Dear Mark,
That's right (about zeros & the midpoint) - I think John was making the point that there might be _something_else_ in the "spm_orig" fields, e.g. text, negative numbers or similar - I've seen that kind of problem before.
Following on from Stefano's mail, even in the absence of the HDR edit possibility in SPM2, you could of course use either SPM99 or some local program (dbedit in case you're here tomorrow) to check/fix things and avoid *mat files (which can be a problem when you're analysing in & out of SPM) - I know it's not generally recommended but you know what you're doing so there should be little risk...
All the best, Alexander
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]]On
Behalf Of Mark Daglish
Sent: 09 March 2005 17:42
To: [log in to unmask]
Subject: Re: [SPM] Display image strangeness
Hi John,
Thanks for the response. These were created by Analyze 6.0 from 130
single slice dicom images from a Philips Intera. I'm away from my image
machine just now, but can send a hdr if it will help.
I thought if the origin field was empty, that SPM assumed the mid-point.
Cheers,
Mark
John Ashburner wrote:
>Dear Mark,
>Where did you get them, and how did you convert them to a format that SPM can
>(try to) read? They have probably been converted using some software that
>puts information in the same place in the header as the ORIGIN field used by
>SPM. One possibility is that they are NIFTI-1 (which SPM2 doesn't recognise
>- but SPM5 will).
>
>Best regards,
>-John
>
>
>
>>I have some (less than ideal) MRI structural images that I want to
>>co-register with PET data. When I display them in SPM2 it is reporting
>>the following:
>>
>>Dimensions: 512x512x130 (correct)
>>Datatype: int16 (correct)
>>Intensity: Y=1X (correct)
>>
>>Vox size: -0.449 x 0.449 x 1.39 (correct)
>>Origin: 1.8e+04 1.77e+04 1.72e+04 (strange)
>>Dir Cos: 1.000 0.000 0.000
>> 0.000 0.540 -0.841
>> 0.000 0.841 0.540
>>
>>The images were acquired approximately coronally, so I re-orient by a
>>ptich rotation of approx -pi/2 before I did this display.
>>If I click on the image and get the crossharis to about were I would
>>like the origin to be the display window reports the crosshair position as:
>>
>>mm: 7973.1 15786.8 -19443.1
>>vx: 253.2 309.1 60.0
>>
>>It seems to me that SPM2 is not handling the voxel to world translation
>>correctly. Can anyone help?
>>
>>Many thanks,
>>
>>Mark
>>
>>
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