Dear Chris,
We have got to the bottom of this issue and it is simply a case of
out-of-date nifti libraries being used in the current FSL release
on the non-Ubuntu/Debian platforms. We will be updating these
soon and hence this problem will disappear.
Hope that it hasn't caused a lot of inconvenience.
All the best,
Mark
On 3 Mar 2011, at 14:47, Chris Adamson wrote:
> No worries.
>
> I'm not sure why the compiled binaries from the fsl website dont have the problem but the Ubuntu packaged versions use the external nifticlib library that already uses char* arrays instead of structs for byteswapping...
>
> Chris.
>
> Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash)
> Research Officer
> Developmental and Functional Brain Imaging, Critical Care and Neurosciences
>
> Murdoch Childrens Research Institute
> The Royal Children’s Hospital
> Flemington Road Parkville Victoria 3052 Australia
> T 9345 4306
> M XXXX XXX XXX
> E [log in to unmask]
> www.mcri.edu.au
>
>
>
>
> -----Original Message-----
> From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson
> Sent: Wed 2/03/2011 12:19 PM
> To: [log in to unmask]
> Subject: Re: [FSL] Help with fslstats error
>
> Dear Chris,
>
> Thank you very much for this - I had not heard of it before and it is quite serious.
> We will definitely be taking action on this.
>
> Thanks,
> Mark
>
>
> On 2 Mar 2011, at 16:34, Chris Adamson wrote:
>
>> I have been able to reliably reproduce the byteswapping error that I said was caused in nifti1_io.c
>>
>> I downloaded fsl-4.1.7-sources.tar.gz
>>
>> extracted it and applied the debian package patches to get it to compile: (none of these apply to the file in question)
>>
>> Description: Fix bashisms in the code.
>> --- a/src/possum/possumX
>> +++ b/src/possum/possumX
>> @@ -98,7 +98,7 @@
>> fi
>>
>> echo "POSSUMDIR (before)" $POSSUMDIR
>> -if [ "${POSSUMDIR}" == "${FSLDEVDIR}" ] ; then
>> +if [ "${POSSUMDIR}" = "${FSLDEVDIR}" ] ; then
>> echo "POSSUMDIR (during)" $POSSUMDIR
>> else
>> export POSSUMDIR=$FSLDIR
>> --- a/src/possum/possumX_postproc.sh
>> +++ b/src/possum/possumX_postproc.sh
>> @@ -77,7 +77,7 @@
>> #$ -m ae
>>
>> echo "POSSUMDIR (before)" $POSSUMDIR
>> -if [ "${POSSUMDIR}" == "${FSLDEVDIR}" ] ; then
>> +if [ "${POSSUMDIR}" = "${FSLDEVDIR}" ] ; then
>> echo "POSSUMDIR (during)" $POSSUMDIR
>> else
>> export POSSUMDIR=$FSLDIR
>>
>>
>> Description: Fix critical syntax error.
