AP and PA DWI Merging

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Hi everyone,
I’m not an expert with DWI images, please help me.
I have two separate AP and PA files for each subject and perform DTIprep for each one separately. Shall I combine these ones with something like FSLMerge? When exactly before DTIPrep running or after that?

2

Hello,

You do not have to merge the files. You can use QSIPrep to preprocess the images (it also has quality control outputs, so you do not have to run DTIPrep). If the phase encoding directions are encoded in the DWI accompanying JSON files (e.g. one has direction “-j” and the other has direction “j”) and the file names have the associated directions in them (e.g. “sub-XXX_dir-AP_dwi.nii.gz” and “sub-XXX_dir-PA_dwi.nii.gz”), QSIPrep will perform susceptibility distortion correction with the two runs (that is, using one run to correct the other), and ultimately produce a single merged output (unless you explicitly want to keep them separate for whatever reason).

Best,
Steven

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Thanks, Steven. I’ll try it.

4

Hi @Steven

I tried to run QSIPrep docker but I wonder why that gives me an error. I change some parameters but it does not work. I know that is a good alternative for DTIprep considering merging AP and PA and I hope that works for me.
I attached log file and code.
Many thanks for your patience
qsiprep.txt (462 Bytes)
qsiprep-log.txt (41.9 KB)
and help. I appreciate that.

5

Hello,

What is the role of -e FSLPython in your command? And are your data BIDS valid?

What did you change?

Best,
Steven

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6

qsip.txt (551 Bytes)
qsip-log.txt (241.2 KB)
Hello @Steven

I removed that part of code.
We have images from different centers, so I found only that one of them works.
I attached code and log, also here is the name of dwi output files for a subject:
sub-3012_confounds.tsv
qsip-log.txt (241.2 KB)

sub-3012_desc-ImageQC_dwi.csv
sub-3012_desc-SliceQC_dwi.json
sub-3012_dwiqc.json
sub-3012_space-T1w_desc-brain_mask.nii.gz
sub-3012_space-T1w_desc-eddy_cnr.nii.gz
sub-3012_space-T1w_desc-preproc_dwi.b
sub-3012_space-T1w_desc-preproc_dwi.bval
sub-3012_space-T1w_desc-preproc_dwi.bvec
sub-3012_space-T1w_desc-preproc_dwi.nii.gz
sub-3012_space-T1w_dwiref.nii.gz

Is everything good? Which ones should I use for tractography? I want to make connectivity matrix, what is next step?

Many thanks for your help and patience.

7

It looks like the outputs are there, but you should check the logs and subject HTML file to see if there were any errors.

Most of those outputs are useful for tractography.

You can use QSIRecon to make whole-brain connectivity matrices. Read more here: Reconstruction — qsiprep version documentation

Also, I noticed in your qsiprep that you only devoted 20 MB of memory? If you meant to do 20 gigabytes, the --mem-mb flag should be 20000.

Best,
Steven

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