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Subject:

Re: mat2file DICOM conversion error

From:

Opher Lubzens <[log in to unmask]>

Reply-To:

Opher Lubzens <[log in to unmask]>

Date:

Mon, 12 Jan 2009 06:47:16 -0800

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (397 lines)

I used it, but apparently last time I forgot to use"make clean"- now the DICOM import is working.Unfortunately other parts of the system are not(I'll be openning a new thread momentarily).

Opher Lubzens 



--- On Thu, 1/8/09, Guillaume Flandin <[log in to unmask]> wrote:

> From: Guillaume Flandin <[log in to unmask]>
> Subject: Re: [SPM] mat2file DICOM conversion error
> To: [log in to unmask]
> Cc: "Opher Lubzens" <[log in to unmask]>
> Date: Thursday, January 8, 2009, 2:25 PM
> Dear Opher,
> 
> could you try to install SPM8b as well and see if you
> observe the same
> error message? The Linux 64bit MEX files provided with
> SPM8b have been
> compiled on a different system than those in SPM5.
> 
> Also, when you compiled the MEX files yourself, did you
> also type "make
> install" after the compilation?
> 
> All the best,
> Guillaume.
> 
> John Ashburner wrote:
> > 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.
> 
> -- 
> Guillaume Flandin, PhD
> Wellcome Trust Centre for Neuroimaging
> University College London
> 12 Queen Square
> London WC1N 3BG


      

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