Hello,
Did you ever figure out the problem?
I too have experienced this same issue when trying to build FSL from source and then trying to install rbet.
I get stuck on the last step as well, after typing "make rbet"
c++ -Wall -ansi -pedantic -Wno-long-long -m64 -O3 -fexpensive-optimizations -m64 -I/data3/transfer/fslbuild/fsl/extras/include/newmat -I/data3/transfer/fslbuild/fsl/extras/include -I../ -I. -I/include -I/data3/transfer/fslbuild/fsl/include -L../meshclass -L/data3/transfer/fslbuild/fsl/extras/lib -L/data3/transfer/fslbuild/fsl/extras/lib -L. -L/lib -L/data3/transfer/fslbuild/fsl/lib -o rbet bet2.o -lmeshclass -lnewimage -lprob -lmiscmaths -lfslio -lniftiio -lznz -lnewmat -lutils -lz
bet2.o: In function `adjust_initial_mesh(NEWIMAGE::volume<float> const&, mesh::Mesh&, double, double, double, double, bool const&, double const&, double const&, double const&)':
bet2.cpp:(.text+0x49fc): undefined reference to `mesh::Mesh::rescale(double, double, double, mesh::Pt)'
collect2: ld returned 1 exit status
make: *** [rbet] Error 1
I've tried just about everything. I'm running Ubuntu 10.04. I've tried to build FSL from source, using the Debian package, etc. Still, no success installing rbet.
Anyone else have success installing it?
D. Michael
On Sun, 24 Feb 2013 20:01:57 +0530, sunil koundal <[log in to unmask]> wrote:
>Dear FSL users ,
> while installing rBET i got problem at last
>step.please suggest any way to fix it :(
> any help would be highly appreciated.
>[root@localhost rbet]# make rbet
>c++ -Wall -ansi -pedantic -Wno-long-long -m64 -O3
>-fexpensive-optimizations -m64 -I/fsl/fsl/extras/include/newmat
>-I/fsl/fsl/extras/include -I../ -I. -I/include -I/fsl/fsl/include -c
>-o bet2.o bet2.cpp
>bet2.cpp: In function ‘bet_parameters adjust_initial_mesh(const
>NEWIMAGE::volume<float>&, mesh::Mesh&, double, double, double, double,
>const bool&, const double&, const double&, const double&)’:
>bet2.cpp:377: warning: suggest parentheses around comparison in operand of ‘&’
>bet2.cpp:377: warning: suggest parentheses around comparison in operand of ‘&’
>bet2.cpp: In function ‘int main(int, char**)’:
>bet2.cpp:746: warning: suggest parentheses around comparison in operand of ‘|’
>c++ -Wall -ansi -pedantic -Wno-long-long -m64 -O3
>-fexpensive-optimizations -m64 -I/fsl/fsl/extras/include/newmat
>-I/fsl/fsl/extras/include -I../ -I. -I/include -I/fsl/fsl/include
>-L../meshclass -L/fsl/fsl/extras/lib -L/fsl/fsl/extras/lib -L. -L/lib
>-L/fsl/fsl/lib -o rbet bet2.o -lmeshclass -lnewimage -lprob
>-lmiscmaths -lfslio -lniftiio -lznz -lnewmat -lutils -lz
>bet2.o: In function `adjust_initial_mesh(NEWIMAGE::volume<float>
>const&, mesh::Mesh&, double, double, double, double, bool const&,
>double const&, double const&, double const&)':
>bet2.cpp:(.text+0x490c): undefined reference to
>`mesh::Mesh::rescale(double, double, double, mesh::Pt)'
>collect2: ld returned 1 exit status
>make: *** [rbet] Error 1
>
>
>
>Regards
>sunil
>
>
>On Fri, Feb 22, 2013 at 5:14 AM, Chan Hoi Fong <[log in to unmask]> wrote:
>> Hi,
>> I also got a problem with initiation of rbet on fsl. I am using OSX and
>> fsl5.0. When I typed the make rbet according to the website's instruction,
>> it shows
>> Billmbp:rbet chanhoifong$ make rbet c++ -Wall -Wno-long-long -ansi -pedantic
>> -arch i386 -arch x86_64 -O3 -fexpensive-optimizations
>> -I/usr/local/fsl/extras/include/newmat -I/usr/local/fsl/extras/include -I../