>> --- a/src/fdt/rotate_bvecs
>> +++ b/src/fdt/rotate_bvecs
>> @@ -18,7 +18,7 @@
>> echo "If you want to force this program to run, please remove the file ${bvecs}_old"
>> echo ""
>> exit 1
>> -done
>> +fi
>> /bin/cp ${bvecs} ${bvecs}_old
>> #/bin/rm -f ${bvecs}
>>
>> Description: Prevent fslmath from crashing with -tfce option set
>> Origin: vendor
>> --- a/src/avwutils/fslmaths.cc 2011-01-13 06:09:39.000000000 -0500
>> +++ b/src/avwutils/fslmaths.cc 2011-03-02 09:03:00.715017995 -0500
>> @@ -940,7 +940,8 @@
>>
>> for(int t=0;t<inputVolume.tsize();t++) {
>> try {
>> - tfce(inputVolume[t], height_power, size_power, connectivity, 0, 0);
>> + /*tfce(input_volume[t], height_power, size_power, connectivity, 0, 0);*/
>> + tfce(inputVolume[t], height_power, size_power, connectivity, 0, inputVolume[t].max()/100.0);
>> }
>> catch(Exception& e) {
>> cerr << "ERROR: TFCE failed, please check your file for valid sizes and voxel values." << e.what() << endl << endl << "Exiting" << endl;
>>
>> Description: Patch to allow building with recent GCC versions
>> --- a/src/fabber/tools.cc
>> +++ b/src/fabber/tools.cc
>> @@ -68,6 +68,7 @@
>>
>> #include "tools.h"
>> #include "easylog.h"
>> +#include <limits>
>>
>> double DescendingZeroFinder::FindZero() const
>> {
>> --- a/src/possum/possumfns.h
>> +++ b/src/possum/possumfns.h
>> @@ -11,9 +11,9 @@
>> void voxel4(const double x,const double y,const double z,
>> const RowVector& tissue,const Matrix& H,const int nreadp,const int v,
>> const double xdim,const double ydim,const double zdim,
>> - const double* b0, const double* b0gxx,const double* b0gyy,const double* b0gzz,
>> + const double* b0time, const double* b0xtime,const double* b0ytime,const double* b0ztime,
>> const double* b0timecourse,const int Nb0,
>> - const double b0, const double b0gxx,const double b0gyy,const double b0gzz,
>> + const double b0, const double b0x,const double b0y,const double b0z,
>> const double* timecourse,const double* activation,const int Nact,
>> const string outputname, const double* table_slcprof, const double dslcp, const double dslcp_first, const int Nslc,
>> const double den,const double RFtrans, const int opt_test,
>>
>> Description: Compatibility with the Debian gdchart package code.
>> --- a/src/libvis/miscplot.cc
>> +++ b/src/libvis/miscplot.cc
>> @@ -79,6 +79,7 @@
>> #include "gd.h"
>> #include "gdc.h"
>> #include "gdchart.h"
>> + #include "gdcpie.h"
>> }
>>
>> namespace MISCPLOT{
>>
>> Description: Cosmetics.
>> --- a/extras/build
>> +++ b/extras/build
>> @@ -107,4 +107,4 @@
>>
>> if [ "X${errorprojs}X" != XX -o "X${errorinstall}X" != XX ] ; then
>> exit 1
>> -fi
>> \ No newline at end of file
>> +fi
>>
>> Description: Cosmetics.
>> --- a/extras/build
>> +++ b/extras/build
>> @@ -107,4 +107,4 @@
>>
>> if [ "X${errorprojs}X" != XX -o "X${errorinstall}X" != XX ] ; then
>> exit 1
>> -fi
>> \ No newline at end of file
>> +fi
>> addo@ada4jc:/data/backup/data/programs/debian/patches$ cat tcl_shell_spec
>> Description: Specific the TCL interpreter.
>> --- a/src/misc_tcl/Runtcl
>> +++ b/src/misc_tcl/Runtcl
>> @@ -1,5 +1,8 @@
>> #!/bin/sh
>>
>> +# Set TCLTKSHELL \
>> +TCLTKSHELL=wish ; export TCLTKSHELL
>> +
>> # Check for display being set \
>> if [ _$DISPLAY = _ ] ; then echo "DISPLAY is not set. Please set your DISPLAY environment variable!" ; exit 1 ; fi
>> # Check for FSLDIR being set \
>>
>> Description: Fix tk problem
