I’m coming with a question about opening an fMRI file which, because of the length of the scan, was exported as classic DICOMs (65322 to be precise). However, 1 file got lost during the export process some time ago and because of that I’m unable to load that file due to the “negative count”. I don’t have a way to retrieve the original data anymore. Is there a way to handle/compensate for the missing data, i.e. 1 file? The TR was 2.5. Will it be possible to further process such data?
I’d appreciate any insight!
If I were you, I would run the following command:
dcm2niix -r y -o /path/to/renamed/DICOMs /path/to/DICOM/inputs
This will rename all of your images based on the instance number. If the missing image is in the first or last 3D volume of your timeseries, you can simply remove all the other images from that volume and convert the remaining files with dcm2niix (if you remove the first volume, reduce your event timings by 2.5s).
If the missing image is not from the first or last volume, you can resolve the problem by replacing the missing file with the corresponding slice from the previous or next volume. So you would make a clone of the image from the previous volume, but set the instance number (DICOM tag 0020,0013) to match the missing image. I would use dcmodify, but you might also try the
replace function of gdcmanon.
Dear @neurolabusc thanks for your tip! The file is indeed in the middle so I will figure out the second option that you suggested.