[MINC-users] nii2mnc problems.

[Mishkin Derakhshan]

Hi Giocanna,
I'm no expert on nii2mnc, and this may be a long shot, but sometimes
if you email/store the .hdr file on a dos based machine it changes the
format. What are the details of the computer which failed, and the
computer which passed?

If you type:
file test_image_00001.hdr
on both computers it should read "ASCII text"

If it says something like "ASCII text, with CRLF line terminators"
then try this:
dos2unix test_image_00001.hdr

And then try nii2mnc again.

Like I said it is long shot, but it may be the problem.
mishkin




On Tue, Apr 14, 2009 at 4:38 PM, Giovanna Pellecchia
<giovanna_p at hotmail.com> wrote:
>
> Thanks for your reply. I am new at this, so I am not sure how to check  the value of dim[0].
> Why would that make a difference from one computer to another?
>
> Giovanna Pellecchia
> Research Analyst
> Toronto Western Hospital
> & Centre for Addiction and Mental Health
>
>> Message: 2
>> Date: Thu, 09 Apr 2009 22:06:27 -0400
>> From: "Roch M. Comeau" <rcomeau at mac.com>
>> Subject: Re: [MINC-users] nii2mnc problems.
>> To: MINC users mailing list <minc-users at bic.mni.mcgill.ca>
>> Message-ID: <FD161774-F86B-4A8C-BD88-EBCAC36BCD7B at mac.com>
>> Content-Type: text/plain; charset=US-ASCII; format=flowed; delsp=yes
>>
>> HI,
>>
>> Maybe have a look at the value of dim[0]. I've seen images where
>> dim[0] is incorrectly set to 0 instead of 3 or 4.
>>
>> Roch Comeau
>> Rogue Research Inc.
>>
>> On 9-Apr-09, at 5:03 PM, Giovanna Pellecchia wrote:
>>
>> >
>> > Howdy all,
>> >
>> > if I try to use nii2mnc I get this interesting error message:
>> >
>> > nii2mnc test_image_00001.hdr
>> > ** ERROR: nifti_convert_nhdr2nim: bad dim[0]
>> > ** ERROR (nifti_image_read): cannot create nifti image from header
>> > 'test_image_00001.hdr'
>> > Segmentation fault
>> > ______________________
>> > The same test image works fine on another computer:
>> > nii2mnc test_image_00001.hdr
>> > orient = 0
>> > <nifti_image
>> >  nifti_type = 'ANALYZE-7.5'
>> >  header_filename = 'test_image_00001.hdr'
>> >  image_filename = 'test_image_00001.img'
>> >  image_offset = '0'
>> >  ndim = '4'
>> >  nx = '163'
>> >  ny = '186'
>> >  nz = '72'
>> >  nt = '1'
>> >  dx = '-1.06677'
>> >  dy = '1.06677'
>> >  dz = '1.87482'
>> >  dt = '1'
>> >  datatype = '16'
>> >  datatype_name = 'FLOAT32'
>> >  nvox = '2182896'
>> >  nbyper = '4'
>> >  byteorder = 'MSB_FIRST'
>> >  cal_min = '0'
>> >  cal_max = '1'
>> >  descrip = 'MINC file'
>> >  num_ext = '0'
>> > />
>> > Unknown XYZ units 0
>> > xspace start:  86.9418 step:  -1.0668 cosines:   1.0000   0.0000
>> > 0.0000
>> > yspace start: -99.2096 step:   1.0668 cosines:   0.0000   1.0000
>> > 0.0000
>> > zspace start: -67.4934 step:   1.8748 cosines:   0.0000   0.0000
>> > 1.0000
>> > (where:
>> > nii2mnc -v
>> > program: 2.0.15
>> > libminc: 2.0.15
>> > netcdf : 3.5.0 of Aug  8 2003 13:03:52 $
>> > HDF5   : 1.6.2 )
>> > (installed from source on Debian Sarge)
>> > ____________________
>> >
>> > My current version:
>> > nii2mnc -v
>> > program: 2.0.15
>> > libminc: 2.0.15
>> > netcdf : "3.6.2" of May 10 2008 09:14:53 $
>> > HDF5   : 1.6.6
>> > (installed using mincbundle on a recent Ubuntu Intrepid install with
>> > all the recommended upgrades).
>> > (I also have an unusual situation, as it turns out that most of the
>> > binaries are located in /bin and the libraries in /usr/lib by
>> > default - no idea why!)
>> >
>> > Hope somebody can point to a solution...
>> > Thanks!
>> > Giovanna.
>
>
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