Dear Paul,
Thank you for the quick reply, I don't get an error regarding fslio anymore :)
I do get an error regarding newimage though. Something about "Undefined symbols for architecture x86_64". It is similar to a post by Erika over a year ago (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind1805&L=FSL&D=0&P=86808). I tried building newimage again by cd to $FSLDIR and running "./build newimage", as well as rebuilding everything from source using "./build". I just had some errors for CiftiLib-master, melodic, flameo and oxford_asl, all linked to the file "libxml++.h" not being found. Not sure if this is related to the issue with compiling unring.
Would you have some suggestions on how to proceed from here ? Here's a snapshot of the output in the terminal when I try to compile unring with the edited Makefile.
Thanks again,
David
> make clean
/bin/rm -f /tmp/fslgrot *.o *.a *.exe core depend.mk
> make
/Users/mri/Programs/fsl/config/common/rules.mk:320: depend.mk: No such file or directory
Building dependency file depend.mk
c++ -Wall -pedantic -arch x86_64 -O3 -I/Users/mri/Programs/fsl/extras/include/boost -I/Users/mri/Programs/fsl/extras/include/armawrap/armawrap -DARMA_USE_LAPACK -DARMA_USE_BLAS -I/Users/mri/Programs/fsl/extras/include/boost -I. -I/Users/mri/Programs/fsl/include -I/Users/mri/Programs/fsl/include -c -o unring.o unring.cc
In file included from unring.cc:51:
In file included from /Users/mri/Programs/fsl/include/newimage/newimageall.h:72:
/Users/mri/Programs/fsl/include/newimage/newimage.h:138:9: warning: unknown pragma ignored [-Wunknown-pragmas]
#pragma interface
^
unring.cc:240:6: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete TV1arr;
^
[]
unring.cc:86:22: note: allocated with 'new[]' here
double *TV1arr = new double[2*nsh+1];
^
unring.cc:241:6: warning: 'delete' applied to a pointer that was allocated with 'new[]'; did you mean 'delete[]'? [-Wmismatched-new-delete]
delete TV2arr;
^
[]
unring.cc:87:22: note: allocated with 'new[]' here
double *TV2arr = new double[2*nsh+1];
^
3 warnings generated.
c++ -Wl,-search_paths_first -arch x86_64 -L/Users/mri/Programs/fsl/extras/lib -framework Accelerate -L. -L/Users/mri/Programs/fsl/lib -L/Users/mri/Programs/fsl/lib -o unring unring.o -lwarpfns -lmeshclass -lbasisfield -lnewimage -lmiscmaths -lprob -lniftiio -lznz -lutils -lnewmat -lm -lz -lfftw3
Undefined symbols for architecture x86_64:
"mat44_to_mat33(mat44)", referenced from:
NEWIMAGE::NiftiGetLeftRightOrder(NiftiHeader const&) in libnewimage.a(generalio.o)
"nifti_mat33_determ(mat33)", referenced from:
NEWIMAGE::NiftiGetLeftRightOrder(NiftiHeader const&) in libnewimage.a(generalio.o)
"nifti_mat44_to_orientation(mat44, int*, int*, int*)", referenced from:
MISCMATHS::get_axis_orientations(armawrap::AWMatrix<double> const&, int, armawrap::AWMatrix<double> const&, int, int&, int&, int&) in libmiscmaths.a(miscmaths.o)
"NiftiHeader::setNiftiVersion(char, bool)", referenced from:
int NEWIMAGE::save_unswapped_vol<NEWIMAGE::volume<char> >(NEWIMAGE::volume<char> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, int) in libnewimage.a(generalio.o)
int NEWIMAGE::save_unswapped_vol<NEWIMAGE::volume<short> >(NEWIMAGE::volume<short> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, int) in libnewimage.a(generalio.o)
int NEWIMAGE::save_unswapped_vol<NEWIMAGE::volume<int> >(NEWIMAGE::volume<int> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, int) in libnewimage.a(generalio.o)
int NEWIMAGE::save_unswapped_vol<NEWIMAGE::volume<float> >(NEWIMAGE::volume<float> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, int) in libnewimage.a(generalio.o)
int NEWIMAGE::save_unswapped_vol<NEWIMAGE::volume<double> >(NEWIMAGE::volume<double> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&, int, int) in libnewimage.a(generalio.o)
NEWIMAGE::save_complexvolume(NEWIMAGE::volume<float> const&, NEWIMAGE::volume<float> const&, std::__1::basic_string<char, std::__1::char_traits<char>, std::__1::allocator<char> > const&) in libnewimage.a(generalio.o)
"NiftiHeader::setQForm(mat44 const&)", referenced from:
int NEWIMAGE::set_fsl_hdr<float>(NEWIMAGE::volume<float> const&, NiftiHeader&) in libnewimage.a(generalio.o)
int NEWIMAGE::set_fsl_hdr<char>(NEWIMAGE::volume<char> const&, NiftiHeader&) in libnewimage.a(generalio.o)
int NEWIMAGE::set_fsl_hdr<short>(NEWIMAGE::volume<short> const&, NiftiHeader&) in libnewimage.a(generalio.o)
int NEWIMAGE::set_fsl_hdr<int>(NEWIMAGE::volume<int> const&, NiftiHeader&) in libnewimage.a(generalio.o)
int NEWIMAGE::set_fsl_hdr<double>(NEWIMAGE::volume<double> const&, NiftiHeader&) in libnewimage.a(generalio.o)
...
"NiftiHeader::getQForm() const", referenced from:
void NEWIMAGE::set_volume_properties<char>(NiftiHeader const&, NEWIMAGE::volume<char>&) in libnewimage.a(generalio.o)
NEWIMAGE::NiftiGetLeftRightOrder(NiftiHeader const&) in libnewimage.a(generalio.o)
void NEWIMAGE::set_volume_properties<short>(NiftiHeader const&, NEWIMAGE::volume<short>&) in libnewimage.a(generalio.o)
void NEWIMAGE::set_volume_properties<int>(NiftiHeader const&, NEWIMAGE::volume<int>&) in libnewimage.a(generalio.o)
void NEWIMAGE::set_volume_properties<float>(NiftiHeader const&, NEWIMAGE::volume<float>&) in libnewimage.a(generalio.o)
void NEWIMAGE::set_volume_properties<double>(NiftiHeader const&, NEWIMAGE::volume<double>&) in libnewimage.a(generalio.o)
"NiftiHeader::getSForm() const", referenced from:
void NEWIMAGE::set_volume_properties<char>(NiftiHeader const&, NEWIMAGE::volume<char>&) in libnewimage.a(generalio.o)
NEWIMAGE::NiftiGetLeftRightOrder(NiftiHeader const&) in libnewimage.a(generalio.o)
void NEWIMAGE::set_volume_properties<short>(NiftiHeader const&, NEWIMAGE::volume<short>&) in libnewimage.a(generalio.o)
void NEWIMAGE::set_volume_properties<int>(NiftiHeader const&, NEWIMAGE::volume<int>&) in libnewimage.a(generalio.o)
void NEWIMAGE::set_volume_properties<float>(NiftiHeader const&, NEWIMAGE::volume<float>&) in libnewimage.a(generalio.o)
void NEWIMAGE::set_volume_properties<double>(NiftiHeader const&, NEWIMAGE::volume<double>&) in libnewimage.a(generalio.o)
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [unring] Error 1
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