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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