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questions > RE: catastrophic error with par/rec - can't find slices
Nov 12, 2019 01:11 PM | Wouter Schellekens
RE: catastrophic error with par/rec - can't find slices
Hi Chris,
I'm encountering a similar issue with Philips PAR/REC files. Only in my case the PAR/REC contains magnitude and phase data (codes 0 & 3). dcm2niix appears unable to read in the phase data (2nd half), giving me a similar error as this topic: "Catastrophic error: found 24300 but expected 48600 slices."
To answer the questions asked below:
1.) version: v1.0.20190902
2.) dicm2nii also does not work.
3.) yes, Philips PAR/REC files. No, undamaged and fully acquired dataset. Using a read binary tool, I could verify that the data is all there.
Do you have any ideas what's going wrong? Shall I upload this dataset somewhere?
Best wishes,
Wouter
Originally posted by Chris Rorden:
I'm encountering a similar issue with Philips PAR/REC files. Only in my case the PAR/REC contains magnitude and phase data (codes 0 & 3). dcm2niix appears unable to read in the phase data (2nd half), giving me a similar error as this topic: "Catastrophic error: found 24300 but expected 48600 slices."
To answer the questions asked below:
1.) version: v1.0.20190902
2.) dicm2nii also does not work.
3.) yes, Philips PAR/REC files. No, undamaged and fully acquired dataset. Using a read binary tool, I could verify that the data is all there.
Do you have any ideas what's going wrong? Shall I upload this dataset somewhere?
Best wishes,
Wouter
Originally posted by Chris Rorden:
1.) First, I would make sure you have the
current stable release version 25-November-2018
(v1.0.20181125)
https://github.com/rordenlab/dcm2niix/releases
2.) If that fails, try dicm2nii:
https://github.com/xiangruili/dicm2nii
3.) Next, are the files you are trying to convert DICOM data or are they Philips proprietary PAR/REC files? I suspect it is a damaged/partial PAR/REC file. In which case you could try to salvage it with
https://github.com/rordenlab/spmScripts/blob/master/nii_rescue_par.m
alternatively, you can manually fix broken PAR/REC files by editing the PAR file with a text editor. I suspect that the core issue is that your scan was interrupted before acquisition was completed, so the PAR file describes more images than stored in the REC file.
https://github.com/rordenlab/dcm2niix/releases
2.) If that fails, try dicm2nii:
https://github.com/xiangruili/dicm2nii
3.) Next, are the files you are trying to convert DICOM data or are they Philips proprietary PAR/REC files? I suspect it is a damaged/partial PAR/REC file. In which case you could try to salvage it with
https://github.com/rordenlab/spmScripts/blob/master/nii_rescue_par.m
alternatively, you can manually fix broken PAR/REC files by editing the PAR file with a text editor. I suspect that the core issue is that your scan was interrupted before acquisition was completed, so the PAR file describes more images than stored in the REC file.
Threaded View
| Title | Author | Date |
|---|---|---|
| Josh Robinson | Apr 11, 2019 | |
| Chris Rorden | Apr 11, 2019 | |
| Wouter Schellekens | Nov 12, 2019 | |