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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