read_fcdc_mri

[Ali Mazaheri]

Thanks Robert,
I think you are correct.... it appears the problem is the new versions
of MRIViewer,
If you save it as the default .MRI  file it can't be read into
fieldtrip. However, when I convert it to CTF v2 it works perfectly.
All the files that didn't open were actually made quite recently..so
this further explains things.

so.... problem solved.

Thanks a bunch !


ali



Robert Oostenveld wrote:
> 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.
>
> Robert
> ----------------------------------
> The aim of this list is to facilitate the discussion between users of
> the FieldTrip  toolbox, to share experiences and to discuss new ideas
> for MEG and EEG analysis.
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>  http://www.ru.nl/fcdonders/fieldtrip/
>
>

----------------------------------
The aim of this list is to facilitate the discussion between users of the FieldTrip  toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis. See also http://listserv.surfnet.nl/archives/fieldtrip.html and http://www.ru.nl/fcdonders/fieldtrip.