>> --- generic/tk.h.orig 2008-02-06 16:31:40.000000000 +0100
>> +++ generic/tk.h 2008-07-24 08:21:46.000000000 +0200
>> @@ -635,17 +635,15 @@
>> *
>> *---------------------------------------------------------------------------
>> */
>> -#define VirtualEvent (LASTEvent)
>> -#define ActivateNotify (LASTEvent + 1)
>> -#define DeactivateNotify (LASTEvent + 2)
>> -#define MouseWheelEvent (LASTEvent + 3)
>> -#define TK_LASTEVENT (LASTEvent + 4)
>> +#define VirtualEvent (MappingNotify + 1)
>> +#define ActivateNotify (MappingNotify + 2)
>> +#define DeactivateNotify (MappingNotify + 3)
>> +#define MouseWheelEvent (MappingNotify + 4)
>> +#define TK_LASTEVENT (MappingNotify + 5)
>>
>> #define MouseWheelMask (1L << 28)
>> -
>> #define ActivateMask (1L << 29)
>> #define VirtualEventMask (1L << 30)
>> -#define TK_LASTEVENT (LASTEvent + 4)
>>
>>
>> /*
>>
>> Then when it compiles it copies the generic configuration to gnu_64-gcc4.4
>> I modified the OPTFLAGS line in systemvars.mk file:
>> OPTFLAGS = -O3 -fexpensive-optimizations ${ARCHFLAGS}
>> ${ARCHFLAGS} is empty
>>
>> So here are the outputs:
>> No optimisations: -O0
>> fslhd data/standard/LowerCingulum_1mm.nii.gz
>> Byte swapping
>> filename data/standard/LowerCingulum_1mm.nii.gz
>>
>> sizeof_hdr 348
>> data_type FLOAT32
>> dim0 3
>> dim1 182
>> dim2 218
>> dim3 182
>> dim4 1
>> dim5 1
>> dim6 1
>> dim7 1
>> vox_units mm
>> time_units s
>> datatype 16
>> nbyper 4
>> bitpix 32
>> pixdim0 0.0000000000
>> pixdim1 1.0000152588
>> pixdim2 1.0000000000
>> pixdim3 1.0000000000
>> pixdim4 1.0000000000
>> pixdim5 1.0000000000
>> pixdim6 1.0000000000
>> pixdim7 1.0000000000
>> vox_offset 352
>> cal_max 4.0000
>> cal_min 0.0000
>> scl_slope 1.000000
>> scl_inter 0.000000
>> phase_dim 0
>> freq_dim 0
>> slice_dim 0
>> slice_name Unknown
>> slice_code 0
>> slice_start 0
>> slice_end 0
>> slice_duration 0.000000
>> time_offset 0.000000
>> intent Unknown
>> intent_code 0
>> intent_name
>> intent_p1 0.000000
>> intent_p2 0.000000
>> intent_p3 0.000000
>> qform_name Unknown
>> qform_code 0
>> qto_xyz:1 1.000015 0.000000 0.000000 0.000000
>> qto_xyz:2 0.000000 1.000000 0.000000 0.000000
>> qto_xyz:3 0.000000 0.000000 1.000000 0.000000
>> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
>> qform_xorient Left-to-Right
>> qform_yorient Posterior-to-Anterior
>> qform_zorient Inferior-to-Superior
>> sform_name Unknown
>> sform_code 0
>> sto_xyz:1 0.000000 0.000000 0.000000 0.000000
>> sto_xyz:2 0.000000 0.000000 0.000000 0.000000
>> sto_xyz:3 0.000000 0.000000 0.000000 0.000000
>> sto_xyz:4 0.000000 0.000000 0.000000 0.000000
>> sform_xorient Unknown
>> sform_yorient Unknown
>> sform_zorient Unknown
>> file_type NIFTI-1+
>> file_code 1
>> descrip FSL3.2beta
>> aux_file Red to yellow?@
>>
>> Optimisations: -O2
>> fslhd data/standard/LowerCingulum_1mm.nii.gz ** ERROR: nifti_convert_nhdr2nim: bad dim[0]
>> ** ERROR (nifti_image_read): cannot create nifti image from header 'data/standard/LowerCingulum_1mm.nii.gz'
>> ** ERROR: nifti_image_open(data/standard/LowerCingulum_1mm): bad header info
>> Error: failed to open file data/standard/LowerCingulum_1mm
>> ERROR: Could not open file
>>
>> Optimisations: -O3 -fexpensive-optimizations
>> fslhd data/standard/LowerCingulum_1mm.nii.gz ** ERROR: nifti_convert_nhdr2nim: bad dim[0]
>> ** ERROR (nifti_image_read): cannot create nifti image from header 'data/standard/LowerCingulum_1mm.nii.gz'
