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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 | |