Hi,
On Thu, Jun 11, 2015 at 2:09 AM, Jalmar Teeuw <jal...@me.com> wrote:
> Hi Matthew,
>
> Thanks for getting back at this. We only process data for our users, so I
> don't have permission to share a sample with you. But I'll ask around to see
> if I can get a scan for you.
>
> To be honest, we aren't quite sure if the problem is with nibabel (v1.3.0). I
> tried to reproduce the problem with one of the scan that was causing this
> problem, but the conversion worked fine for me (same data, same script,
> different platform). Although recently we had the same issue cropping up
> again for another user where only part of the data was affected by this
> problem. All we know is that the description field of the NIFTI header starts
> at the right offset, the magic number bytes are off by +one byte, and the
> brain looks skewed; hence the assumption of an extra byte in one of the
> transform fields.
>
> Alternatively, we were wondering what happens if the content of the
> description field exceeded 80 characters
>
> descr = "%s;%s;%s;%s" % (
> pr_hdr.general_info['exam_name'],
> pr_hdr.general_info['patient_name'],
> pr_hdr.general_info['exam_date'].replace(' ',''),
> pr_hdr.general_info['protocol_name'])
> nhdr.structarr['descrip'] = descr[:80]
>
> The python code neatly truncates the description to 80 characters. Could it
> be possible that an extra '\0' null byte gets written to terminate the
> string, causing the description field to be 81 bytes long?
I am fairly sure that there is no way to extend the structure by 1
byte with that command. The header is effectively a C structure,
wrapped by numpy, so even if numpy allowed you to overflow the field
length, it would still only overwrite the next field, and should not
extend the structure.
So - any help you can give to debug this would be great - I don't have
any good ideas at the moment... For example - can you send a header
from an affected file?
Cheers,
Matthew
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