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 zkaufman@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 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 magnitudemap
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 tofieldmap_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.edumailto: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 errorand
the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sentto
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 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/
Oh, Sorry about that, I was unaware you were using freesurfer v5.1 on an older RedHat system.
Freesurfer v5.1 was released quite awhile ago and its entirely possible that the newest development version of the freesurfer binaries are not compatible with it. But here is a link to our centos4 build which in theory has the best shot of working on your system:
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos4_x86_64/mri_coreg
Please give it a shot, and sorry for the initial confusion.
-Zeke
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 zkaufman@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 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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 personto
whom it is addressed. If you believe this e-mail was sent to you in errorand
the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail wassent
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 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/
Hi Zeke, thanks for providing the link, and sorry for not clarifying which version I am using earlier. The centos4 version you provided now does not throw the previous errors. Thanks again, Caspar
2015-11-23 14:54 GMT-05:00 zkaufman@nmr.mgh.harvard.edu:
Oh, Sorry about that, I was unaware you were using freesurfer v5.1 on an older RedHat system.
Freesurfer v5.1 was released quite awhile ago and its entirely possible that the newest development version of the freesurfer binaries are not compatible with it. But here is a link to our centos4 build which in theory has the best shot of working on your system:
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos4_x86_64/mri_coreg
Please give it a shot, and sorry for the initial confusion.
-Zeke
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 zkaufman@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 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 > > > _______________________________________________ > 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
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-- 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/
freesurfer@nmr.mgh.harvard.edu
-
Caspar M. Schwiedrzik -
zkaufman＠nmr.mgh.harvard.edu