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physimals / oxford_asl

A command line tool for quantification of perfusion from ASL data
Apache License 2.0
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Error with oxford_asl --iaf option #6

Closed YukoNakamuraDDS closed 4 years ago

YukoNakamuraDDS commented 5 years ago

Dear Experts,

To practice asl analysis, I downloaded sample data (singlePLDpcASL) from BASIL website and tried to run oxford_asl. I tried to run the following line as the website showed. oxford_asl -i asltc -o oxasl --wp --casl --iaf=tc --tis=3.6 --bolus=1.8 --slicedt=0.0452 --spatial --moco -c aslcalib --tr 4.8 --cblip=aslcalib_PA --pedir=y --echospacing=0.06

Then I've got the following error. Error! Unrecognised option on command line: --iaf

I searched oxford_asl file and checked it if it would have --iaf option. Then I've found it in the file.

My environment is the following. I downloaded the latest version of oxford_asl (from this website; https://github.com/ibme-qubic/oxford_asl/files/2302429/oxford_asl-3.9.17-osx.tar.gz) and overwrite it on the old version of oxford_asl.

I also installed wxpython, matplotlib, numpy and nibabel, and checked fslpython (it worked). So I'm wondering if someone would have any idea about this error (--iaf option problem).

Thank you so much for your time.

Best wishes, Yuko

mcraig-ibme commented 4 years ago

Hi, apologies for the lack of response, I have not been getting GitHub notifications and a number of issues have been raised here without me realising.

If this issue is still present in current versions of oxford_asl (FSL 6.0.1 or later) then please let me know - otherwise I will close the issue. --iaf should definitely be recognized as an option.

mcraig-ibme commented 4 years ago

Closing historical issue