>> -I. -I/include -I/usr/local/fsl/include -c -o bet2.o bet2.cpp clang:
>> warning: argument unused during compilation: '-fexpensive-optimizations' In
>> file included from bet2.cpp:81: In file included from
>> /usr/local/fsl/include/newimage/newimageall.h:72:
>> /usr/local/fsl/include/newimage/newimage.h:111:9: warning: unknown pragma
>> ignored [-Wunknown-pragmas] #pragma interface ^ In file included from
>> bet2.cpp:81: In file included from
>> /usr/local/fsl/include/newimage/newimageall.h:73:
>> /usr/local/fsl/include/newimage/newimageio.h:863:14: warning: & has lower
>> precedence than ==; == will be evaluated first [-Wparentheses] if (retval &
>> 1 == 1) { handle_read_error(retval,filename); } ^~~~~~~~
>> /usr/local/fsl/include/newimage/newimageio.h:863:14: note: place parentheses
>> around the == expression to silence this warning if (retval & 1 == 1) {
>> handle_read_error(retval,filename); } ^ ( )
>> /usr/local/fsl/include/newimage/newimageio.h:863:14: note: place parentheses
>> around the & expression to evaluate it first if (retval & 1 == 1) {
>> handle_read_error(retval,filename); } ^ ( )
>> /usr/local/fsl/include/newimage/newimageio.h:871:14: warning: & has lower
>> precedence than ==; == will be evaluated first [-Wparentheses] if (retval &
>> 1 == 1) { handle_read_error(retval,filename); } ^~~~~~~~
>> /usr/local/fsl/include/newimage/newimageio.h:871:14: note: place parentheses
>> around the == expression to silence this warning if (retval & 1 == 1) {
>> handle_read_error(retval,filename); } ^ ( )
>> /usr/local/fsl/include/newimage/newimageio.h:871:14: note: place parentheses
>> around the & expression to evaluate it first if (retval & 1 == 1) {
>> handle_read_error(retval,filename); } ^ ( ) In file included from
>> bet2.cpp:81: In file included from
>> /usr/local/fsl/include/newimage/newimageall.h:74:
>> /usr/local/fsl/include/newimage/newimagefns.h:1402:148: error: redefinition
>> of default argument ...int num_usan,volume<T>* usan_area = new
>> volume<T>(1,1,1),volume<T>... ^ ~~~~~~~~~~~~~~~~~~~~
>> /usr/local/fsl/include/newimage/newimagefns.h:366:142: note: previous
>> definition is here ...int num_usan,volume<T>* usan_area = new
>> volume<T>(1,1,1),volume<T>... ^ ~~~~~~~~~~~~~~~~~~~~
>> /usr/local/fsl/include/newimage/newimagefns.h:1402:191: error: redefinition
>> of default argument ...= new volume<T>(1,1,1),volume<T>
>> usan_vol1=volume<T>(1,1,1), const float... ^ ~~~~~~~~~~~~~~~~
>> /usr/local/fsl/include/newimage/newimagefns.h:366:185: note: previous
>> definition is here ...= new volume<T>(1,1,1),volume<T>
>> usan_vol1=volume<T>(1,1,1), const float... ^ ~~~~~~~~~~~~~~~~
>> /usr/local/fsl/include/newimage/newimagefns.h:1402:230: error: redefinition
>> of default argument ...usan_vol1=volume<T>(1,1,1),const float
>> sigmab1sq=0,volume<T> usan_vol2 =... ^ ~
>> /usr/local/fsl/include/newimage/newimagefns.h:366:224: note: previous
>> definition is here ...usan_vol1=volume<T>(1,1,1),const float
>> sigmab1sq=0,volume<T> usan_vol2 =... ^ ~
>> /usr/local/fsl/include/newimage/newimagefns.h:1402:252: error: redefinition
>> of default argument ...float sigmab1sq=0,volume<T> usan_vol2 =
>> volume<T>(1,1,1),const float... ^ ~~~~~~~~~~~~~~~~
>> /usr/local/fsl/include/newimage/newimagefns.h:366:246: note: previous
>> definition is here ...float sigmab1sq=0,volume<T> usan_vol2 =
>> volume<T>(1,1,1),const float... ^ ~~~~~~~~~~~~~~~~
>> /usr/local/fsl/include/newimage/newimagefns.h:1402:293: error: redefinition
