Greetings,
I have an issue related to asl_file and oxford_asl while using the --rpts option:
I have a PCASL sequence with 5 PLDs. The PLDs repeat with the following pattern 2,2,2,3,3 in a tag-control pairs order. That is, I have a total of 24 volumes/images + 1 M0 image as the first volume in the sequence as a control. This PCASL sequence is acquired using a Siemens 3T Prisma MRI scanner using two different software versions: MRE11 and the newer XA30.
Here is the issue:
Running the following asl_file command works great for PCASL scans collected using the MRE11 Siemens software:
asl_file --data=Subj_asl_TC.nii.gz --iaf=tc --ibf=tis --ntis=5 --rpts=2,2,2,3,3 --diff --out=Subj_asl_TC_Subtr.nii.gz
Here, the "Subj_asl_TC_Subtr.nii.gz" file consists of 5 volumes, representing the 5 PLDs following subtraction and averaging.
Running the same command for PCASL scans collected using the XA30 Siemens software yields an output file with 12 volumes, indicating that either the --rpts option was ignored or something else went wrong.
Visual inspection of a raw XA30 PCASL sequence seems accurate and identical to the MRE11 variant (same parameters)
I have also tried the following but nothing worked so far for the XA30 sequences:
Exporting the DICOMs in both enhanced and interoperability mode from the scanner
Comparing the NIFTI headers between MRE11 and XA30 for differences but there are none
Using different versions of FSL (FSL 6.0.1 and 6.0.4)
Has anyone encountered this error before with Siemens XA30 PCASL sequences and is anyone aware of a workaround?
We are currently manually subtracting the the tag-control pairs, averaging them and passing the output to oxford_asl, but it might be good to know why the --rpts option doesn't work for the XA30 PCASL sequences.
Any help will be appreciated,
Thank you,
Valentinos Zachariou
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