Hi - please see MJ's reply from before....
Cheers.
On 2 Jan 2014, at 10:26, 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
> [nmrsu@dhcppc4 ~]$ make rBet
> make: *** No rule to make target `rbet'. Stop.
> regards
>
>
> On 2/25/13, Mark Jenkinson <[log in to unmask]> wrote:
>> Hi,
>>
>> I'm afraid this isn't code that was produced by the FSL team, so you will
>> have to rely on help from the authors.
>>
>> All the best,
>> Mark
>>
>>
>> On 24 Feb 2013, at 14:31, 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
>>
>>
>
>
> --
> Sunil Koundal
> Senior Research Fellow
> NMR Research Centre
> INMAS, DRDO
> DELHI-54
> Mobile number -+919910969525
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FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
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