If you also installed the updates and have a suitable version of MATLAB
installed that is compatible with your version of Linux (see MathWorks web
pages), then I'm all out of ideas. I still have an old computer, and have no
experience of compiling for 64 bit.
Best regards,
-John
On Thursday 08 January 2009 09:58, Opher Lubzens wrote:
> I reinstalled SPM5 and remade it using the Makefile included, and I still
> get the same error and output, including for the template T1.nii file.Had
> anybody here had SPM show such problems with Linux64?
>
> Opher Lubzens
>
> --- On Tue, 1/6/09, John Ashburner <[log in to unmask]> wrote:
> > From: John Ashburner <[log in to unmask]>
> > Subject: Re: [SPM] mat2file DICOM conversion error
> > To: [log in to unmask]
> > Date: Tuesday, January 6, 2009, 6:28 PM
> > I think Kathy could be on to something here. It is possible
> > that re-installing
> > SPM could help, because this segmentation fault should not
> > normally occur.
> > Try displaying one of the image files released with SPM.
> > If this does not
> > work, then an installation problem could be a likely cause.
> > Another
> > possibility is if your data are stored on some unusual sort
> > of filesystem.
> >
> > Best regards,
> > -John
> >
> > On Tuesday 06 January 2009 15:34, Kathy Pearson wrote:
> > > Opher,
> > >
> > > I once had a similar problem when placing the SPM5
> >
> > distribution code into
> >
> > > CVS on Linux without first tagging the binaries as
> >
> > such. This caused
> >
> > > inappropriate conversion of the binary equivalent
> >
> > Carriage Return and Line
> >
> > > Feed text characters, leading to a crash. The same
> >
> > kind of thing might
> >
> > > happen if you've unzipped the distribution with
> >
> > WinZip using the "Smart
> >
> > > Tar" option to automatically translate what might
> >
> > be text files with UNIX
> >
> > > LF to Windows CR/LF.
> > >
> > > Kathy Pearson
> > > UAB Psychology
> > >
> > > -----Original Message-----
> > > From: SPM (Statistical Parametric Mapping)
> >
> > [mailto:[log in to unmask]] On
> >
> > > Behalf Of Opher Lubzens
> > > Sent: Tuesday, January 06, 2009 7:48 AM
> > > To: [log in to unmask]
> > > Subject: Re: [SPM] mat2file DICOM conversion error
> > >
> > > Correction: I was using the wrong file-a foo.img from
> >
> > a previous attempt at
> >
> > > conversion to ANALYZE rather then a regular foo.nii
> >
> > file.When I use the
> >
> > > foo.nii with these commands I get this result:
> > >
> > > N =
> > >
> > > NIFTI object: 1-by-1
> > > dat: [181x217x181 file_array]
> > > mat: [4x4 double]
> > > mat_intent: 'Aligned'
> > > mat0: [4x4 double]
> > > mat0_intent: 'Aligned'
> > > timing: [1x1 struct]
> > > descrip: 'AVERAGE:'
> > > cal: [0 32767]
> > >
> > >
> > >
> > > ans =
> > >
> > > fname: 't1.nii'
> > > dim: [181 217 181]
> > > dtype: 'INT16-LE'
> > > offset: 352
> > > scl_slope: 1
> > > scl_inter: 0
> >
> > ------------------------------------------------------------------------
> >
> > > Segmentation violation detected at Tue Jan 6
> >
> > 15:34:35 2009
> >
> > ------------------------------------------------------------------------
> >
> > > Configuration:
> > > MATLAB Version: 7.5.0.338 (R2007b)
> > > MATLAB License: 567156
> > > Operating System: Linux 2.6.22.5-31-default #1 SMP
> >
> > 2007/09/21 22:29:00
> >
> > > UTC x86_64
> > > GNU C Library: 2.6.1 stable
> > > Window System: The X.Org Foundation (70200000),
> >
> > display :0.0
> >
> > > Current Visual: 0x23 (class 4, depth 16)
> > > Processor ID: x86 Family 6 Model 7 Stepping 7,
> >
> > GenuineIntel
> >
> > > Virtual Machine: Java 1.6.0 with Sun Microsystems
> >
> > Inc. Java HotSpot(TM)
> >
> > > 64-Bit Server VM mixed mode
> > > Default Charset: UTF-8
> > >
> > > Register State:
> > > rax = 0000000000000000 rbx = 0000000000000001
> > > rcx = 000000000634b4b0 rdx = 00002aaad032c160
> > > rbp = 00000000407f76d0 rsi = 00000000407f83d4
> > > rdi = 0000000000000000 rsp = 00000000407f7688
> > > r8 = 0000000000000001 r9 = 0000000000000000
> > > r10 = 00002aaad032c160 r11 = 000000000633e090
> > > r12 = 0000000000000001 r13 = 00000000407f77d0
> > > r14 = 00000000407f7bd0 r15 = 0000000000000004
> > > rip = 00002aaacb37c55d flg = 0000000000010246
> > >
> > > Stack Trace:
> > > [0] file2mat.mexa64:0x00002aaacb37c55d(0x407f7700,
> >
> > 0, 0x2aaad032c160,
> >
> > > 0x407f83d4)
> > > [1] file2mat.mexa64:0x00002aaacb37c5e2(0x10e43879f,
> >
> > 0, 0x2aaad032c160,
> >
> > > 0x407f83d4)
> > >
> > >
> > >
> > >
> > > Thank you for taking taking time to help me so
> >
> > closely.
