Hi guys, I have the raw PAR REC and DICOM files from the scanner. I converted the PAR REC files to mgz and ran recon-all but it exited with errors. But when I converted the DICOM files into mgz and ran recon-all, it was running fine. Can anyone tell me why this is happening.
Regards, Sameer
is there any reason you can't just start with the dicom? You can check the orientation on the converted files to see if it's wrong - that's usually what happens. How did you convert from PAR REC?
cheers, Bruce
On Fri, 26 Jun 2009, sameer kumar wrote:
Hi guys, I have the raw PAR REC and DICOM files from the scanner. I converted the PAR REC files to mgz and ran recon-all but it exited with errors. But when I converted the DICOM files into mgz and ran recon-all, it was running fine. Can anyone tell me why this is happening.
Regards, Sameer
Hi Bruce, I used mricro to convert from PAR REC. The problem is that when I tried to convert the results back to the native space, they are flipped, and are not in the same orientation as the original.
Hi Sameer,
can you just use the dicom?
Bruce On Fri, 26 Jun 2009, sameer kumar wrote:
Hi Bruce, I used mricro to convert from PAR REC. The problem is that when I tried to convert the results back to the native space, they are flipped, and are not in the same orientation as the original.
Yes, I used the dicom to run recon-all. I converted the results back to native space, using mri_convert -rl orig/001.mgz XX.mgz XX_native.mgz
the images in the native space are not in the same orientation as 001.mgz, which i got from the dicoms.
how do you know they are not in the same orientation? What are you using to check? On Fri, 26 Jun 2009, sameer kumar wrote:
Yes, I used the dicom to run recon-all. I converted the results back to native space, using mri_convert -rl orig/001.mgz XX.mgz XX_native.mgz
the images in the native space are not in the same orientation as 001.mgz, which i got from the dicoms.
The 001.mgz should already be in native space.
sameer kumar wrote:
Yes, I used the dicom to run recon-all.
I converted the results back to native space, using
mri_convert -rl orig/001.mgz XX.mgz XX_native.mgz
the images in the native space are not in the same orientation as 001.mgz, which i got from the dicoms.
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