[MINC-users] nii2mnc

[Trisanna Sprung-Much]

thanks, Robert. Will see if I can get the original dicoms instead.

Best

Trisanna

--
Ph.D. Candidate
McGill University
Integrated Program in Neuroscience
Psychology


On Fri, Jul 22, 2016 at 8:35 AM, Robert D. Vincent <
robert.d.vincent at mcgill.ca> wrote:

> Hi Trisanna,
>
> It looks like your file does not contain a specification of a spatial
> transform from voxel to world space - the code to handle this in nii2mnc
> was broken a while back. It's fixed now, but I don't think that version has
> been officially released yet.
>
>     -bert
>
> On Thu, Jul 21, 2016 at 5:03 PM, Vladimir S. FONOV <
> vladimir.fonov at gmail.com
> > wrote:
>
> > Hello,
> >
> > it could fail for many reasons....
> > You can try itk_convert - see if it helps.
> >
> >
> > On 2016-07-21 03:06 PM, Trisanna Sprung-Much wrote:
> >
> >> Hello
> >>
> >> I recently tried to use nii2mnc on some ex-vivo scans and the command
> >> seems
> >> to fail. Any ideas as to why? I think it has to do with the format of my
> >> nifti file?
> >>
> >> many thanks
> >>
> >> Trisanna
> >>
> >> nii2mnc: Convert NIfTI-1 files to MINC format
> >> usage: nii2mnc [options] filename.nii [filename.mnc]
> >>  nii2mnc Merv_7T.nii Merv_7T.mnc
> >> <nifti_image
> >>   nifti_type = 'NIFTI-1+'
> >>   header_filename = 'Merv_7T.nii'
> >>   image_filename = 'Merv_7T.nii'
> >>   image_offset = '352'
> >>   ndim = '3'
> >>   nx = '280'
> >>   ny = '280'
> >>   nz = '80'
> >>   dx = '0.428571'
> >>   dy = '0.428571'
> >>   dz = '1.5'
> >>   datatype = '4'
> >>   datatype_name = 'INT16'
> >>   nvox = '6272000'
> >>   nbyper = '2'
> >>   byteorder = 'LSB_FIRST'
> >>   scl_slope = '1'
> >>   scl_inter = '0'
> >>   xyz_units = '2'
> >>   xyz_units_name = 'mm'
> >>   time_units = '8'
> >>   time_units_name = 's'
> >>   descrip = 'FSL5.0'
> >>   num_ext = '0'
> >> />
> >> Segmentation fault (core dumped)
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> >>
> >
> > --
> > Best regards,
> >
> >  Vladimir S. FONOV ~ vladimir.fonov <at> gmail.com
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
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