ASL not supported?

[dkp]

Hi,
We have a study that includes ASL images. The bids community suggested to me that they should be treated as func images and tagged with acq-asl. I'm having trouble getting this to work with reproin. Can reproin support such files, and if so, how should I name them?
Thanks

[laurenbreithaupt]

@dkp were you able to find a workaround for ASL images and reproin?

[yarikoptic]

Unfortunately personally I have not approached ASL yet, so lack "first hand" experience.
There is BEP005 aiming to standardize ASL files naming in BIDS. So it seems that per single ASL sequence you will need to end up with multiple files.
if you could describe the details of trouble, may be we could assist to either make it compatible with BEP005 looking to go forward, or workaround somehow via those loosely defined _acq and other fields while starting with a simple func_task-YYY_run-XXX_acq-asl if you are interested in functional ASL.
Having some sample dicoms acquired on phantoms would be of help.

[dkp]

Hi Yaraslov, Thanks for getting back to me. You can use the dicom dataset I have posted (all my brain, so no deidentification issues): https://arizona.app.box.com/file/370103948316 You will find JJWANG ASL images (JJWANGS_pCASL*) and Siemens ASL sequence (Perfusion_Weighted*) included in that dataset. I was hoping for some sort of reproin solution going forward. Currently, I can use heudiconv and convertall.py (see here: https://neuroimaging-core-docs.readthedocs.io/en/latest/pages/heudiconv.html) to treat the ASL images as a variety of functional image: asl = create_key('sub-{subject}/{session}/func/sub-{subject}_{session}_acq-asl_run-01') asl_post = create_key('sub-{subject}/{session}/func/sub-{subject}_{session}_acq-asl_run-02') to get something like this: |-- func | | |-- sub-219_ses-itbs_acq-asl_run-01.json | | |-- sub-219_ses-itbs_acq-asl_run-01.nii.gz | | |-- sub-219_ses-itbs_acq-asl_run-02.json | | |-- sub-219_ses-itbs_acq-asl_run-02.nii.gz But reproin seems to make more stringent assumptions about what kinds of files can end up in the func directory, and so I am not sure how to name these files at the console to handle this elegantly. I conclude that reproin is not the best solution if you have any nonstandard sequences....but I presume that eventually this will be handled by reproin when ASL becomes a standard part of the BIDS. Please tell me if I'm missing the point. So, I have a solution, just not a really cool reproin solution ; )

…

-Dianne

On Thu, Apr 18, 2019 at 7:25 AM Yaroslav Halchenko ***@***.***> wrote: Unfortunately personally I have not approached ASL yet, so lack "first hand" experience. There is BEP005 <https://docs.google.com/document/d/15tnn5F10KpgHypaQJNNGiNKsni9035GtDqJzWqkkP6c/edit#heading=h.prrzvwchfio6> aiming to standardize ASL files naming in BIDS. So it seems that per single ASL sequence you will need to end up with multiple files. if you could describe the details of trouble, may be we could assist to either make it compatible with BEP005 looking to go forward, or workaround somehow via those loosely defined _acq and other fields while starting with a simple func_task-YYY_run-XXX_acq-asl if you are interested in functional ASL. Having some sample dicoms acquired on phantoms would be of help. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#31 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAHLUQENPISFQJFQM5O54UTPRCAG3ANCNFSM4GXLUNIA> .

-- Dianne Patterson, Ph.D. Research Scientist [email protected] <[email protected]> or [email protected] University of Arizona Speech and Hearing Science 314 1131 E 2nd Street, Building #71 (Just East of Harvill) ============== If you don't hear back from me (and you expected to), I blame the University's new SPAM filter. Please write to my gmail account. ============== Antipiphany: That moment when you realize how little you actually know ==============

[tsalo]

Now that ASL-BIDS has been merged, I think it might be a good time to circle back to this. Has any progress been made on ASL naming/conversion with ReproIn?

[yarikoptic]

Unfortunately I had no time @tsalo and as I personally do not do ASL - no personal drive. But it must be quite easy to tune reproin for anyone who knows what to expect/want from ASL and where to place it. @dkp -- may be with all your experience with it, you could extend the https://github.com/nipy/heudiconv/blob/master/heudiconv/heuristics/reproin.py#L382 and there on to support ASL? I would be very grateful.

[dkp]

@yarikoptic and @tsalo Thank you for your responses! I might have too much on my plate and not enough Python experience, but I'll add it to my list, and let you know if I succeed.

[tsalo]

I think the naming could be straightforward. The two elements that concern me are (1) certain metadata fields may require user input (e.g., LabelingEfficiency) and (2) volume-wise scaling should be applied as part of the BIDS curation (e.g., GE M0 scans should be multiplied by 32 * TotalAcquiredPairs). @yarikoptic would you consider those steps within heudiconv/reproin's scrope?

[yarikoptic]

Re 1: I don't think we should introduce interaction there but we could add "TODO" value.

2. Why it isn't done by dcm2niix --bids?