[MINC-users] nii2mnc error on CBRAIN.

[Yang Ding]

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.* *
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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,
Douglas Mental Health University Institute
6875 LaSalle Blvd.
Verdun, Quebec, Canada, H4H 1R3
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