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 <zkaufman@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 <greve@nmr.mgh.harvard.edu
>> >> <mailto:greve@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
>> >>
>> >>
>> >> _______________________________________________
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>> >> <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >>
>> >>
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>> >>
>> >>
>> >> _______________________________________________
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>> >> Freesurfer@nmr.mgh.harvard.edu
>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>> >
>> > --
>> > Douglas N. Greve, Ph.D.
>> > MGH-NMR Center
>> > greve@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/
>> >
>> >
>> >
>>
>>
>