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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
[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 [log in to unmask]">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