Hi - this _may_ be a problem with our libraries, but more likely it is
just that you need a 64-bit machine to run this, because of memory
requirements.
Cheers.
On 12 Mar 2008, at 10:21, Hedok Lee wrote:
> Dear Brian,
>
> Thanks for your response. Please refer to the screen shot (40KB) for
> raw image, and also segmentation done by Centos4 64 bit.
>
> Image is acquired axially and its resolution is 1mm x 1mm x 1.5mm.
> It also contains slight motion artifacts.
> Let me know if you find something unusual about the image.
>
> With this image, I don't run into the problem with the 64-bit OS but
> RedHat4 32 bit machine always fails to complete, so I thought it's
> related with platform specific issue. I tested the same image with
> Fedora 5 32bit, and resulted the same error.
>
>
> Thanks for your help.
>
> Hedok
>
>
> Brian Patenaude wrote:
>> Hi,
>>
>> The images for which the brain stem fails, how far down is the
>> brainstem
>> truncated by the image.
>> My best guess without looking at the data is that the model is
>> extending
>> beyond the image, and it fails when it attempts to sample those
>> voxels
>> that don't exist.
>>
>> Cheers,
>>
>> Brian
>>
>>
>>
>>
>>> Dear FSLers:
>>>
>>> I'm still struggling with one scan that is persistently causing an
>>> error
>>> (segmentation fault). So I decided to try a few things.
>>>
>>> #1 Upgraded from 4.0.1 to 4.0.3 This did not help. Same problem as
>>> before.
>>>
>>> #2 Compile FIRST.
>>>
>>> After typing " make" in "/src/first/", it produced two binaries
>>> ("first" and "first_utils"). I then moved those two binaries to
>>> "/usr/fsl/bin" directories, and ran "run_first_all" again. Is
>>> this right?
>>>
>>> It's now giving me error like this " *** glibc detected *** free():
>>> invalid pointer: 0x081e7140 *"
>>>
>>> I'm sure I made mistakes somewhere in the process. I appreciate if
>>> someone can help me with what I did wrong here.
>>>
>>> Thanks,
>>> Hedok
>>>
>>> ***After running make, this is what I get***
>>> /usr/local/fsl/config/common/rules.mk:320: depend.mk: No such file
>>> or
>>> directory
>>> Building dependency file depend.mk
>>> c++ -Wall -ansi -pedantic -Wno-long-long -march=i686 -mcpu=i686
>>> -O3
>>> -fexpensive-optimizations -march=i686 -mcpu=i686
>>> -I/usr/local/fsl/extras/include/newmat -I. -I/include
>>> -I/usr/local/fsl/include -c -o first.o first.cc
>>> c++ -Wall -ansi -pedantic -Wno-long-long -march=i686 -mcpu=i686
>>> -O3
>>> -fexpensive-optimizations -march=i686 -mcpu=i686
>>> -I/usr/local/fsl/extras/include/newmat -I. -I/include
>>> -I/usr/local/fsl/include -L/usr/local/fsl/extras/lib -L. -L/lib
>>> -L/usr/local/fsl/lib -o first first.o -lshapeModel -lmeshclass
>>> -lnewimage -lprob -lmiscmaths -lfslio -lniftiio -lznz -lnewmat -
>>> lutils
>>> -lz
>>> c++ -Wall -ansi -pedantic -Wno-long-long -march=i686 -mcpu=i686
>>> -O3
>>> -fexpensive-optimizations -march=i686 -mcpu=i686
>>> -I/usr/local/fsl/extras/include/newmat -I. -I/include
>>> -I/usr/local/fsl/include -c -o first_utils.o first_utils.cc
>>> c++ -Wall -ansi -pedantic -Wno-long-long -march=i686 -mcpu=i686
>>> -O3
>>> -fexpensive-optimizations -march=i686 -mcpu=i686
>>> -I/usr/local/fsl/extras/include/newmat -I. -I/include
>>> -I/usr/local/fsl/include -L/usr/local/fsl/extras/lib -L. -L/lib
>>> -L/usr/local/fsl/lib -o first_utils first_utils.o -lshapeModel
>>> -lmeshclass -lnewimage -lprob -lmiscmaths -lfslio -lniftiio -lznz
>>> -lnewmat -lutils -lz
>>>
>>>
>>> ***After running run_first_all with newly compiled binaries, this is
>>> what I get***
>>> [matlab@hyperion test2]$ run_first_all mSPGR_MiTa102507 3
>>> mSPGR_MiTa102507
>>> /usr/local/fsl/bin/first_flirt mSPGR_MiTa102507
>>> mSPGR_MiTa102507_to_std
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7140 ***
>>> *** glibc detected *** free(): invalid pointer: 0x081e7c80 ***
>>> 16593
>>>
>>>
>>>
>>>
>>>
>>>
>>> Hedok Lee wrote:
>>>
>>>> Dear FSLers
>>>>
>>>> I’m having a problem with completing “run_first_all”, and I hope
>>>> someone
>>>> can help me with this. I’m running the command with default
>>>> options, and
>>>> occasionally it fails to complete. The problem comes and goes,
>>>> so I
>>>> looked
>>>> into the script “run_first_all” today to track down exactly where
>>>> it
>>>> fails.
>>>>
>>>> After registering input file with the standard brain, there is a
>>>> loop
>>>> where
>>>> it runs “run_first” for every structure, and commands are stored in
>>>> “com”
>>>> file. The "com" file looks fine except it fails to execute with
>>>> “Brain
>>>> stem”. This is what I get when I run the command stored in the
>>>> “com”
>>>> file
>>>> manually. It works fine except brain stem. Note also that it only
>>>> happens
>>>> occasionally(10% of time).
>>>>
>>>>
>>>> /usr/local/fsl/bin/run_first -i mSPGR_MiTa102507 -t
>>>> mSPGR_MiTa102507_to_std.mat -n 40 -o mSPGR_MiTa102507-
>>>> BrStem_first -
>>>> m /usr/local/fsl/data/first/models_317_bin/BrStem_bin.bmv
>>>> /usr/local/fsl/bin/run_first: line 144: 27190 Segmentation fault
>>>> ${FSLDIR}/bin/first --baam -i $image -l $trmat -m $model -k
>>>> $outname -s
>>>> 8 -
>>>> g $modes -y $lb -z $ub -a -777 $verbose $comExtras
>>>>
>>>> As you can see I get the segmentation fault.
>>>>
>>>> This problem occurred when I used RedHat 4 32bit, but disappeared
>>>> with
>>>> Centos 4 64bit.
>>>>
>>>> There is another thread reporting similar problem but I couldn’t
>>>> find
>>>> any
>>>> follow up on that, so let me know if anyone has a solution for
>>>> this.
>>>> http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0802&L=FSL&P=R30689&I=-3
>>>>
>>>>
>>>> I checked the registration quality and it looks fine to me.
>>>> See the attachment for the screenshot.
>>>>
>>>>
>>>> Thanks,
>>>>
>>>> Hedok
>>>>
>>>>
>>>
>
> <Screen_shot.JPG>
---------------------------------------------------------------------------
Stephen M. Smith, Professor of Biomedical Engineering
Associate Director, Oxford University FMRIB Centre
FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
+44 (0) 1865 222726 (fax 222717)
[log in to unmask] http://www.fmrib.ox.ac.uk/~steve
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