[MINC-users] nii2mnc error on CBRAIN.

[Gang Liang]

fsl have 2 data types: niftii and analyze(old)

to convert analyze format to nii, use fslchfiletype, then use nii2mnc to
convert it to minc
to convert analyze format to minc, use analyze2mnc or ana2mnc

Hope this help

Gang

On Fri, Mar 2, 2012 at 11:51 AM, Yang Ding <yang.ding at mail.mcgill.ca> wrote:

> Dear all,
>
> I am a new user to CBrain and encountered error with nii2mnc tool
> implemented there. I keep running into error when trying to convert
> "img/hdr" type of NIFTI files into MINC.* *
> *
> *
> *
> *
> *
> *
> Technical Details about the Error:
>
> While executing command: *nii2mnc CNSCNSA02.003494.0002an.img
>  CNSCNSA02.003494.0002an.img.mnc*
>
> *** ERROR (nifti_image_read): failed to find header file for
> > 'CNSCNSA02.003494.0002an.img' *
>
> */opt/gridengine/cbrain/spool/brainstorm/job_scripts/5865: line 48: 17390
> > Segmentation fault (core dumped) nii2mnc CNSCNSA02.003494.0002an.img
> > CNSCNSA02.003494.0002an.img.mnc*
>
>
> The headerfile *'CNSCNSA02.003494.0002an.hdr'* is in the same directory as
> IMG files and assigned with the proper project. I was also able open this
> img/hdr file pair in SPM8 without issue locally (not on the server).
>
>
> While executing command: *nii2mnc CNSCNSA02.003494.0002an.hdr
>  CNSCNSA02.003494.0002an.hdr.mnc*
>
> *** ERROR (nifti_image_load_prep): cannot open data file
> > 'CNSCNSA02.003494.0002an.img'
> > ** nifti_image_load, failed load_prep
> > /opt/gridengine/cbrain/spool/brainstorm/job_scripts/5866: line 48: 17803
> > Segmentation fault (core dumped) nii2mnc CNSCNSA02.003494.0002an.hdr
> > CNSCNSA02.003494.0002an.hdr.mnc*
>
>
> The "data file" is again, located in the same directory as IMG files and
> assigned with the proper project. I was also able open this img/hdr file
> pair in SPM8 without issue.
>
> Anyone with more experience of the tool on CBRAIN, please feel free to
> comment.
>
>
> Things I have tried:
>
>   - Setting permission on the files to read/write instead of read only.
>   - Use a shorter name (e.g. Sub01.img/hdr from another project of mine
>   failed too)
>   - Convert to .nii using MRIcroN before using the nii2mnc tool. *This
>   actually worked* but MRIcroN does not do batch conversion of .img/hdr to
>   .nii for the 100 subjects that I have to work with...
>
>
> Please let me know if you have any other suggestions to resolve this
> problem. Thank you very much for all the support.
>
>
>
>
> Sincerely,
>
> Yang Ding
>
>
> Graduate Student
> Integrated Program in Neuroscience
>
> McGill Group for Suicide Studies (MGSS)
>
> 514-761-6131 ext 6197
>
> Rm. F-3145, Frank B Common Pavilion,
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> 6875 LaSalle Blvd.
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>
>