> >
> > > Opher Lubzens
> > >
> > > --- On Tue, 1/6/09, John Ashburner
> >
> > <[log in to unmask]> wrote:
> > > > From: John Ashburner
> >
> > <[log in to unmask]>
> >
> > > > Subject: Re: [SPM] mat2file DICOM conversion
> >
> > error
> >
> > > > To: [log in to unmask]
> > > > Date: Tuesday, January 6, 2009, 2:22 PM
> > > > If SPM won't convert your DICOM files, then
> >
> > maybe it is
> >
> > > > worth trying to figure
> > > > out what is wrong with the foo.img file. Try
> >
> > pasting this
> >
> > > > into MATLAB and
> > > > reporting back the results:
> > > >
> > > > P='foo.img';
> > > > N=nifti(P)
> > > > N.dat
> > > > N.dat(1,1,1)
> > > > t=dir(P)
> > > >
> > > > Best regards,
> > > > -John
> > > >
> > > > On Tuesday 06 January 2009 12:12, Opher Lubzens
> >
> > wrote:
> > > > > This error message is all the data I get.At
> >
> > first I
> >
> > > > thought it was because
> > > >
> > > > > the indices were int16 and the data was
> >
> > int32, but
> >
> > > > when I change them to
> > > >
> > > > > match I get an "Incompatible class
> >
> > types"
> >
> > > > error.And when I try to display
> > > >
> > > > > the dcm2nii nifti I get a "foo.img
> >
> > cannot be
> >
> > > > resampled" warning, followed
> > > >
> > > > > by a "wrong handle dimentions"
> >
> > error if I
> >
> > > > click anywhere in the view
> > > >
> > > > > windows.
> > > > >
> > > > > Opher Lubzens
> > > > >
> > > > > --- On Mon, 1/5/09, John Ashburner
> > > >
> > > > <[log in to unmask]> wrote:
> > > > > > From: John Ashburner
> > > >
> > > > <[log in to unmask]>
> > > >
> > > > > > Subject: Re: [SPM] mat2file DICOM
> >
> > conversion
> >
> > > > error
> > > >
> > > > > > To: [log in to unmask]
> > > > > > Date: Monday, January 5, 2009, 8:11 PM
> > > > > > Was there anything more to the error
> >
> > message?
> >
> > > > Also, what
> > > >
> > > > > > sort of errors does
> > > > > > SPM produce when you try to use NIfTI
> >
> > files
> >
> > > > generated by
> > > >
> > > > > > dcm2nii ?
> > > > > >
> > > > > > Best regards,
> > > > > > -John
> > > > > >
> > > > > > On Sunday 04 January 2009 11:19, Opher
> >
> > Lubzens
> >
> > > > wrote:
> > > > > > > Hello, I've been trying to
> >
> > import an
> >
> > > > inplane
> > > >
> > > > > > anatomy that I have in DICOM
> > > > > >
> > > > > > > format into nifti using the SPM5
> >
> > native
> >
> > > > DICOM import
> > > >
> > > > > > function.
> > > > > >
> > > > > > > Unfortunately I get a
> >
> > "Subscripted
> >
> > > > assignment
> > > >
> > > > > > dimension mismatch (2)" error
> > > > > >
> > > > > > > from mat2file, and I can't
> >
> > understand
> >
> > > > the
> > > >
> > > > > > mat2file.c code, since my copy
> > > > > >
> > > > > > > doesn't include
> >
> > documentation.Does
> >
> > > > anyone know of
> > > >
> > > > > > solution to this problem?
> > > > > >
> > > > > > > Opher Lubzens
> > > > > > >
> > > > > > > PS.I've tried using dcm2nii
> >
> > but SPM was
> >
> > > > unable to
> > > >
> > > > > > read the resulting nifti.
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