>> ** ERROR: nifti_image_open(data/standard/LowerCingulum_1mm): bad header info
>> Error: failed to open file data/standard/LowerCingulum_1mm
>> ERROR: Could not open file
>>
>> to test this I turned on debugging in src/niftiio/nifti1_io.c
>>
>> line 299: static nifti_global_options g_opts = { 4, 0 };
>>
>> ** find_file_ext: failed for name 'data/standard/LowerCingulum_1mm'
>> -d image_read from 'data/standard/LowerCingulum_1mm', read_data = 0, HAVE_ZLIB = 1
>> ** find_file_ext: failed for name 'data/standard/LowerCingulum_1mm'
>> ** find_file_ext: failed for name 'data/standard/LowerCingulum_1mm'
>> ** find_file_ext: failed for name 'data/standard/LowerCingulum_1mm'
>> -d nifti_image_read: found header filename 'data/standard/LowerCingulum_1mm.nii.gz'
>> ** bad swapped d0 = 768, unswapped = 768
>> ** ERROR: nifti_convert_nhdr2nim: bad dim[0]
>> ** ERROR (nifti_image_read): cannot create nifti image from header 'data/standard/LowerCingulum_1mm.nii.gz'
>> ** ERROR: nifti_image_open(data/standard/LowerCingulum_1mm): bad header info
>> Error: failed to open file data/standard/LowerCingulum_1mm
>> ERROR: Could not open file
>>
>> It just fails to perform the byteswapping i.e. d0 is the same swapped as unswapped. To solve the problem I changed the byteswapping code to use char* arrays rather than structs, as follows:
>>
>> nifti1_io.c:
>>
>> 1962 void nifti_swap_2bytes( int n , void *ar ) /* 2 bytes at a time */
>> 1963 {
>> 1964 /*register int ii ;
>> 1965 register twobytes *tb = (twobytes *)ar ;
>> 1966 register unsigned char tt ;
>> 1967
>> 1968 for( ii=0 ; ii < n ; ii++ ){
>> 1969 tt = tb[ii].a ; tb[ii].a = tb[ii].b ; tb[ii].b = tt ;
>> 1970 }*/
>> 1971 int ii;
>> 1972 unsigned char tt;
>> 1973 unsigned char* uc = (unsigned char*)ar;
>> 1974 for(ii = (n - 1) * 2; ii >= 0; ii -= 2){
>> 1975 tt = uc[ii]; uc[ii] = uc[ii + 1]; uc[ii + 1] = tt;
>> 1976 }
>> 1977
>> 1978 return ;
>> 1979 }
>>
>> and similar patches for all the other sizes (4, 8, 16)
>>
>> It is particularly strange because the sizeof operators return the correct values, i.e. sizeof(twobytes) = 2, sizeof(fourbytes) = 4 ... etc
>>
>> I have been able to do this on
>> Intel Xeon E5335 and Intel i7-920 64-bit processors and on the Intel Atom N270 32-bit processor.
>>
>> My operating system is Ubuntu Maverick 10.10.
>>
>> g++ --version:
>> g++ (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
>>
>> gcc --version:
>> gcc (Ubuntu/Linaro 4.4.4-14ubuntu5) 4.4.5
>>
>> Interestingly I haven't had this problem with the ubuntu package version or the binary versions off the FSL website.
>>
>> Chris Adamson.
>>
>> Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash)
>> Research Officer
>> Developmental and Functional Brain Imaging, Critical Care and Neurosciences
>>
>> Murdoch Childrens Research Institute
>> The Royal Children's Hospital
>> Flemington Road Parkville Victoria 3052 Australia
>> T 9345 4306
>> M XXXX XXX XXX
>> E [log in to unmask]
>> www.mcri.edu.au
>>
>>
>>
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library on behalf of Chris Adamson
>> Sent: Tue 1/03/2011 10:54 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] Help with fslstats error
>>
>> The problem occurred when I ran fslhd ${FSLDIR}/data/standard/LowerCingulum_1mm.nii.gz
>> It would crash with the same error as in the other post.
>> I will redownload and compile the original source to try and reproduce the error.