>> of default argument ...usan_vol2 = volume<T>(1,1,1),const float sigmab2sq=0)
>> ^ ~ /usr/local/fsl/include/newimage/newimagefns.h:366:287: note: previous
>> definition is here ...usan_vol2 = volume<T>(1,1,1),const float sigmab2sq=0);
>> ^ ~ /usr/local/fsl/include/newimage/newimagefns.h:2050:91: error:
>> redefinition of default argument ...const volume<S>& kernel, bool
>> seperable=false, bool renormalise=true) ^ ~~~~~
>> /usr/local/fsl/include/newimage/newimagefns.h:369:91: note: previous
>> definition is here ...const volume<S>& kernel, bool seperable=false, bool
>> renormalise=true); ^ ~~~~~
>> /usr/local/fsl/include/newimage/newimagefns.h:2050:113: error: redefinition
>> of default argument ...const volume<S>& kernel, bool seperable=false, bool
>> renormalise=true) ^ ~~~~
>> /usr/local/fsl/include/newimage/newimagefns.h:369:113: note: previous
>> definition is here ...const volume<S>& kernel, bool seperable=false, bool
>> renormalise=true); ^ ~~~~ 3 warnings and 7 errors generated. make: ***
>> [bet2.o] Error 1
>>
>> Anyone have idea what's wrong here?
>> Many thanks!
>> Hoifong
>>
>> 2013-2-21 下午11:09 於 "D. Michael" <[log in to unmask]> 寫道:
>>
>>> Hello,
>>>
>>> I had the deny permission issue initally as well. I registered an account
>>> with the nitrc group early in the morning, but by the afternoon it accepted
>>> the password.
>>>
>>> However, I'm having some issues getting rbet to run.
>>>
>>> I followed the instructions and when i typed "make rbet".
>>>
>>> I received this message:
>>>
>>> Makefile:2: /default.mk: No such file or directory
>>> make: *** No rule to make target `/default.mk'. Stop.
>>>
>>>
>>> I have FSL setup through the Debian package on Ubuntu 10.04. I could not
>>> locate the default.mk file.
>>>
>>> Also, it is my understanding that it needed the environmental variables,
>>> $FSLCONFDIR and $FSLMACHTYPE, set for the "make rbet" to work.
>>>
>>> How are these variables assigned. They currently aren't in our setup.
>>>
>>> Anyone else have the same issues?
>>>
>>> Thanks,
>>>
>>> D. Michael
>>>
>>> On Wed, 20 Feb 2013 22:15:05 +0800, Chan Hoi Fong <[log in to unmask]>
>>> wrote:
>>>
>>> >Se�n
>>> > Thanks for your help. But i have some problem with the installation. I
>>> >have registered on NITRC and do the git clone as the website mention. But
>>> >during the installation on terminal , after i typed the
>>> > *git clone ssh:[log in to unmask] . *
>>> >( i have changed the user to my user name) ,it required me to type my
>>> >password. It just show permission denied and the dont let me complete the
>>> >installation. Do i need to apply the tool in their website?
>>> >hoifong
>>> >
>>> >
>>> >
>>> >On Wed, Feb 20, 2013 at 4:19 PM, Sean F Walsh <[log in to unmask]> wrote:
>>> >
>>> >> Hi Hoi Fong,
>>> >>
>>> >> You may also want to try Toby Wood's optimisation of BET for the rodent
>>> >> brain, available here:
>>> >>
>>> >>
>>> >> http://www.kcl.ac.uk/iop/depts/neuroimaging/research/imaginganalysis/Software/rBET.aspx
>>> >>
>>> >> All the best,
>>> >>
>>> >> Se�n
>>> >>
>>> >
>>> >
>>> >
>>> >--
>>> >Hoi Fong, Chan, MD
>>> >En Chu Kong hospital, Department of neurology
>>> >National Taiwan University , Department of anatomy and cell biology
>>> >Taipei
>>> >
>
>
>
>--
>Sunil Koundal
>Senior Research Fellow
>NMR Research Centre
>INMAS, DRDO
>DELHI-54
>Mobile number -+919910969525
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