fieldmap0001.nii > >> >>> Setting mov orientation to RIA > >> >>> Tmov: -------------------- > >> >>> -0.547 0.000 0.000 17.500; > >> >>> 0.000 0.000 0.547 -17.500; > >> >>> 0.000 -0.547 0.000 17.500; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> mkheaderreg = 1, float2int = 0 > >> >>> Computing reg from header (and possibly input matrix) > >> >>> ---- Input registration matrix (computed) -------- > >> >>> -1.000 0.000 0.000 -0.587; > >> >>> 0.000 1.000 0.000 -2.150; > >> >>> 0.000 0.000 1.000 -2.188; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> --------------------------------------- > >> >>> ---- Input registration matrix -------- > >> >>> -1.000 0.000 0.000 -0.587; > >> >>> 0.000 1.000 0.000 -2.150; > >> >>> 0.000 0.000 1.000 -2.188; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> Determinant -1 > >> >>> subject = rat > >> >>> RegMat --------------------------- > >> >>> 1.000 0.000 0.000 -0.587; > >> >>> 0.000 1.000 0.000 -2.150; > >> >>> 0.000 0.000 1.000 -2.188; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> FSLOUTPUTTYPE NIFTI_GZ > >> >>> tkreg2FSL: mov det = 0.163555, ref det = 0.154688 > >> >>> INFO: FSL2FreeSurfer: Mov volume is NIFTI with positive det, > >> >>> applying LR flip to registration matrix. > >> >>> INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det, > >> >>> applying LR flip to registration matrix. > >> >>> > >> >>> here is what I get from fsl_rigid_register: > >> >>> $Id: fsl_rigid_register,v 1.31 2011/03/02 20:16:39 nicks Exp $ > >> >>> Thu Nov 19 17:13:48 EST 2015 > >> >>> fieldmap0001_reg.nii > >> >>> Reference is nifti, not converting > >> >>> Input is nifti, not converting > >> >>> Output is nifti, not converting > >> >>> -------------------------------------- > >> >>> /Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap > >> >>> calling eval flirt.fsl -in ./fieldmap0001.hdr -out > >> >>> ./fieldmap0001_reg.hdr -bins 256 -cost corratio -searchrx -10 10 > >> >>> -searchry -10 10 -searchrz -10 10 -interp trilinear -dof 6 -ref > >> >>> ./epi.hdr -init initxfm.fslmat -omat ./fieldmap0001_reg.fslmat > >> >>> /Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap > >> >>> mri_copy_params --pulse fieldmap0001_reg.nii fieldmap0001.nii > >> >>> fieldmap0001_reg.nii > >> >>> only copying pulse parameters > >> >>> WARNING: volume sizes are different > >> >>> in_vol : 80, 80, 22 > >> >>> temp_vol : 64, 64, 64 > >> >>> WARNING: voxel sizes are different > >> >>> in_vol : 0.375, 0.375, 1.1 > >> >>> temp_vol : 0.546875, 0.546875, 0.546875 > >> >>> -------------------------------------- > >> >>> /Freiwald/cschwiedrz/rodent/test/Rat_673b_Baseline/Phasemap > >> >>> tkregister2_cmdl --targ epi.nii --mov fieldmap0001.nii --reg > >> >>> ./fsl_rigid_register.28592/reg.dat --fslreg > >> >>> fieldmap0001_reg.nii.fslmat --noedit > >> >>> tkregister_tcl > >> >>> > >> > /Freiwald/lab_files/opt/freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0-full/tktools/tkregister2.tcl > >> >>> ---- FSL registration matrix -------- > >> >>> 0.987 -0.164 0.002 0.247; > >> >>> 0.157 0.943 -0.295 -5.691; > >> >>> 0.046 0.291 0.956 7.475; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> --------------------------------------- > >> >>> target volume epi.nii > >> >>> movable volume fieldmap0001.nii > >> >>> reg file ./fsl_rigid_register.28592/reg.dat > >> >>> LoadVol 0 > >> >>> ZeroCRAS 0 > >> >>> $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ > >> >>> Diagnostic Level -1 > >> >>> INFO: loading target epi.nii > >> >>> 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 fieldmap0001.nii > >> >>> Tmov: -------------------- > >> >>> -0.547 0.000 0.000 17.500; > >> >>> 0.000 0.000 0.547 -17.500; > >> >>> 0.000 -0.547 0.000 17.500; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> mkheaderreg = 0, float2int = 0 > >> >>> FSLOUTPUTTYPE NIFTI > >> >>> fsl2TkReg: mov det = 0.163555, ref det = 0.154688 > >> >>> INFO: FSL2FreeSurfer: Mov volume is NIFTI with positive det, > >> >>> applying LR flip to registration matrix. > >> >>> INFO: FSL2FreeSurfer: Ref volume is NIFTI with positive det, > >> >>> applying LR flip to registration matrix. > >> >>> ---- Input registration matrix (computed) -------- > >> >>> -0.987 0.046 -0.157 0.692; > >> >>> -0.002 0.956 0.295 -19.148; > >> >>> -0.164 -0.291 0.943 -0.998; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> --------------------------------------- > >> >>> ---- Input registration matrix -------- > >> >>> -0.987 0.046 -0.157 0.692; > >> >>> -0.002 0.956 0.295 -19.148; > >> >>> -0.164 -0.291 0.943 -0.998; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> Determinant -1 > >> >>> subject = subject-unknown > >> >>> RegMat --------------------------- > >> >>> 0.987 0.046 -0.157 0.692; > >> >>> 0.002 0.956 0.295 -19.148; > >> >>> 0.164 -0.291 0.943 -0.998; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> Cleaning up > >> >>> > >> >>> Started at Thu Nov 19 17:13:48 EST 2015 > >> >>> Ended at Thu Nov 19 17:13:50 EST 2015 > >> >>> > >> >>> fsl_rigid_register Done > >> >>> > >> >>> if I check the results here using tkmedit -f epi.nii -aux > >> >>> fieldmap0001_reg.nii > >> >>> the orientation of fieldmap0001_reg.nii is already wrong. > >> >>> > >> >>> here is what I get from mri_vol2vol: > >> >>> movvol fieldmap_rads.nii.gz > >> >>> targvol epi.nii > >> >>> outvol fieldmap_rads_reg.nii.gz > >> >>> regfile mag_2_mocovol.register.dat > >> >>> invert 0 > >> >>> tal 0 > >> >>> talres 2 > >> >>> regheader 0 > >> >>> noresample 0 > >> >>> interp trilinear (1) > >> >>> precision float (3) > >> >>> Gdiag_no -1 > >> >>> Synth 0 > >> >>> SynthSeed 1448209916 > >> >>> > >> >>> Final tkRAS-to-tkRAS Matrix is: > >> >>> 0.987 0.046 -0.157 0.692; > >> >>> 0.002 0.956 0.295 -19.148; > >> >>> 0.164 -0.291 0.943 -0.998; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> > >> >>> > >> >>> Vox2Vox Matrix is: > >> >>> 0.676 -0.108 -0.093 8.999; > >> >>> 0.112 0.646 0.586 -2.959; > >> >>> -0.002 -0.202 1.922 -16.003; > >> >>> 0.000 0.000 0.000 1.000; > >> >>> > >> >>> Resampling > >> >>> Output registration matrix is identity > >> >>> INFO: wAriting registration matrix to > >> fieldmap_rads_reg.nii.gz.reg > >> >>> > >> >>> checking the result with > >> >>> tkregister2 --mov fieldmap_rads_reg.nii.gz --targ epi.nii --reg > >> >>> fieldmap_rads_reg.nii.gz.reg > >> >>> also yields the wrong orientation, obviously. > >> >>> > >> >>> In this case, I am changing the fieldmap to RIA orientation, > >> >>> although it is actually IPL; doing the same steps with the > >> >>> original IPL orientation gives the same faulty results. > >> >>> > >> >>> this is the code: > >> >>> > >> >>> tkregister2 --s rat \ > >> >>> --targ $epi \ > >> >>> --mov fieldmap0001.nii \ > >> >>> --reg mag_2_mocovol.register.dat \ > >> >>> --fslregout initxfm.fslmat \ > >> >>> --noedit \ > >> >>> --regheader \ > >> >>> --mov-orientation $fieldmap_orient \ > >> >>> --targ-orientation $epi_orient > >> >>> > >> >>> flirt_opts="-maxangle 10 -dof 6 -interp trilinear -bins 256 > >> -cost > >> >>> corratio" > >> >>> fsl_rigid_register -r $epi \ > >> >>> -i fieldmap0001.nii \ > >> >>> -o fieldmap0001_reg.nii \ > >> >>> -regmat mag_2_mocovol.register.dat \ > >> >>> -initxfm initxfm.fslmat \ > >> >>> ${flirt_opts} > >> >>> > >> >>> # apply registration to phase > >> >>> mri_vol2vol --mov fieldmap_rads.nii.gz --targ $epi --o > >> >>> fieldmap_rads_reg.nii.gz --reg mag_2_mocovol.register.dat > >> --trilin > >> >>> > >> >>> Any advice would be appreciated. > >> >>> Thanks! Caspar > >> >>> > >> >>> > >> >>> > >> >>> _______________________________________________ > >> >>> Freesurfer mailing list > >> >>> Freesurfer@nmr.mgh.harvard.edu > >> >>> <mailto:Freesurfer@nmr.mgh.harvard.edu> > >> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> >> > >> >> > >> >> _______________________________________________ > >> >> Freesurfer mailing list > >> >> Freesurfer@nmr.mgh.harvard.edu > >> >> <mailto:Freesurfer@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. > >> >> > >> >> > >> >> > >> >> > >> >> _______________________________________________ > >> >> Freesurfer mailing list > >> >> Freesurfer@nmr.mgh.harvard.edu > >> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > > >> > -- > >> > Douglas N. Greve, Ph.D. > >> > MGH-NMR Center > >> > gr...@nmr.mgh.harvard.edu > >> > Phone Number: 617-724-2358 > >> > Fax: 617-726-7422 > >> > > >> > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > >> > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > >> > Outgoing: > >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > >> > > >> > > >> > > >> > >> > > > >
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