Robert Oostenveld r.oostenveld at FCDONDERS.RU.NL
Mon May 7 13:56:40 CEST 2007

Hi Ali

On 7 May 2007, at 13:40, Ali Mazaheri wrote:
> I am coming across this error when I use the read_fcdc_mri
> {Undefined function or variable "orientation"
> mri=ipermute(mri,orientation)
> This happens only for some of my MRI files... and not others..
> which makes me think that there is a step
> somewhere I am missing when making my MRI files ( I use the
> instruction provided)
> any suggestions/remedies would be greatly appreciated.

Searching for the code that relates to your error message, I only see
   fcdc-roboos> grep ipermute *.m
   read_asa_mri.m:mri = ipermute(mri, orientation);
   read_asa_mri.m:seg = ipermute(seg, orientation);

So it seems that you are trying to read ASA format *.mri files, which
I know that you are not doing.

The file format detection (fieldtrip/private/filetype.m)
automatically determines the format, and read_fcdc_mri then uses the
corresponding low-level function (in this case for ASA). The likely
cause is that you are using a file with extension *.mri which is not
being recognized as CTF MRI file. That can be the case if the binary
file does not start with the string 'CTF_MRI_FORMAT VER 2.2'. Please
open the mri file in a robust text editor or type "strings
<filename>" on the linux prompt and see whether that is the case.

The new version of MRIConverter/MRIViewer can write files in a new
CTF format (probably what you have) and in the old v2.2 format (which
the code seems to support). I don't know the difference between the
formats. You might try read_ctf_mri on the file directly.


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