JiscMail Logo
Email discussion lists for the UK Education and Research communities

Help for SPM Archives


SPM Archives

SPM Archives


SPM@JISCMAIL.AC.UK


View:

Message:

[

First

|

Previous

|

Next

|

Last

]

By Topic:

[

First

|

Previous

|

Next

|

Last

]

By Author:

[

First

|

Previous

|

Next

|

Last

]

Font:

Proportional Font

LISTSERV Archives

LISTSERV Archives

SPM Home

SPM Home

SPM  January 2009

SPM January 2009

Options

Subscribe or Unsubscribe

Subscribe or Unsubscribe

Log In

Log In

Get Password

Get Password

Subject:

Re: mat2file DICOM conversion error

From:

Kathy Pearson <[log in to unmask]>

Reply-To:

Kathy Pearson <[log in to unmask]>

Date:

Tue, 6 Jan 2009 09:34:05 -0600

Content-Type:

text/plain

Parts/Attachments:

Parts/Attachments

text/plain (181 lines)

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.


      

Top of Message | Previous Page | Permalink

JiscMail Tools


RSS Feeds and Sharing


Advanced Options


Archives

October 2019
September 2019
August 2019
July 2019
June 2019
May 2019
April 2019
March 2019
February 2019
January 2019
December 2018
November 2018
October 2018
September 2018
August 2018
July 2018
June 2018
May 2018
April 2018
March 2018
February 2018
January 2018
December 2017
November 2017
October 2017
September 2017
August 2017
July 2017
June 2017
May 2017
April 2017
March 2017
February 2017
January 2017
December 2016
November 2016
October 2016
September 2016
August 2016
July 2016
June 2016
May 2016
April 2016
March 2016
February 2016
January 2016
December 2015
November 2015
October 2015
September 2015
August 2015
July 2015
June 2015
May 2015
April 2015
March 2015
February 2015
January 2015
December 2014
November 2014
October 2014
September 2014
August 2014
July 2014
June 2014
May 2014
April 2014
March 2014
February 2014
January 2014
December 2013
November 2013
October 2013
September 2013
August 2013
July 2013
June 2013
May 2013
April 2013
March 2013
February 2013
January 2013
December 2012
November 2012
October 2012
September 2012
August 2012
July 2012
June 2012
May 2012
April 2012
March 2012
February 2012
January 2012
December 2011
November 2011
October 2011
September 2011
August 2011
July 2011
June 2011
May 2011
April 2011
March 2011
February 2011
January 2011
December 2010
November 2010
October 2010
September 2010
August 2010
July 2010
June 2010
May 2010
April 2010
March 2010
February 2010
January 2010
December 2009
November 2009
October 2009
September 2009
August 2009
July 2009
June 2009
May 2009
April 2009
March 2009
February 2009
January 2009
December 2008
November 2008
October 2008
September 2008
August 2008
July 2008
June 2008
May 2008
April 2008
March 2008
February 2008
January 2008
December 2007
November 2007
October 2007
September 2007
August 2007
July 2007
June 2007
May 2007
April 2007
March 2007
February 2007
January 2007
2006
2005
2004
2003
2002
2001
2000
1999
1998


JiscMail is a Jisc service.

View our service policies at https://www.jiscmail.ac.uk/policyandsecurity/ and Jisc's privacy policy at https://www.jisc.ac.uk/website/privacy-notice

Secured by F-Secure Anti-Virus CataList Email List Search Powered by the LISTSERV Email List Manager