AFNI version info (afni -ver): Version AFNI_23.0.07 'Commodus'
Hi AFNI team,
I am currently trying to convert Dicom file to BRIK/HEAD file.
I recently changed fMRI protocol from Siemens Magnetom Prisma to Siemens Magnetom Numaris/X.
The problem is that my old code does not work anymore. Below is my old code for converting Dicom to BRIK file and slice timing correction.
Dimon -infile_pattern '*.dcm' -gert_outdir ${BRIKDir} -gert_to3d_prefix ${FileName} -GERT_Reco -quit -gert_create_dataset
3dTshift -tzero $stcShift -heptic -prefix ${filename}+orig.HEAD
When I run the code, the error is as Figure A below.
As far as I know, new fMRI protocol saves as enhanced Dicom file which does not use mosaic format anymore. I guess that this is why Dimon cannot make 2d slices to 3d.
I searched for solution in AFNI board, and I found that dcm2niix_afni might help, so I tried as below.
dcm2niix_afni $dataDir -o $origBRIKDir -f ${DicomFile} $dataDir
3dcopy ${NIFTIfile}.nii ${BRIKFile}+orig
3dTshift -tzero $stcShift -heptic -prefix ${newFile}+orig.HEAD
With new code, I could convert the Dicom to NIFTI and then to BRIK/HEAD format, but slice timing correction did not go well as Figure B below.
The error message says that dataset is already aligned in time. However when I opened the BRIK file, all the time offset were 0.
Is there any solution for converting enhanced Dicom to BRIK format and also do the slice timing correction?