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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