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/ > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