>>
>>
>>
>> Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash)
>> Research Officer
>> Developmental and Functional Brain Imaging, Critical Care and Neurosciences
>>
>> Murdoch Childrens Research Institute
>> The Royal Children's Hospital
>> Flemington Road Parkville Victoria 3052 Australia
>> T 9345 4306
>> M XXXX XXX XXX
>> E [log in to unmask]
>> www.mcri.edu.au
>>
>>
>>
>>
>> -----Original Message-----
>> From: FSL - FMRIB's Software Library on behalf of Mark Jenkinson
>> Sent: Tue 1/03/2011 5:22 PM
>> To: [log in to unmask]
>> Subject: Re: [FSL] Help with fslstats error
>>
>> Dear Chris,
>>
>> I'm really surprised to hear this.
>> I've never experienced this problem or even heard about it.
>> It is really quite concerning.
>> Are you sure that this is the case, and if so is it ever something
>> you can replicate reliably?
>>
>> All the best,
>> Mark
>>
>> P.S. Jesse - I would check to see if your images are corrupt
>> first. That is the most likely explanation. Try loading them
>> into FSLView and see if they view OK.
>>
>>
>>
>> On 1 Mar 2011, at 20:28, Chris Adamson wrote:
>>
>>> Assuming you are on an intel-based machine, check the image to see if the header is in big endian byte order. I have found that the byte swapping routines in nifti1_io.c do not always work when optimisations are turned on.
>>>
>>> Dr Christopher Adamson, PhD (Melb.), B Software Engineering (Hons., Monash)
>>> Research Officer
>>> Developmental and Functional Brain Imaging, Critical Care and Neurosciences
>>>
>>> Murdoch Childrens Research Institute
>>> The Royal Children's Hospital
>>> Flemington Road Parkville Victoria 3052 Australia
>>> T 9345 4306
>>> M XXXX XXX XXX
>>> E [log in to unmask]
>>> www.mcri.edu.au
>>>
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: FSL - FMRIB's Software Library on behalf of Jesse Bledsoe
>>> Sent: Tue 1/03/2011 3:12 PM
>>> To: [log in to unmask]
>>> Subject: [FSL] Help with fslstats error
>>>
>>> Hi everyone,
>>>
>>> I am receiving the following error for some data and would appreciate any
>>> insights into the error:
>>>
>>> [bledsoej@circ Grey_White]$ fslstats EF0136_brain_pve_1.nii.gz -m -v
>>> ** ERROR (nifti_image_read): short header read 'EF0136_brain_pve_1.nii.gz'
>>> ** ERROR: nifti_image_open(EF0136_brain_pve_1): bad header info
>>> Error: failed to open file EF0136_brain_pve_1
>>> ERROR: Could not open image EF0136_brain_pve_1
>>> Image Exception : #22 :: Failed to read volume EF0136_brain_pve_1.nii.gz
>>> terminate called after throwing an instance of 'RBD_COMMON::BaseException'
>>> Abort (core dumped)
>>>
>>> Any suggestions are greatly appreciated,
>>>
>>> Jesse
>>>
>>>
>>> ______________________________________________________________________
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>>>
>>>
>>> ______________________________________________________________________
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>>> ______________________________________________________________________
>>>
>>
>> ______________________________________________________________________
>> This email has been scanned by the MessageLabs Email Security System.
>> For more information please visit http://www.messagelabs.com/email
>>
>> If you have any question, please contact MCRI IT Helpdesk for further assistance.
>> ______________________________________________________________________
>>
>>
>> ______________________________________________________________________
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>> ______________________________________________________________________
>>
>> ______________________________________________________________________
>> This email has been scanned by the MessageLabs Email Security System.
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>> If you have any question, please contact MCRI IT Helpdesk for further assistance.
>> ______________________________________________________________________
>>
>>
>> ______________________________________________________________________
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>
> ______________________________________________________________________
> This email has been scanned by the MessageLabs Email Security System.
> For more information please visit http://www.messagelabs.com/email
>
> If you have any question, please contact MCRI IT Helpdesk for further assistance.
> ______________________________________________________________________
>
>
> ______________________________________________________________________
> This email has been scanned by the MessageLabs Email Security System.
> For more information please visit http://www.messagelabs.com/email
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