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
|